Publications

Horizontal Tabs

2012

Original Research Papers

Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nat Protoc. 2012;7:45-61. Abstract

Barlow AJ, Dixon J, Dixon M, Trainor PA. Balancing neural crest cell intrinsic processes with those of the microenvironment in Tcof1 haploinsufficient mice enables complete enteric nervous system formation [published ahead of print January 10 2012]. Hum Mol Genet. 2012 Abstract
Chen G, Bradford WD, Seidel CW, Li R. Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy [published ahead of print January 31 2012]. Nature.2012. Abstract
Kumar S, Sandell LL, Trainor PA, Koentgen F, Duester G. Alcohol and aldehyde dehydrogenases: Retinoid metabolic effects in mouse knockout models. Biochim Biophys Acta.2012;1821:198-205. Abstract

Majumdar A, Cesario WC, White-Grindley E, Jiang H, Ren F, Khan MR, Li L, Choi EM, Kannan K, Guo F, Unruh J, Slaughter B, Si K. Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory [published ahead of print January 31 2012]. Cell. 2012. Abstract

Wynn ML, Kulesa PM, Schnell S. Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour [published ahead of print January 4 2012]. J R Soc Interface. 2012. Abstract

Reviews, Commentaries or Chapters

Abmayr SM, Pavlath GK. Myoblast fusion: lessons from flies and mice. Development. 2012;139:641-656. Abstract

Achilleos A, Trainor PA. Neural crest stem cells: discovery, properties and potential for therapy [published ahead or print]. Cell Res. 2012. Abstract

Mak HY. Lipid droplets as fat storage organelles in Caenorhabditis elegans: Thematic Review Series: Lipid Droplet Synthesis and Metabolism: from Yeast to Man. J Lipid Res. 2012;53:28-33. Abstract

2011

Original Research Papers

Bear J, Rubinstein B, Fel L. Capillary Pressure Curve for Liquid Menisci in a Cubic Assembly of Spherical Particles Below Irreducible Saturation. Transport in Porous Media.2011;89:63-73. Abstract

Benazeraf B, Francois P, Denans N, Little CD, Pourquie O. [A non directional cell migration gradient in the presomitic mesoderm contributes to axis elongation in chicken embryos]. Biol Aujourdhui. 2011;205:95-103. Abstract

Berdygulova Z, Westblade LF, Florens L, Koonin EV, Chait BT, Ramanculov E, Washburn MP, Darst SA, Severinov K, Minakhin L. Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45. J Mol Biol.2011;405:125-142. Abstract

Brown WRA, Liti G, Rosa C, James S, Roberts I, Robert V, Jolly N, Tang W, Baumann P, Green C, Schlegel K, Young J, Hirchaud F, Leek S, Thomas G, Blomberg A, Warringer J. A geographically diverse collection of Schizosaccharomyces pombe isolates shows limited phenotypic variation but extensive karyotypic diversity. G3 Genes, Genomes, Genetics. 2011;1:615-626. Abstract

Capotosti F, Guernier S, Lammers F, Waridel P, Cai Y, Jin J, Conaway JW, Conaway RC, Herr W. O-GlcNAc Transferase Catalyzes Site-Specific Proteolysis of HCF-1. Cell. 2011;144:376-388. Abstract

Castranova D, Lawton A, Lawrence C, Baumann DP, Best J, Coscolla J, Doherty A, Ramos J, Hakkesteeg J, Wang C, Wilson C, Malley J, Weinstein BM. The Effect of Stocking Densities on Reproductive Performance in Laboratory Zebrafish (Danio rerio). Zebrafish. 2011;8:141-146. Abstract

Charles C, Hovorakova M, Ahn Y, Lyons DB, Marangoni P, Churava S, Biehs B, Jheon A, Lesot H, Balooch G, Krumlauf R, Viriot L, Peterkova R, Klein OD. Regulation of tooth number by fine-tuning levels of receptor-tyrosine kinase signaling. Development.2011;138:4063-4073. Abstract

Chen L, Cai Y, Jin J, Florens L, Swanson SK, Washburn MP, Conaway JW, Conaway RC. Subunit Organization of the Human INO80 Chromatin Remodeling Complex: AN EVOLUTIONARILY CONSERVED CORE COMPLEX CATALYZES ATP-DEPENDENT NUCLEOSOME REMODELING.J Biol Chem. 2011;286:11283-11289. Abstract

Costessi A, Mahrour N, Tijchon E, Stunnenberg R, Stoel MA, Jansen PW, Sela D, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC, Stunnenberg HG. The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters. EMBO J. 2011;30:3786-3798. Abstract

Cunningham TJ, Chatzi C, Sandell LL, Trainor PA, Duester G. Rdh10 mutants deficient in limb field retinoic acid signaling exhibit normal limb patterning but display interdigital webbing. Dev Dyn.2011;240:1142-1150. Abstract

Farjo KM, Moiseyev G, Nikolaeva O, Sandell LL, Trainor PA, Ma JX. RDH10 is the primary enzyme responsible for the first step of embryonic Vitamin A metabolism and retinoic acid synthesis. Dev Biol. 2011;357:347-355. Abstract

Friederichs JM, Ghosh S, Smoyer CJ, McCroskey S, Miller BD, Weaver KJ, Delventhal KM, Unruh J, Slaughter BD, Jaspersen SL. The SUN Protein Mps3 Is Required for Spindle Pole Body Insertion into the Nuclear Membrane and Nuclear Envelope Homeostasis. PLoS Genet. 2011;7:e1002365. Abstract

Gao JT, Guimera R, Li H, Pinto IM, Sales-Pardo M, Wai SC, Rubinstein B, Li R. Modular coherence of protein dynamics in yeast cell polarity system. Proc Natl Acad Sci U S A. 2011;108:7647-7652. Abstract

Gardner JM, Smoyer CJ, Stensrud ES, Alexander R, Gogol M, Wiegraebe W, Jaspersen SL. Targeting of the SUN protein Mps3 to the inner nuclear membrane by the histone variant H2A.Z.J Cell Biol. 2011;193:489-507. Abstract

Gibson WT, Veldhuis JH, Rubinstein B, Cartwright HN, Perrimon N, Brodland GW, Nagpal R, Gibson MC. Control of mitotic cleavage plane by local epithelial topology. Cell. 2011;144:427-438. Abstract

Gilmore JM, Sardiu ME, Venkatesh S, Stutzman B, Peak A, Seidel CW, Workman JL, Florens L, Washburn MP. Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses [published ahead of print December 22 2011].Mol Cell Proteomics. 2011. Abstract

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2011;471:473-479. Abstract

Hao Y, Xu N, Box A, Schaefer L, Kannan K, Zhang Y, Florens L, Seidel C, Washburn M, Wiegraebe W, Mak HY. Nuclear cGMP-Dependent Kinase Regulates Gene Expression via Activity-Dependent Recruitment of a Conserved Histone Deacetylase Complex. PLoS Genet. 2011;7:e1002065. Abstract

Haralalka S, Shelton C, Cartwright HN, Katzfey E, Janzen E, Abmayr SM. Asymmetric Mbc, active Rac1 and F-actin foci in the fusion-competent myoblasts during myoblast fusion in Drosophila. Development. 2011;138:1551 - 1562. Abstract

He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet.2011;43:414-420. Abstract

Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, Clouthier D, Cunningham ML, Dixon M, Donahue LR, Fraser SE, Hallgrimsson B, Iwata J, Klein O, Marazita ML, Murray JC, Murray S, de Villena FP, Postlethwait J, Potter S, Shapiro L, Spritz R, Visel A, Weinberg SM, Trainor PA. The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol.2011;355:175-182. Abstract

Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, Florens L, Washburn MP, Skowronski J. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature. 2011;474:658-661. Abstract

Hughes SE, Beeler JS, Seat A, Slaughter BD, Unruh JR, Bauerly E, Matthies HJ, Hawley RS. Gamma-Tubulin Is Required for Bipolar Spindle Assembly and for Proper Kinetochore Microtubule Attachments during Prometaphase I in Drosophila Oocytes. PLoS Genet. 2011;7:e1002209. Abstract

Kannan L, Li H, Mushegian A. A polynomial-time algorithm computing lower and upper bounds of the rooted subtree prune and regraft distance. J Comput Biol. 2011;18:743-757. Abstract

Keck JM, Jones MH, Wong CC, Binkley J, Chen D, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates JR, 3rd, Winey M. A cell cycle phosphoproteome of the yeast centrosome. Science.2011;332:1557-1561. Abstract

Kirilly D, Wang S, Xie T. Self-maintained escort cells form a germline stem cell differentiation niche. Development. 2011;138:5087-5097. Abstract

Kim S, Ma L, Yu CR. Requirement of Calcium-Activated Chloride Channels in the Activation of the Mouse Vomeronasal Neuron. Nat Commun [serial online]. 2011;2:365. doi:10.1038/ncomms1368. Abstract, Full Text

Kristensen DM, Cai X, Mushegian A. Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts.J Bacteriol. 2011;193:1806-1814. Abstract

Krol AJ, Roellig D, Dequeant ML, Tassy O, Glynn E, Hattem G, Mushegian A, Oates AC, Pourquie O. Evolutionary plasticity of segmentation clock networks. Development. 2011;138:2783-2792. Abstract

Lake CM, Nielsen RJ, Hawley RS. The Drosophila zinc finger protein trade embargo is required for double strand break formation in meiosis. PLoS Genet. 2011;7:e1002005. Abstract

Lee KK, Sardiu ME, Swanson SK, Gilmore JM, Torok M, Grant PA, Florens L, Workman JL, Washburn MP. Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes. Mol Syst Biol. 2011;7:503. Abstract Full Text

Lin C, Garrett AS, De Kumar B, Smith ER, Gogol M, Seidel C, Krumlauf R, Shilatifard A. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev. 2011;25:1486-1498. Abstract

Litovchick L, Florens LA, Swanson SK, Washburn MP, DeCaprio JA. DYRK1A protein kinase promotes quiescence and senescence through DREAM complex assembly. Genes Dev. 2011;25:801-813. Abstract

Lutes AA, Baumann DP, Neaves WB,Baumann P. From the Cover: Laboratory synthesis of an independently reproducing vertebrate species. Proc Natl Acad Sci U S A.2011;108:9910-9915. Abstract

McKinney MC, Stark DA, Teddy J, Kulesa PM. Neural crest cell communication involves an exchange of cytoplasmic material through cellular bridges revealed by photoconversion of KikGR. Dev Dyn. 2011;240:1391-1401. Abstract

McKinney MC, Kulesa PM. In vivo calcium dynamics during neural crest cell migration and patterning using GCaMP3. Dev Biol.2011;358:309-317. Abstract

Meyer EJ, Ikmi A, Gibson MC. Interkinetic Nuclear Migration Is a Broadly Conserved Feature of Cell Division in Pseudostratified Epithelia. Curr Biol. 2011;21:485-491. Abstract

Mohan M, Herz HM, Smith ER, Zhang Y, Jackson J, Washburn MP, Florens L, Eissenberg JC, Shilatifard A. The COMPASS Family of H3K4 Methylases in Drosophila. Mol Cell Biol.2011;31:4310-4318. Abstract

Mosley AL, Sardiu ME, Pattenden SG, Workman JL, Florens L, Washburn MP. Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes. Mol Cell Proteomics.2011;10:M110 000687. Abstract

Parrish M, Unruh J, Krumlauf R. BAC modification through serial or simultaneous use of CRE/Lox technology.J Biomed Biotechnol. 2011;2011:924068. Abstract

Perry JM, He XC, Sugimura R, Grindley JC, Haug JS, Ding S, Li L. Cooperation between both Wnt/{beta}-catenin and PTEN/PI3K/Akt signaling promotes primitive hematopoietic stem cell self-renewal and expansion. Genes Dev.2011;25:1928-1942. Abstract

Potapova TA, Sivakumar S, Flynn JN, Li R, Gorbsky GJ. Mitotic progression becomes irreversible in prometaphase and collapses when Wee1 and Cdc25 are inhibited.Mol Biol Cell. 2011;22:1191-1206. Abstract

Remboutsika E, Elkouris M, Iulianella A, Andoniadou CL, Poulou M, Mitsiadis TA, Trainor PA, Lovell-Badge R. Flexibility of neural stem cells. Front Physiol.2011;2:16. Abstract

Rubinstein BY, Leshansky AM. Rupture of thin liquid films: Generalization of weakly nonlinear theory. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;83:031603. Abstract

Sandell LL, Iulianella A, Melton KR, Lynn M, Walker M, Inman KE, Bhatt S, Leroux-Berger M, Crawford M, Jones NC, Dennis JF, Trainor PA. A phenotype-driven ENU mutagenesis screen identifies novel alleles with functional roles in early mouse craniofacial development. Genesis. 2011;49:342-359. Abstract

Sardiu ME, Washburn MP. Building protein-protein interaction networks with proteomics and informatics tools. J Biol Chem. 2011;286:23645-23651. Abstract

Shivaraju M, Camahort R, Mattingly M, Gerton JL. Scm3 is a centromeric nucleosome assembly factor. J Biol Chem. 2011;286:12016-12023. Abstract

Smith ER, Lin C, Garrett AS, Thornton J, Mohaghegh N, Hu D, Jackson J, Saraf A, Swanson SK, Seidel C, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. The little elongation complex regulates small nuclear RNA transcription. Mol Cell.2011;44:954-965. Abstract

Sugimura R, Li L. Bone Metastasis Targets The Endosteal Hematopoietic Stem Cell Niche. IBMS BoneKEy. 2011;8:381-384. Abstract

Szuperak M, Salah S, Meyer EJ, Nagarajan U, Ikmi A, Gibson MC. Feedback regulation of Drosophila BMP signaling by the novel extracellular protein Larval Translucida. Development. 2011;138:715-724. Abstract

Takahashi YH, Westfield GH, Oleskie AN, Trievel RC, Shilatifard A, Skiniotis G. Structural analysis of the core COMPASS family of histone H3K4 methylases from yeast to human. Proc Natl Acad Sci U S A.2011;108:20526-20531. Abstract

Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CA, Kong SE, Szutorisz H, Swanson SK, Martin-Brown S, Washburn MP, Florens L, Seidel CW, Lin C, Smith ER, Shilatifard A, Conaway RC, Conaway JW. Human Mediator Subunit MED26 Functions as a Docking Site for Transcription Elongation Factors. Cell. 2011;146:92-104. Abstract

Takahashi YH, Schulze JM, Jackson J, Hentrich T, Seidel C, Jaspersen SL, Kobor MS, Shilatifard A. Dot1 and Histone H3K79 Methylation in Natural Telomeric and HM Silencing. Mol Cell. 2011;42:118-126. Abstract

Takeo S, Lake CM, Morais-de-Sa E, Sunkel CE, Hawley RS. Synaptonemal Complex-Dependent Centromeric Clustering and the Initiation of Synapsis in Drosophila Oocytes. Curr Biol. 2011. Abstract

Taliaferro JM, Alvarez N, Green RE, Blanchette M, Rio DC. Evolution of a tissue-specific splicing network. Genes Dev. 2011;25:608-620. Abstract

Wang X, Pan L, Wang S, Zhou J, McDowell W, Park J, Haug J, Staehling K, Tang H, Xie T. Histone H3K9 Trimethylase Eggless Controls Germline Stem Cell Maintenance and Differentiation. PLoS Genet. 2011;7:e1002426. Abstract

Weake VM, Dyer JO, Seidel C, Box A, Swanson SK, Peak A, Florens L, Washburn MP, Abmayr SM, Workman JL. Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation. Genes Dev.2011;25:1499-1509. Abstract

Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr AR, Florens L, Schirmer EC. Several novel nuclear envelope transmembrane proteins identified in skeletal muscle have cytoskeletal associations. Mol Cell Proteomics.2011;10:M110 003129. Abstract

Wood C, Huff J, Marshall W, Yu EQ, Unruh J, Slaughter B, Wiegraebe W. Fluorescence correlation spectroscopy as tool for high-content-screening in yeast (HCS-FCS). Proc SPIE; 2011;7905, 79050H. Abstract

Yi K, Unruh JR, Deng M, Slaughter BD, Rubinstein B, Li R. Dynamic maintenance of asymmetric meiotic spindle position through Arp2/3-complex-driven cytoplasmic streaming in mouse oocytes. Nat Cell Biol. 2011;13:1252-1258. Abstract

Yu Y, Srinivasan M, Nakanishi S, Leatherwood J, Shilatifard A, Sternglanz R. A Conserved Patch near the C Terminus of Histone H4 Is Required for Genome Stability in Budding Yeast. Mol Cell Biol.2011;31:2311-2325. Abstract

Zhou C, Slaughter BD, Unruh JR, Eldakak A, Rubinstein B, Li R. Motility and segregation of hsp104-associated protein aggregates in budding yeast. Cell. 2011;147:1186-1196. Abstract

Zhu HH, Ji K, Alderson N, He Z, Li S, Liu W, Zhang DE, Li L, Feng GS. Kit-Shp2-Kit signaling acts to maintain a functional hematopoietic stem and progenitor cell pool. Blood. 2011;117:5350-5361. Abstract

Reviews, Commentaries or Chapters

Bryan TM, Baumann P. G-quadruplexes: from guanine gels to chemotherapeutics. Mol Biotechnol. 2011;49:198-208. Abstract

Chen S, Wang S, Xie T. Restricting self-renewal signals within the stem cell niche: multiple levels of control. Curr Opin Genet Dev.2011;21:684-689. Abstract

Conaway RC, Conaway JW. Origins and activity of the Mediator complex. Semin Cell Dev Biol. 2011;22:729-734. Abstract

Conaway RC, Conaway JW. Function and regulation of the Mediator complex. Curr Opin Genet Dev. 2011;21:225-230. Abstract

Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science. 2011;333:1758-1760. Abstract

Haralalka S, Cartwright HN, Abmayr SM. Recent advances in imaging embryonic myoblast fusion in Drosophila [published ahead of print August 30 2011]. Methods. 2011. Abstract

Hawley RS. Molecular biology. Hitting a tiny target in the dark. Science 2011;331:870-871. Abstract

Hawley RS. Oogenesis: when most is good enough. Curr Biol. 2011;21:R288-290. Abstract

Hawley RS. Solving a Meiotic LEGO(R) Puzzle: Transverse Filaments and the Assembly of the Synaptonemal Complex in Caenorhabditis elegans. Genetics. 2011;189:405-409. Abstract

Hewawasam GS, Gerton JL. Cse4 gets a kiss-of-death from Psh1. Cell Cycle. 2011;10:566-567. Abstract

Henikoff S, Shilatifard A. Histone modification: cause or cog? Trends Genet. 2011;27:389-396. Abstract

Jaspersen SL, Hawley RS. Meiotic pairing as a polo match. Dev Cell. 2011;21:805-806. Abstract

Krull CE, Su F, Swartz M, Eberhart J, McLennan R, Chen Y, Trainor PA. Electroporation of Chick and Mouse Embryos. In: J Sharpe, and RO Wong, eds. Imaging in Developmental Biology: A Laboratory Manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2011.

Kulesa PM, Dickinson ME, Hadjantonakis AK. Highlights of the special imaging issue. Genesis.2011;49:479-483. Abstract

Kwak J, Workman JL, Lee D. The proteasome and its regulatory roles in gene expression. Biochim Biophys Acta. 2011;1809:88-96. Abstract

Kwon SH, Workman JL. HP1c casts light on dark matter. Cell Cycle. 2011;10:625-630. Abstract

Kwon SH, Workman JL. The changing faces of HP1: From heterochromatin formation and gene silencing to euchromatic gene expression: HP1 acts as a positive regulator of transcription. BioEssays. 2011;33:280-289. Abstract

Lin CH, Workman JL. Suppression of cryptic intragenic transcripts is required for embryonic stem cell self-renewal. EMBO J. 2011;30:1420-1421. Abstract

Ma L, Haga-Yamanaka S, Yu Q-E, Qiu Q, Kim S, Yu CR. Imaging neuronal responses in slice preparations of vomeronasal organ expressing a genetically encoded calcium sensor. J Vis Exp.2011;58. Abstract

Mushegian A, Conaway JW. Thematic minireview series on computational systems biology. J Biol Chem.2011;286:23621-23622. Abstract

Neaves WB, Baumann P. Unisexual reproduction among vertebrates. Trends Genet. 2011;27:81-88. Abstract

Ramisetty SR, Washburn MP. Unraveling the dynamics of protein interactions with quantitative mass spectrometry. Crit Rev Biochem Mol Biol. 2011;46:216-228. Abstract

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Muller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Comparative functional genomics of the fission yeasts. Science.2011;332:930-936. Abstract

Sardiu ME, Washburn MP. Construction of protein interaction networks based on the label-free quantitative proteomics. Methods Mol Biol. 2011;781:71-85. Abstract

Shivaraju M, Gerton GL. The dynamics of the Cse4 chaperone Scm3. Cell Cycle. 2011;10:3369-3378. Abstract

Strizzi L, Hardy KM, Seftor EA, Margaryan NV, Kirschmann DA, Kirsammer GT, Bailey CM, Kasemeier-Kulesa JC, Kulesa PM, Seftor REB, Hendrix MJC. Lessons from Embyogenesis. In: A Bosserhoff, ed. Melanoma Development - Molecular Biology, Genetics and Clinical Applications: Springer-Verlag/Wien; 2011:281-296. Abstract

Slaughter BD, Unruh JR, Li R. Fluorescence fluctuation spectroscopy and imaging methods for examination of dynamic protein interactions in yeast. Methods Mol Biol. 2011;759:283-306. Abstract

Smith E, Lin C, Shilatifard A. The super elongation complex (SEC) and MLL in development and disease. Genes Dev. 2011;25:661-672. Abstract

Smolle M, Workman JL. Signaling through Chromatin: Setting the Scene at Kinetochores. Cell.2011;146:671-672. Abstract

Suganuma T, Workman JL. Signals and combinatorial functions of histone modifications. Annu Rev Biochem.2011;80:473-499. Abstract

Washburn MP. Driving biochemical discovery with quantitative proteomics. Trends Biochem Sci. 2010;36:170-177. Abstract

Weake VM, Workman JL. SAGA function in tissue-specific gene expression [published ahead of print December 27 2011]. Trends Cell Biol. 2011. Abstract
Xiong B. Spc25: How the kinetochore protein plays during oocyte meiosis. Cell Cycle. 2011;10:1031-1030. Abstract

Xu XP, Rouiller I, Slaughter BD, Egile C, Kim E, Unruh JR, Fan X, Pollard TD, Li R, Hanein D, Volkmann N. Three-dimensional reconstructions of Arp2/3
complex with bound nucleation promoting factors [published ahead of print September 20 2011]. EMBO J. 2011. Abstract

Yun M, Wu J, Workman JL, Li B. Readers of histone modifications. Cell Res.2011;21:564-578. Abstract
Zhou Y, Lu T, Xie T. A PGC-1 Tale: Healthier Intestinal Stem Cells, Longer Life. Cell Metab.2011;14:571-572. Abstract

Book

Richards JE, Hawley RS. The Human Genome, A User's Guide. Third ed: Academic Press; 2011.

2010

Original Research Papers

Ahn Y, Sanderson BW, Klein OD, Krumlauf R. Inhibition of Wnt signaling by Wise (Sostdc1) and negative feedback from Shh controls tooth number and patterning. Development. 2010;137:3221-3231. Abstract

Blin G, Nury D, Stefanovic S, Neri T, Guillevic O, Brinon B, Bellamy V, Rucker-Martin C, Barbry P, Bel A, Bruneval P, Cowan C, Pouly J, Mitalipov S, Gouadon E, Binder P, Hagege A, Desnos M, Renaud JF, Menasche P, Puceat M. A purified population of multipotent cardiovascular progenitors derived from primate pluripotent stem cells engrafts in postmyocardial infarcted nonhuman primates. J Clin Invest.2010;120:1125-1139. Abstract

Bosl WJ, Li R. The role of noise and positive feedback in the onset of autosomal dominant diseases. BMC Syst Biol. 2010;4:93. Abstract

Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L, Washburn MP, Conaway JW, Conaway RC. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem.2010;285:4268-4272. Abstract

Chen S, Kaneko S, Ma X, Chen X, Ip YT, Xu L, Xie T. Lissencephaly-1 controls germline stem cell self-renewal through modulating bone morphogenetic protein signaling and niche adhesion. Proc Natl Acad Sci U S A. 2010;107:19939-19944. Abstract

D'Angiolella V, Donato V, Vijayakumar S, Saraf A, Florens L, Washburn MP, Dynlacht B, Pagano M. SCF(Cyclin F) controls centrosome homeostasis and mitotic fidelity through CP110 degradation. Nature.2010;466:138-142. Abstract

Egli D, Eggan K. Recipient cell nuclear factors are required for reprogramming by nuclear transfer. Development.2010;137:1953-1963. Abstract

Eldakak A, Rancati G, Rubinstein B, Paul P, Conaway V, Li R. Asymmetrically inherited multidrug resistance transporters are recessive determinants in cellular replicative ageing. Nat Cell Biol. 2010;12:799-805. Abstract

Fournier ML, Paulson A, Pavelka N, Mosley AL, Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, Seidel C, Florens L, Washburn MP. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol Cell Proteomics.2010;9:271-284. Abstract

Govind CK, Qiu H, Ginsburg DS, Ruan C, Hofmeyer K, Hu C, Swaminathan V, Workman JL, Li B, Hinnebusch AG. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes.Mol Cell. 2010;39:234-246. Abstract

He J, Ma L, Kim S, Schwartz J, Santilli M, Wood C, Durnin MH, Yu CR. Distinct Signals Conveyed to Pheromone Concentrations to the Mouse Vomeronasal Organ. J Neurosci.2010;30:7473-7483. Abstract

Helston RM, Box JA, Tang W, Baumann P. Schizosaccharomyces cryophilus sp. nov., a new species of fission yeast. FEMS Yeast Res. 2010;10:779-786. Abstract

Herz HM, Madden LD, Chen Z, Bolduc C, Buff E, Gupta R, Davuluri R, Shilatifard A, Hariharan IK, Bergmann A. The H3K27me3 demethylase dUTX is a suppressor of Notch- and Rb-dependent tumors in Drosophila. Mol Cell Biol. 2010;30:2485-2497. Abstract

Hewawasam G, Shivaraju M, Mattingly M, Venkatesh S, Martin-Brown S, Florens L, Workman JL, Gerton JL. Psh1 Is an E3 Ubiquitin Ligase that Targets the Centromeric Histone Variant Cse4. Mol Cell. 2010;40:444-454. Abstract

Ikmi A, Gibson MC. Identification and in vivo characterization of NvFP-7R, a developmentally regulated red fluorescent protein of Nematostella vectensis. PLoS One. 2010;5:E11807. Abstract

Kasemeier-Kulesa JC, McLennan R, Romine MH, Kulesa PM, Lefcort F. CXCR4 controls ventral migration of sympathetic precursor cells. J Neurosci. 2010;30:13078-13088. Abstract

Kim JH, Saraf A, Florens L, Washburn M, Workman JL. Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2. Genes Dev. 2010;24:2766-2771. Abstract

Korfali N, Wilkie GS, Swanson SK, Srsen V, Batrakou DG, Fairley EA, Malik P, Zuleger N, Goncharevich A, de Las Heras J, Kelly DA, Kerr AR, Florens L, Schirmer EC. The leukocyte nuclear envelope proteome varies with cell activation and contains novel transmembrane proteins that affect genome architecture. Mol Cell Proteomics. 2010;9:2571-2585. Abstract

Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010;26:1481-1487. Abstract

Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol.2010;18:11-19. Abstract
Kulesa PM, Gammill LS. Neural crest migration: Patterns, phases and signals.Dev Biol. 2010;344:566-568. Abstract

Kulesa PM, Teddy JM, Smith M, Alexander R, Cooper CH, Lansford R, McLennan R. Multispectral fingerprinting for improved in vivo cell dynamics analysis. BMC Dev Biol. 2010;10:101. Abstract

Kwon SH, Florens L, Swanson SK, Washburn MP, Abmayr SM, Workman JL. Heterochromatin protein 1 (HP1) connects the FACT histone chaperone complex to the phosphorylated CTD of RNA polymerase II. Genes Dev. 2010;24:2133-2145. Abstract

Lang C, Grava S, Finlayson M, Trimble R, Philippsen P, Jaspersen SL. Structural mutants of the spindle pole body cause distinct alteration of cytoplasmic microtubules and nuclear dynamics in multinucleated hyphae. Mol Biol Cell.2010;21:753-766. Abstract

Lang C, Grava S, van den Hoorn T, Trimble R, Philippsen P, Jaspersen SL. Mobility, microtubule nucleation and structure of microtubule-organizing centers in multinucleated hyphae of Ashbya gossypii. Mol Biol Cell.2010;21:18-28. Abstract

Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, Washburn MP, Conaway JW, Conaway RC, Shilatifard A. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol Cell.2010;37:429-437. Abstract

Lu S, Goering M, Gard S, Xiong B, McNairn AJ, Jaspersen SL, Gerton JL. Eco1 is important for DNA damage repair in S. cerevisiae. Cell Cycle.2010;9:1-13.

Lutes AA, Neaves WB, Baumann DP, Wiegraebe W, Baumann P. Sister chromosome pairing maintains heterozygosity in parthenogenetic lizards. Nature.2010;464:283-286. Abstract

Mallanna SK, Ormsbee BD, Iacovino M, Gilmore JM, Cox JL, Kyba M, Washburn MP, Rizzino A. Proteomic analysis of Sox2-associated proteins during early stages of mouse embryonic stem cell differentiation identifies Sox21 as a novel regulator of stem cell fate. Stem Cells. 2010;28:1715-1727. Abstract

Mastushita-Sakai T, White-Grindley E, Samuelson J, Seidel C, Si K. Drosophila Orb2 targets genes involved in neuronal growth, synapse formation, and protein turnover. Proc Natl Acad Sci U S A.2010;107:11987-11992. Abstract

McLennan R, Kulesa PM. Neuropilin-1 interacts with the second branchial arch microenvironment to mediate chick neural crest cell dynamics. Dev Dyn.2010;239:1664-1673. Abstract

McLennan R, Teddy JM, Kasemeier-Kulesa JC, Romine MH, Kulesa PM. Vascular endothelial growth factor (VEGF) regulates cranial neural crest migration in vivo. Dev Biol.2010;339:114-125. Abstract

Mogilner A, Rubinstein B. Actin disassembly 'clock' and membrane tension determine cell shape and turning: a mathematical model. J Phys Condensed Matter.2010;22:194118. Abstract

Mohan M, Herz HM, Takahashi YH, Lin C, Lai KC, Zhang Y, Washburn MP, Florens L, Shilatifard A. Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev.2010;24:574-589. Abstract

Niakan KK, Ji H, Maehr R, Vokes SA, Rodolfa KT, Sherwood RI, Yamaki M, Dimos JT, Chen AE, Melton DA, McMahon AP, Eggan K. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev.2010;24:312-326. Abstract

Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzen Y, Seidel C, Wright AP, Forsburg SL. Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. BMC Genomics.2010;11:59. Abstract

Ozbudak EM, Tassy O, Pourquie O. Spatiotemporal compartmentalization of key physiological processes during muscle precursor differentiation. Proc Natl Acad Sci U S A. 2010;107:4224-4229. Abstract

Pattenden SG, Gogol MM, Workman JL. Features of cryptic promoters and their varied reliance on bromodomain-containing factors. PLoS One.2010;5:e12927. Abstract
Pavelka N, Rancati G, Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature. 2010;468:321-325. Abstract

Pyrgaki C, Trainor P, Hadjantonakis AK, Niswander L. Dynamic imaging of mammalian neural tube closure. Dev Biol. 2010;344:941-947. Abstract

Sauliere J, Haque N, Harms S, Barbosa I, Blanchette M, Le Hir H. The exon junction complex differentially marks spliced junctions. Nat Struct Mol Biol.2010;17:1269-1271. Abstract

Si K, Choi YB, White-Grindley E, Majumdar A, Kandel ER. Aplysia CPEB can form prion-like multimers in sensory neurons that contribute to long-term facilitation. Cell.2010;140:421-435. Abstract

Smith KT, Martin-Brown SA, Florens L, Washburn MP, Workman JL. Deacetylase inhibitors dissociate the histone-targeting ING2 subunit from the Sin3 complex. Chem Biol (Lond).2010;17:65-73. Abstract

Suganuma T, Mushegian A, Swanson SK, Abmayr SM, Florens L, Washburn MP, Workman JL. The ATAC Acetyltransferase Complex Coordinates MAP Kinases to Regulate JNK Target Genes. Cell. 2010;142:726-736. Abstract

Takeo S, Hawley RS, Aigaki T. Calcineurin and its regulation by Sra/RCAN is required for completion of meiosis in Drosophila. Dev Biol.2010;344:957-967. Abstract

Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010;7:618-630. Abstract

Witkin KL, Friederichs JM, Cohen-Fix O, Jaspersen SL. Changes in the Nuclear Envelope Environment Affect Spindle Pole Body Duplication in Saccharomyces cerevisiae. Genetics. 2010;186:867-883. Abstract

Xia S, Li X, Johnson T, Seidel C, Wallace DP, Li R. Polycystin-dependent fluid flow sensing targets histone deacetylase 5 to prevent the development of renal cysts. Development.2010;137:1075-1084. Abstract

Xiong B, Lu S, Gerton JL. Hos1 is a lysine deacetylase for the smc3 subunit of cohesin. Curr Biol. 2010;20:1660-1665. Abstract

Zeng Y, Li H, Schweppe NM, Hawley RS, Gilliland WD. Statistical analysis of nondisjunction assays in Drosophila. Genetics. 2010;186:505-513. Abstract

Zhang D, O'Neil M F, Cunningham MT, Fan F, Olyaee M, Li L. Abnormal Wnt signaling and stem cell activation in reactive lymphoid tissue and low-grade marginal zone lymphoma. Leuk Lymphoma.2010;51:906-910. Abstract

Zhang SO, Mathur S, Hattem G, Tassy O, Pourquie O. Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos. BMC Genomics.2010;11:13. Abstract

Zhang SO, Trimble R, Guo F, Mak HY. Lipid droplets as ubiquitous fat storage organelles in C. elegans. BMC Cell Biol. 2010;11:96. Full Text

Zhang Y, Wen Z, Washburn MP, Florens L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem.2010;82:2272-2281. Abstract

Reviews, Commentaries or Chapters

Aulehla A, Pourquie O. Signaling gradients during paraxial mesoderm development. Cold Spring Harb Perspect Biol.2010;2:a000869.. Abstract

Baumann P, Price C. Pot1 and telomere maintenance. FEBS Lett. 2010;584:3779-3784. Abstract

Benazeraf B, Francois P, Baker RE, Denans N, Little CD, Pourquie O. A random cell motility gradient downstream of FGF controls elongation of an amniote embryo. Nature.2010;466:248-252. Abstract

Bose T, Gerton J. Cohesinopathies, gene expression, and chromatin organization. J Cell Biol.2010;189:201-210. Abstract

Bryan TM, Baumann P. G-quadruplexes: from guanine gels to chemotherapeutics. Methods Mol Biol.2010;608:1-16. Abstract

Eissenberg JC, Shilatifard A. Histone H3 lysine 4 (H3K4) methylation in development and differentiation. Dev Biol.2010;339:240-249. Abstract

Gilmore JM, Washburn MP. Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics. 2010;73:2078-2091. Abstract

Haralalka S, Abmayr SM. Myoblast fusion in Drosophila. Exp Cell Res. 2010;316:3007-3013. Abstract

Herz HM, Shilatifard A. The JARID2-PRC2 duality. Genes Dev.2010;24:857-861. Abstract

Ichida JK, Kiskinis E, Eggan K. Shushing down the epigenetic landscape towards stem cell differentiation. Development.2010;137:2455-2460. Abstract

Inman K, Ezin M, Bronner-Fraser M, Trainor P. Role of Cardiac Neural Crest Cells in Morphogenesis of the Heart and Great Vessels. Heart Development and Regeneration. 1st ed. Amsterdam: Elsevier/Academic Press; 2010;1:417-434.

Kim JH, Workman JL. Histone acetylation in heterochromatin assembly. Genes Dev.2010;24:738-740. Abstract
Kiskinis E, Eggan K. Progress toward the clinical application of patient-specific pluripotent stem cells. J Clin Invest.2010;120:51-59.Abstract

Krumlauf R, Levine M. Gene expression and development. Special introduction. Dev Biol.2010;339:224. Abstract

Kulesa PM, Bailey CM, Cooper C, Fraser SE. In ovo live imaging of avian embryos. Cold Spring Harb Protoc.2010;2010:pdb prot5446. Abstract

Kulesa PM, Bailey CM, Kasemeier-Kulesa JC, McLennan R. Cranial neural crest migration: New rules for an old road. Dev Biol. 2010;344:543-554. Abstract

Lee JS, Smith E, Shilatifard A. The language of histone crosstalk. Cell. 2010;142:682-685. Abstract

Li L, Clevers H. Coexistence of quiescent and active adult stem cells in mammals. Science.2010;327:542-545. Abstract

Li R. Myosin-II Puts the Squeeze on Asymmetric Cell Division. Dev Cell. 2010;19:639-640. Abstract

Li R, Bowerman B. Symmetry breaking in biology. Cold Spring Harb Perspect Biol.2010;2:a003475. Abstract

Mohan M, Lin C, Guest E, Shilatifard A. Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis. Nat Rev Cancer. 2010;10:721-728. Abstract

Pavelka N, Rancati G, Li R. Dr Jekyll and Mr Hyde: role of aneuploidy in cellular adaptation and cancer. Curr Opin Cell Biol.2010;22:809-15. Abstract

Perry JM, Li L. Functional assays for hematopoietic stem cell self-renewal. Methods Mol Biol.2010;636:45-54. Abstract

Sardiu ME, Washburn MP. Enriching quantitative proteomics with SI(N).Nat Biotechnol. 2010;28:40-42. Abstract

Sarthy JF, Baumann P. Apollo-Taking the Lead in Telomere Protection. Mol Cell. 2010;39:489-491. Abstract

Shen R, Xie T. NANOS: a germline stem cell's Guardian Angel. J Mol Cell Biol.2010;2:76-77. Abstract

Slaughter BD, Li R. Toward Quantitative "in vivo biochemistry" with Fluorescence Fluctuation Spectroscopy. Mol Biol Cell. 2010;21:4306-4311. Abstract

Slaughter BD, Smith SE, Li R. Symmetry breaking in the life cycle of the budding yeast. In: R Li, and B Bowerman, eds. Symmetry Breaking in Biology. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2010:99-116.

Smith E, Shilatifard A. The Chromatin Signaling Pathway: Diverse Mechanisms of Recruitment of Histone-Modifying Enzymes and Varied Biological Outcomes. Mol Cell. 2010;40:689-701. Abstract

Steen J, Morrison JA, Kulesa PM. Multi-position photoactivation and multi-time acquisition for large-scale cell tracing in avian embryos. Cold Spring Harb Protoc.2010;2010:pdb prot5447. Abstract

Suganuma T, Workman JL. Features of the PHF8/KIAA1718 histone demethylase. Cell Res.2010;20:861-862. Abstract

Suganuma T, Workman JL. WD40 repeats arrange histone tails for spreading of silencing. J Mol Cell Biol.2010;2:81-83. Abstract

Sugimura R, Li L. Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases. Birth Defects Res C Embryo Today. 2010;90:243-256. Abstract
Sugimura R, Li L. Shifting in balance between osteogenesis and adipogenesis substantially influences hematopoiesis. J Mol Cell Biol.2010;2:61-62. Abstract

Takahashi YH, Shilatifard A. Structural basis for H3K4 trimethylation by yeast Set1/COMPASS. Adv Enzyme Regul.2010;50:104-110. Abstract

Tenzen T, Zembowicz F, Cowan CA. Genome modification in human embryonic stem cells. J Cell Physiol.2010;222:278-281. Abstract

Trainor PA. Craniofacial birth defects: The role of neural crest cells in the etiology and pathogenesis of Treacher Collins syndrome and the potential for prevention. Am J Med Genet A. 2010;152A:2984-2994. Abstract

Vilhais-Neto GC, Maruhashi M, Smith KT, Vasseur-Cognet M, Peterson AS, Workman JL, Pourquie O. Rere controls retinoic acid signalling and somite bilateral symmetry. Nature.2010;463:953-957. Abstract

Weake VM, Workman JL. Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet. 2010;11:426-437. Abstract

Xiong B, Gerton JL. Regulators of the cohesin network. Annu Rev Biochem.2010;79:131-153. Abstract

Yin T, Li L. Fountain of Youth: aged blood-forming stem cells could be rejuvenated by young microenvironment. Cell Res.2010;20:504-505. Abstract

Zeitlinger J, Stark A. Developmental gene regulation in the era of genomics. Dev Biol.2010;339:230-239. Abstract

Zhang SO, Box AC, Xu N, Le Men J, Yu J, Guo F, Trimble R, Mak HY. Genetic and dietary regulation of lipid droplet expansion in Caenorhabditis elegans. Proc Natl Acad Sci U S A.2010;107:4640-4645. Abstract

Book

Baumann P. G-Quadruplex DNA. Vol 608: Springer Verlag, Humana Press; 2010.

Li R, Bowerman B. Symmetry Breaking in Biology, 1st ed. Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press. 2010.

2009

Original Research Papers

Anderson JA, Gilliland WD, Langley CH. Molecular population genetics and evolution of Drosophila meiosis genes. Genetics.2009;181:177-185. Abstract

Asai-Coakwell M, French CR, Ye M, Garcha K, Bigot K, Perera AG, Staehling-Hampton K, Mema SC, Chanda B, Mushegian A, Bamforth S, Doschak MR, Li G, Dobbs MB, Giampietro PF, Brooks BP, Vijayalakshmi P, Sauve Y, Abitbol M, Sundaresan P, van Heyningen V, Pourquié O, Underhill TM, Waskiewicz AJ, Lehmann OJ. Incomplete penetrance and phenotypic variability characterize Gdf6-attributable oculo-skeletal phenotypes. Hum Mol Genet. 2009;18:1110-1121. Abstract

Aygun O, Xu X, Liu Y, Takahashi H, Kong SE, Conaway RC, Conaway JW, Svejstrup JQ. Direct inhibition of RNA polymerase II transcription by RECQL5. J Biol Chem.2009;284:23197-23203. Abstract

Blanchette M, Green RE, Macarthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell.2009;33:438-449. Abstract

Blumenstiel JP, Noll AC, Griffiths JA, Perera AG, Walton KN, Gilliland WD, Hawley RS, Staehling-Hampton K. Identification of EMS-induced mutations in Drosophila melanogaster by whole-genome sequencing. Genetics.2009;182:25-32. Abstract

Butcher RA, Ragains JR, Li W, Ruvkun G, Clardy J, Mak HY. Biosynthesis of the Caenorhabditis elegans dauer pheromone. Proc Natl Acad Sci U S A.2009;106:1875-1879. Abstract

Camahort R, Shivaraju M, Mattingly M, Li B, Nakanishi S, Zhu D, Shilatifard A, Workman JL, Gerton JL. Cse4 is part of an octameric nucleosome in budding yeast. Mol Cell.2009;35:794-805. Abstract

Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, Zhang K, Melton DA, Eggan K. Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. Cell Stem Cell 2009;4:103-106. Abstract

Cochran JC, Sindelar CV, Mulko NK, Collins KA, Kong SE, Hawley RS, Kull FJ. ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement. Cell.2009;136:110-122. Abstract

Dang W, Steffen KK, Perry R, Dorsey JA, Johnson FB, Shilatifard A, Kaeberlein M, Kennedy BK, Berger SL. Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature.2009;459:802-807. Abstract

Deng M, Gao J, Suraneni P, Li R. Kinetochore-independent chromosome poleward movement during anaphase of meiosis II in mouse eggs. PLoS ONE.2009;4:e5249. Abstract

Deng M, Li R. Sperm chromatin-induced ectopic polar body extrusion in mouse eggs after ICSI and delayed egg activation. PLoS One.2009;4:e7171. Abstract

Ding N, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Boyer TG. MED19 and MED26 are synergistic functional targets of the RE1 silencing transcription factor in epigenetic silencing of neuronal gene expression. J Biol Chem.2009;284:2648-2656. Abstract

Dinglasan RR, Devenport M, Florens L, Johnson JR, McHugh CA, Donnelly-Doman M, Carucci DJ, Yates JR, 3rd, Jacobs-Lorena M. The Anopheles gambiae adult midgut peritrophic matrix proteome. Insect Biochem Mol Biol.2009;39:125-134. Abstract

Egli D, Sandler VM, Shinohara ML, Cantor H, Eggan K. Reprogramming after chromosome transfer into mouse blastomeres. Curr Biol.2009;19:1403-1409. Abstract

Ferreira ME, Prochasson P, Berndt KD, Workman JL, Wright APH. Activator-binding domains of the SWI/SNF chromatin remodeling complex characterizedin vitro are required for its recruitment to promotersin vivo. FEBS J.2009;276:2557-2565. Abstract

Gard S, Light W, Xiong B, Bose T, McNairn AJ, Harris B, Fleharty B, Seidel C, Brickner JH, Gerton JL. Cohesinopathy mutations disrupt the subnuclear organization of chromatin. J Cell Biol.2009;187:455-462. Abstract

Gibb S, Zagorska A, Melton K, Tenin G, Vacca I, Trainor P, Maroto M, Dale JK. Interfering with Wnt signalling alters the periodicity of the segmentation clock. Dev Biol.2009;330:21-31. Abstract

Gilliland WD, Hughes SF, Vietti DR, Hawley RS. Congression of achiasmate chromosomes to the metaphase plate in Drosophila melanogaster oocytes. Dev Biol.2009;325:122-128. Abstract

Gilliland WD, Vietti DL, Schweppe NM, Guo F, Johnson TJ, Hawley RS. Hypoxia transiently sequesters Mps1 and Polo to collagenase-sensitive filaments in Drosophila prometaphase oocytes. PLoS One.2009;4:e7544. Abstract

Gottschalk AJ, Timinszky G, Kong SE, Jin J, Cai Y, Swanson SK, Washburn MP, Florens L, Ladurner AG, Conaway JW, Conaway RC. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci U S A.2009;106:13770-13774. Abstract

Harreman M, Taschner M, Sigurdsson S, Anindya R, Reid J, Somesh B, Kong SE, Banks CAS, Conaway RC, Conaway JW, Svejstrup JQ. Distinct ubiquitin ligases act sequentially for RNA polymerase II polyubiquitylation. Proc Natl Acad Sci U S A.2009;106:20705-20710. Abstract

Hartmann B, Castelo R, Blanchette M, Boue S, Rio DC, Valcarcel J. Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells. Genome Biol.2009;10:R11. Abstract

Hughes SE, Gilliland WD, Cotitta JL, Takeo S, Collins KA, Hawley RS. Heterochromatic threads connect oscillating chromosomes during prometaphase I in Drosophila oocytes. PLoS Genet.2009;5:e1000348. Abstract

Ichida JK, Blanchard J, Lam K, Son EY, Chung JE, Egli D, Loh KM, Carter AC, Di Giorgio FP, Koszka K, Huangfu D, Akutsu H, Liu DR, Rubin LL, Eggan K. A small-molecule inhibitor of Tgf-β signaling replaces Sox2 in reprogramming by inducing Nanog. Cell Stem Cell.2009;5:491-503. Abstract

Iulianella A, Sharma M, Vanden Heuvel GB, Trainor PA. Cux2 functions downstream of Notch signaling to regulate dorsal interneuron formation in the spinal cord. Development.2009;136:2329-2334. Abstract

Kim J, Guermah M, McGinty RK, Lee JS, Tang Z, Milne TA, Shilatifard A, Muir TW, Roeder RG. RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell.2009;137:459-471. Abstract

Kulesa PM, Stark DA, Steen J, Lansford R, Kasemeier-Kulesa JC. Watching the assembly of an organ a single cell at a time using confocal multi-position photoactivation and multi-time acquisition. Organogenesis.2009;5:238-247. Abstract

Lee KK, Swanson SK, Florens L, Washburn MP, Workman JL. Yeast Sgf73/Ataxin-7 serves to anchor the deubiquitination module into both SAGA and Slik(SALSA) HAT complexes. Epigenetics Chromatin.2009;2:2. Abstract

Li B, Jackson J, Simon MD, Fleharty B, Gogol M, Seidel C, Workman JL, Shilatifard A. Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription. J Biol Chem.2009;284:7970-7976. Abstract

Li H, Kristensen DM, Coleman MK, Mushegian A. Detection of biochemical pathways by probabilistic matching of phyletic vectors. PLoS ONE.2009;4:e5326. Abstract

Magill G, Neaves WB. Ontological and ethical implications of direct nuclear reprogramming. Kennedy Inst Ethics J.2009;19:23-32.

McNairn AJ, Gerton JL. Intersection of ChIP and FLIP, genomic methods to study the dynamics of the cohesin proteins. Chromosome Res.2009;17:155-163. Abstract

Mosley AL, Florens L, Wen Z, Washburn MP. A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus. J Proteomics.2009;72:110-120. Abstract

Mosley AL, Pattenden SG, Carey M, Venkatesh S, Gilmore JM, Florens L, Workman JL, Washburn MP. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell.2009;34:168-178. Abstract

Nakanishi S, Lee JS, Gardner KE, Gardner JM, Takahashi YH, Chandrasekharan MB, Sun ZW, Osley MA, Strahl BD, Jaspersen SL, Shilatifard A. Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1. J Cell Biol.2009;186:371-377. Abstract

Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev.2009;23:912-927. Abstract

Patel AB, Gibson WT, Gibson MC, Nagpal R. Modeling and inferring cleavage patterns in proliferating epithelia. PLoS Comput Biol.2009;5:e1000412. Abstract

Resnick TD, Dej KJ, Xiang Y, Hawley RS, Ahn C, Orr-Weaver TL. Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration in Drosophila female meiosis. Genetics.2009;181:875-887. Abstract

Rubinstein B, Fournier MF, Jacobson K, Verkhovsky AB, Mogilner A. Actin-myosin viscoelastic flow in the keratocyte lamellipod. Biophys J.2009;97:1853-1863. Abstract

Rubinstein B, Larripa K, Sommi P, Mogilner A. The elasticity of motor-microtubule bundles and shape of the mitotic spindle. Phys Biol.2009;6:016005. Abstract

Sardiu ME, Florens L, Washburn MP. Evaluation of clustering algorithms for protein complex and protein interaction network assembly. J Proteome Res.2009;8:2944-2952. Abstract

Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP. Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One.2009;4:e7310. Abstract

Sarthy J, Bae NS, Scrafford J, Baumann P. Human RAP1 inhibits non-homologous end joining at telomeres. EMBO J.2009;28:3390-3399. Abstract

Schulze JM, Jackson J, Nakanishi S, Gardner JM, Hentrich T, Haug J, Johnston M, Jaspersen SL, Kobor MS, Shilatifard A. Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell.2009;35:626-641. Abstract

Shelton C, Kocherlakota KS, Zhuang S, Abmayr SM. The immunoglobulin superfamily member Hbs functions redundantly with Sns in interactions between founder and fusion-competent myoblasts. Development.2009;136:1159-1168. Abstract

Shen R, Weng C, Yu J, Xie T. eIF4A controls germline stem cell self-renewal by directly inhibiting BAM function in the Drosophila ovary. Proc Natl Acad Sci U S A.2009;106:11623-11628. Abstract

Shi M, Vivian CJ, Lee KJ, Ge C, Morotomi-Yano K, Manzl C, Bock F, Sato S, Tomomori-Sato C, Zhu R, Haug JS, Swanson SK, Washburn MP, Chen DJ, Chen BP, Villunger A, Florens L, Du C. DNA-PKcs-PIDDosome: a nuclear caspase-2-activating complex with role in G2/M checkpoint maintenance. Cell.2009;136:508-520. Abstract **Retracted**

Skaar JR, Richard DJ, Saraf A, Toschi A, Bolderson E, Florens L, Washburn MP, Khanna KK, Pagano M. INTS3 controls the hSSB1-mediated DNA damage response. J Cell Biol.2009;187:25-32. Abstract

Slaughter BD, Das A, Schwartz JW, Rubinstein B, Li R. Dual modes of Cdc42 recycling fine-tune polarized morphogenesis. Dev Cell.2009;17:823-835. Abstract

Takahashi H, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC. Proteomics reveals a physical and functional link between hepatocyte nuclear factor 4α and transcription factor IID. J Biol Chem.2009;284:32405-32412. Abstract

Takahashi YH, Lee JS, Swanson SK, Saraf A, Florens L, Washburn MP, Trievel RC, Shilatifard A. Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1. Mol Cell Biol.2009;29:3478-3486. Abstract

Trainor PA, Dixon J, Dixon MJ. Treacher Collins syndrome: etiology, pathogenesis and prevention. Eur J Hum Genet.2009;17:275-283. Abstract

Tsoy O, Ravcheev D, Mushegian A. Comparative genomics of ethanolamine utilization. J Bacteriol.2009;191:7157-7164. Abstract

Wai SC, Gerber SA, Li R. Multisite phosphorylation of the guanine nucleotide exchange factor Cdc24 during yeast cell polarization. PLoS One.2009;4:e6563. Abstract

Wang P, Lin C, Smith ER, Guo H, Sanderson BW, Wu M, Gogol M, Alexander T, Seidel C, Wiedemann LM, Ge K, Krumlauf R, Shilatifard A. Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Mol Cell Biol.2009;29:6074-6085. Abstract

Weake VM, Swanson SK, Mushegian A, Florens L, Washburn MP, Abmayr SM, Workman JL. A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression. Genes Dev.2009;23:2818-2823. Abstract

Wiegraebe W, Xie Y, Yin T, Stark D, Perko K, Alexander R, Schwartz J, He XC, Li L. Two-Photon Microscopy and Spectral Detection for Ex Vivo Imaging of Individual Stem Cells. Nature Protocols in Protocols Network. 2009. Available at: http://www.natureprotocols.com/2009/02/19/twophoton_microscopy_and_spect.php. Accessed September 28, 2009.

Xie Y, Yin T, Wiegraebe W, He XC, Miller D, Stark D, Perko K, Alexander R, Schwartz J, Grindley JC, Park J, Haug JS, Wunderlich JP, Li H, Zhang S, Johnson T, Feldman RA, Li L. Detection of functional haematopoietic stem cell niche using real-time imaging. Nature.2009;457:97-101. Abstract

Zhang Y, Wen Z, Washburn MP, Florens L. Effect of Dynamic Exclusion Duration on Spectral Count Based Quantitative Proteomics. Anal Chem.2009;81:6317-6326. Abstract

Zhuang S, Shao H, Guo F, Trimble R, Pearce E, Abmayr SM. Sns and Kirre, the Drosophila orthologs of Nephrin and Neph1, direct adhesion, fusion and formation of a slit diaphragm-like structure in insect nephrocytes. Development.2009;136:2335-2344. Abstract

Reviews, Commentaries or Chapters

Alexander T, Nolte C, Krumlauf R. Hox Alexander T, Nolte C, Krumlauf R. Hox genes and segmentation of the hindbrain and axial skeleton. Annu Rev Cell Dev Biol.2009;25:431-456. Abstract

Baumann P. Journal club. A molecular biologist explores ways to revolutionize agriculture. Nature.2009;462:547. Abstract

Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. An operational definition of epigenetics. Genes Dev.2009;23:781-783. Abstract

Conaway RC, Conaway JW. Mediator comes out from the shadows. Structure.2009;17:485-486. Abstract

Conaway RC, Conaway JW. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci.2009;34:71-77. Abstract

Gibson WT, Gibson MC. Cell topology, geometry, and morphogenesis in proliferating epithelia. Curr Top Dev Biol.2009;89:87-114. Abstract

Hall HE, Hawley RS. The hows and Ys of genome integrity. Cell.2009;138:830-832. Abstract

Hawley RS. A direct measurement of crossingover in human orophase oocytes. F1000 Biol Rpts[serial online].2009;1:86. Available at:http://F1000.com/Reports/Biology/content/1/86., Accessed November 16, 2009.

Hawley RS, Gilliland WD. Homologue pairing: getting it right. Nat Cell Biol.2009;11:917-918. Abstract

Hawley RS. Review of "Life Illuminated: Selected Papers from Cold Spring Harbor," Volume 2, 1972-1994, edited by J. Witkowski et al. Q Rev Biol.2009;84:183.

Herz HM, Nakanishi S, Shilatifard A. The curious case of bivalent marks. Dev Cell.2009;17:301-303. Abstract

Hughes SE, Hawley RS. Heterochromatin: a rapidly evolving species barrier. PLoS Biol.2009;7:e1000233. Abstract

Iimura T, Denans N, Pourquie O. Establishment of Hox vertebral identities in the embryonic spine precursors. Curr Top Dev Biol.2009;88:201-234. Abstract

Jackson J, Shilatifard A. Global proteomic analysis of Saccharomyces cerevisiae identifies molecular pathways of histone modifications. Methods Mol Biol.2009;548:175-186. Abstract

Jaspersen SL, Hawley RS. Pushing and pulling: microtubules mediate meiotic pairing and synapsis. Cell.2009;139:861-863. Abstract

Korfali N, Fairley EA, Swanson SK, Florens L, Schirmer EC. Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification. Methods Mol Biol.2009;528:201-225.

Kulesa PM, Lefcort F, Kasemeier-Kulesa JC. The migration of autonomic precursor cells in the embryo. Auton Neurosci.2009;151:3-9. Abstract

Lawrence C, Sanders GE, Varga ZM, Baumann DP, Freeman A, Baur B, Francis M. Regulatory compliance and the zebrafish. Zebrafish.2009;6:453-456. Abstract

Li R, Wedlich-Soldner R. Bem1complexes and the complexity of yeast cell polarization. Curr Biol.2009;19:R194-R195.

Liu Y, Conaway JW. When transcription meets recombination: a lesson from the human RECQ protein complexes. F1000 Biol Rpts [serial online].2009;1.76. Available at: http://f1000biology.com/reports/10.3410/b1-76/, Accessed October 14, 2009.

Parrish M, Nolte C, Krumlauf R. Hox genes expression. In: L Squire, ed. New Encyclopedia of Neuroscience. 4th ed: Academic Press; 2009:1221-1231.

Ross J, Li L. HSC mobilization: new incites and insights. Blood.2009;114:1283-1284. Abstract

Sakai D, Trainor PA. Treacher Collins syndrome: Unmasking the role of Tcof1/treacle. Int J Biochem Cell Biol.2009;41:1229-1232. Abstract

Slaughter BD, Smith SE, Li R. Symmetry breaking in the life cycle of the budding yeast. ColdSpring HarborPerspect Biol.2009;1:a003384. Abstract

Smith E, Shilatifard A. Developmental biology. Histone cross-talk in stem cells. Science.2009;323:221-222. Abstract

Smith KT, Workman JL. Histone deacetylase inhibitors: Anticancer compounds. Int J Biochem Cell Biol.2009;41:21-25. Abstract

Smith KT, Workman JL. Introducing the acetylome. Nat Biotechnol.2009;27:917-919. Abstract

Swanson SK, Florens L, Washburn MP. Generation and analysis of multidimensional protein identification technology datasets. Methods Mol Bol.2009;492:1-20. Abstract

Trainor P. Facial birth defects unmasked. Australas Sci.2009:29-32.

Trievel RC, Shilatifard A. WDR5, a complexed protein. Nat Struct Mol Biol.2009;16:678-680. Abstract

Tümpel S, Wiedemann LM, Krumlauf R. Hox genes and segmentation of the vertebrate hindbrain. Curr Top Dev Biol. 2009/08/05 ed; 2009;88:103-137. Abstract

Wang J, Rodova M, Gardner BM, Lu Q, Trainor PA, Yost JG. Wnt/β-catenin signaling plays an essential role in bone sialoprotein-elicited osteoblast differentiation and mineralization. Bone. 2009;44:S158-S159.

Weake VM, Workman JL. Histone ubiquitination. In: RA Bradshaw, and EA Dennis, eds. Handbook of Cell Signaling. 2nd ed: Oxford: Academic Press; 2009:2449-2460.

Weake VM, Workman JL. Hit and run: X marks the spot! Nat Struct Mol Biol.2009;16:801-803. Abstract

Xie T. Stem cell in the adult Drosophila hindgut: just a sleeping beauty. Cell Stem Cell.2009;5:227-228. Abstract

Xie T, Song X, Jin Z, Pan L, Weng C, Chen S, Zhang N. Interactions between stem cells and their niche in the Drosophila ovary. Abstracts of papers presented at the LXXIII Cold Spring Harbor Symposium on Quantitative Biology: Control & Regulation of Stem Cells: May 28-June 2, 2008. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory. 2009;72:39-47.

Yin T, Xie Y, Li L. Visualize eHPCs in different zones. Blood.2009;114:230-231. Abstract

Zhang N, Xie T. Extrinsic and intrinsic control of germline stem cell regulation in the Drosophila ovary. In: VK Rajasekhar, and MC Vemuri, eds. Regulatory Networks in Stem Cells 1st ed. New York: Humana; 2009:155-163. Table of Contents

Book

Pourquié O, ed. Hox Genes, 1st ed. San Diego, Academic Press. 2009.

2008

Original Research Papers

Aulehla A, Wiegraebe W, Baubet V, Wahl MB, Deng C, Taketo M, Lewandoski M, Pourquié O. A beta-catenin gradient links the clock and wavefront systems in mouse embryo segmentation. Nat Cell Biol.2008;10:186-193. Abstract

Baumann D, Cook M, Ma L, Mushegian A, Sanders E, Schwartz J, Yu CR. A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae. Biol Direct.2008;3:28. Abstract

Black JC, Mosley A, Kitada T, Washburn M, Carey M. The SIRT2 deacetylase regulates autoacetylastion of p300. Mol Cell.2008;32:449-455. Abstract

Blumenstiel JP, Fu R, Theurkauf WE, Hawley RS. Components of the RNAi machinery that mediate long-distance chromosomal associations are dispensable for meiotic and early somatic homolog pairing in Drosophila melanogaster. Genetics.2008;180:1355-1365. Abstract

Bogni S, Trainor P, Natarajan D, Krumlauf R,Pachnis V. Non-cell-autonomous effects of Ret deletion in early enteric neurogenesis. Development.2008;135:3007-3011. Abstract

Box JA, Bunch JT, Tang W, Baumann P. Spliceosomal cleavage generates the 3' end of telomerase RNA. Nature.2008;456:910-914. Abstract

Box JA, Bunch JT, Zappulla DC, Glynn EF, Baumann P. A flexible template boundary element in the RNA subunit of fission yeast telomerase. J Biol Chem.2008;283:24224-24233. Abstract

Cornier AS, Staehling-Hampton K, Delventhal KM, Saga Y, Caubet JF, Sasaki N, Ellard S, Young E, Ramirez N, Carlo SE, Torres J, Emans JB, Turnpenny PD, Pourquié O. Mutations in the MESP2 gene cause spondylothoracic dysostosis/Jarcho-Levin syndrome. Am J Hum Genet.2008;82:1334-1341. Abstract

Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS ONE.2008;3:e2856. Abstract

Fan X, Martin-Brown S, Florens L, Li R. Intrinsic capability of budding yeast cofilin to promote turnover of tropomyosin-bound actin filaments. PLoS ONE.2008;3:e3641. Abstract

Geisbrecht ER, Haralalka S, Swanson SK, Florens L, Washburn MP, Abmayr SM. Drosophila ELMO/CED-12 interacts with Myoblast city to direct myoblast fusion and ommatidial organization. Dev Biol.2008;314:137-149. Abstract

Goldbeter A, Pourquié O. Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol.2008;252:574-585.
Abstract

Gomez C, Özbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquié O. Control of segment number in vertebrate embryos. Nature.2008;454:335-339. Abstract

Haug JS, He XC, Grindley JC, Wunderlich JP, Gaudenz K, Ross JT, Paulson A, Wagner KP, Xie Y, Zhu R, Yin T, Perry JM, Hembree MJ, Redenbaugh EP, Radice GL, Seidel C, Li L. N-cadherin expression level distinguishes reserved versus primed states of hematopoietic stem cells. Cell Stem Cell.2008;2:367-379. Abstract

He J, Ma L, Kim S, Nakai J, Yu CR. Encoding gender and individual information in the mouse vomeronasal organ. Science. 2008;320:535-538. Abstract

Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A.2008;105:7762-7767. Abstract

Inoue T, Inoue YU, Asami J, Izumi H, Nakamura S, Krumlauf R. Analysis of mouse Cdh6 gene regulation by transgenesis of modified bacterial artificial chromosomes. Dev Biol.2008;315:506-520. Abstract

Iulianella A, Sharma M, Durnin M, Vanden Heuvel GB, Trainor PA. Cux2 (Cutl2) integrates neural progenitor development with cell-cycle progression during spinal cord neurogenesis. Development.2008;135:729-741. Abstract

Jin Z, Kirilly D, Weng C, Kawase E, Smith S, Schwartz J, Xie T. Differentiation-defective stem cells outcompete normal stem cells for niche occupancy in the Drosophila ovary. Cell Stem Cell.2008;2:39-49. Abstract

Jones NC, Lynn ML, Gaudenz K, Sakai D, Aoto K, Rey JP, Glynn EF, Ellington L, Du C, Dixon J, Dixon MJ, Trainor PA. Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function. Nat Med.2008;14:125-133. Abstract

Kasemeier-Kulesa JC, Teddy JM, Postovit LM, Seftor EA, Seftor RE, Hendrix MJ, Kulesa PM. Reprogramming multipotent tumor cells with the embryonic neural crest microenvironment. Dev Dyn.2008;237:2657-2666. Abstract

Kocherlakota KS, Wu JM, McDermott J, Abmayr SM. Analysis of the cell adhesion molecule sticks-and-stones reveals multiple redundant functional domains, protein-interaction motifs and phosphorylated tyrosines that direct myoblast fusion in Drosophila melanogaster. Genetics.2008;178:1371-1383. Abstract

Koutelou E, Sato S, Tomomori-Sato C, Florens L, Swanson SK, Washburn MP, Kokkinaki M, Conaway RC, Conaway JW, Moschonas NK. Neuralized-like 1 (Neurl1) targeted to the plasma membrane by N-Myristoylation regulates the Notch ligand Jagged1. J Biol Chem.2008;283:3846-3853. Abstract

Kulesa PM, Teddy JM, Stark DA, Smith SE, McLennan R. Neural crest invasion is a spatially-ordered progression into the head with higher cell proliferation at the migratory front as revealed by the photoactivatable protein, KikGR. Dev Biol.2008;316:275-287. Abstract

Leonardi J, Box JA, Bunch JT, Baumann P. TER1, the RNA subunit of fission yeast telomerase. Nat Struct Mol Biol.2008;15:26-33. Abstract

Li H, Guo F, Rubinstein B, Li R. Actin-driven chromosomal motility leads to symmetry breaking in mammalian meiotic oocytes. Nat Cell Biol.2008;10:1301-1308. Abstract

Li H, Zhu D, Cook M. A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data. BMCGenomics.2008;9:188. Abstract

Li X, Magenheimer BS, Xia S, Johnson T, Wallace DP, Calvet JP, Li R. A tumor necrosis factor-alpha-mediated pathway promoting autosomal dominant polycystic kidney disease. Nat Med.2008;14:863-868. Abstract

Lin CH, Li B, Swanson S, Zhang Y, Florens L, Washburn MP, Abmayr SM, Workman JL. Heterochromatin Protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase. Mol Cell.2008;32:696-706. Abstract

Liu WL, Coleman RA, Grob P, King DS, Florens L, Washburn MP, Geles KG, Yang JL, Ramey V, Nogales E, Tjian R. Structural changes in TAF4b-TFIID correlate with promoter selectivity. Mol Cell.2008;29:81-91. Abstract

Mahrour N, Redwine WB, Florens L, Swanson SK, Martin-Brown S, Bradford WD, Staehling-Hampton K, Washburn MP, Conaway RC, Conaway JW. Characterization of Cullin-box sequences that direct recruitment of Cul2-Rbx1 and Cul5-Rbx2 modules to Elongin BC-based ubiquitin ligases. J Biol Chem.2008;283:8005-8013. Abstract

Minakhin L, Goel M, Berdygulova Z, Ramanculov E, Florens L, Glazko G, Karamychev VN, Slesarev AI, Kozyavkin SA, Khromov I, Ackermann HW, Washburn M, Mushegian A, Severinov K. Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol.2008;378:468-480.Abstract

Nakanishi S, Sanderson BW, Delventhal KM, BradfordWD, Staehling-Hampton K, Shilatifard A. A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation. Nat Struct Mol Biol. 2008;15:881-888. Abstract

Page SL, Khetani RS, Lake CM, Nielsen RJ, Jeffress JK, Warren WD, Bickel SE, Hawley RS. corona is required for higher-order assembly of transverse filaments into full-length synaptonemal complex in Drosophila Oocytes. PLoS Genet. 2008;4:e1000194. Abstract

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics.2008;7:631-644. Abstract

Rancati G, Pavelka N, Fleharty B, Noll A, Trimble R, Walton K, Perera A, Staehling-Hampton K, Seidel CW, Li R. Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor. Cell.2008;135:879-893. Abstract

Roux MM, Radeke MJ, Goel M, Mushegian A, Foltz KR. 2DE identification of proteins exhibiting turnover and phosphorylation dynamics during sea urchin egg activation. Dev Biol.2008;313:630-647. Abstract

Rubinstein BY. Expression for restricted partition function through Bernoulli polynomials. Ramanujan J.2008;15:177-185.

Sansό M, Gogol M, Ayte J, Seidel C, Hidalgo E. Transcription factors Pcr1 and Atf1 have distinct roles in stress- and Sty1-dependent gene regulation. Eukaryot Cell. 2008;7::826-835. Abstract

Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP. Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A.2008;105:1454-1459. Abstract

Savalia D, Westblade LF, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan JC, Chait BT, Washburn MP, Ackermann HW, Mushegian A, Gabisonia T, Molineux I, Severinov K. Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. J Mol Biol.2008;377:774-789. Abstract

Slaughter BD, Huff JM, Wiegraebe W, Schwartz JW, Li R. SAM domain-based protein oligomerization observed by live-cell fluorescence fluctuation spectroscopy. PLoS ONE.2008;3:e1931. Abstract

Smith ER, Lee MG, Winter B, Droz NM, Eissenberg JC, Shiekhattar R, Shilatifard A. Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II. Mol Cell Biol.2008;28:1041-1046. Abstract

Smith ER, Winter B, Eissenberg JC, Shilatifard A. Regulation of the transcriptional activity of poised RNA polymerase II by the elongation factor ELL. Proc Natl Acad Sci U S A.2008;105:8575-8579. Abstract

Srivastava S, Swanson SK, Manel N, Florens L, Washburn MP, Skowronski J. Lentiviral Vpx accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection. PLoS Pathog.2008;4:e1000059. Abstract

Suganuma T, Gutierrez JL, Li B, Florens L, Swanson SK, Washburn MP, Abmayr SM, Workman JL. ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding. Nat Struct Mol Biol.2008;15:364-372.

Tümpel S, Cambronero F, Sims C, Krumlauf R, Wiedemann LM. A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc Natl Acad Sci U S A.2008;105:20077-20082.Abstract

Wang P, Bowl MR, Bender S, Peng J, Farber L, Chen J, Ali A, Zhang Z, Alberts AS, Thakker RV, Shilatifard A, Williams BO, Teh BT. Parafibromin, a component of the human PAF complex, regulates growth factors and is required for embryonic development and survival in adult mice. Mol Cell Biol.2008;28:2930-2940. Abstract

Wang X, Baumann P. Chromosome fusions following telomere loss are mediated by single-strand annealing. Mol Cell.2008;31:463-473.

Weake VM, Lee KK, Guelman S, Lin CH, Seidel C, Abmayr SM, Workman JL. SAGA-mediated H2B deubiquitination controls the development of neuronal connectivity in the Drosophila visual system. Embo J.2008;27:394-405. Abstract

Wu M, Wang PF, Lee JS, Martin-Brown S, Florens L, Washburn M, Shilatifard A. Molecular regulation of H3K4 trimethylation by Wdr82, a component of the human Set1/COMPASS. Mol Cell Biol.2008;24:7337-7344. Abstract

Xie T. Physiology. Burn fat, live longer. Science.2008;322:865-866. Abstract

Yao T, Song L, Jin J, Cai Y, Takahashi H, Swanson SK, Washburn MP, Florens L, Conaway RC, Cohen RE, Conaway JW. Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Mol Cell.2008;31:909-917. Abstract

Reviews, Commentaries and Chapters

Abmayr SM, Zhuang S, Geisbrecht ER. Myoblast fusion in Drosophila. Methods Mol Biol.2008;475:75-97. Abstract

Aulehla A, Pourquié O. Oscillating signaling pathways during embryonic development. Curr Opin Cell Biol.2008;20:632-637. Abstract

Benazeraf B, Pourquié O. Developmental biology: cell intercalation one step beyond. Curr Biol.2008;18:R119-R121. Abstract

Bhattacharyya S, Kulesa PM, Fraser SE. Vital labeling of embryonic cells using fluorescent dyes and proteins. Methods Cell Biol. 2008;87:187-210.

Dequéant ML, Pourquié O. Segmental patterning of the vertebrate embryonic axis. Nat Rev Genet.2008;370-382. Abstract

Emmert-Streib F, Dehmer M. Detecting pathological pathways of a complex disease by a comparative analysis of networks. In: F Emmert-Streib, and M Dehmer, eds. Analysis of Microarray Data: A Network-Based Approach. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA; 2008:285-305.

Florens L, Korfali N, Schirmer EC. Subcellular fractionation and proteomics of nuclear envelopes. Methods Mol Biol. 2008;432:117-137. Abstract

Geng C. New advances in stem cell biology: a perspective from gametogenesis. Fly.2008;2:145-148. Abstract

Gottschalk AJ, Conaway RC, Conaway JW. New clues to actin function in chromatin regulation. Nat Struct Mol Biol.2008;15:432-433. Abstract

Iimura T, Pourquié O. Manipulation and electroporation of the avian segmental plate and somites in vitro. Methods Cell Biol. 2008;87:257-270.Abstract

Jaspersen SL, Stearns T. Exploring the pole: an EMBO conference on centrosomes and spindle pole bodies. Nat Cell Biol.2008;10:1375-1378. Abstract

Kwon SH, Workman JL. The heterochromatin protein 1 (HP1) family: put away a bias toward HP1. Mol Cells.2008;26:217-227. Abstract

Leyser O, Pourquié O. Pattern formation and developmental mechanisms. Curr Opin Genet Dev.2008;18:285-286. Abstract

Li R, Gundersen GG. Beyond polymer polarity: how the cytoskeleton builds a polarized cell. Nat Rev Mol Cell Biol.2008;9:860-873. Abstract

McNairn AJ, Gerton JL. The chromosome glue gets a little stickier. Trends Genet.2008;24:382-389. Abstract

McNairn AJ, Gerton JL. Cohesinopathies: one ring, many obligations. Mutat Res.2008;647:103-111.

Mehrotra S, Hawley RS, McKim KS. Synapsis, double strand breaks, and domains of crossover control in Drosophila females. In: R Egel, ed. Recombination and Meiosis: Crossing-Over and Disjunction. Heidelberg: Springer Verlag 2008;2:125-151.

Mushegian A. Gene content of LUCA, the last universal common ancestor. Front Biosci.2008;13:4657-4666. Abstract

Nagpal R, Patel A, Gibson MC. Problems and paradigms: epithelial topology. BioEssays.2008;30:260-266. Abstract

Neaves WB. When does a person become a person? Natl Cathol Report.2008;December 26, 2008:10-11.

Özbudak EM, Pourquié O. The vertebrate segmentation clock: the tip of the iceberg. Curr Opin Genet Dev.2008;18:317-323. Abstract

Perry JM, Li L. Self-renewal versus transformation: Fbxw7 deletion leads to stem cell activation and leukemogenesis. Genes Dev.2008;22:1107-1109. Abstract

Scoville DH, Sato T, He XC, Li L. Current view: intestinal stem cells and signaling. Gastroenterology.2008;134:849-864. Abstract

Seidel C. Introduction to DNA microarrays. In: F Emmert-Streib, and M Dehmer, eds. Analysis of Microarray Data: A Network-Based Approach. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA; 2008:1-26.

Shen R, Xie T. Stem cell self-renewal versus differentiation: tumor suppressor Mei-P26 and miRNAs control the balance. Cell Res.2008;18:713-715. Abstract

Shilatifard A. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol.2008;20:341-348.Abstract.

Smith SK, Jaspersen SL, Hawley RS. Matrimony ties Polo down: can this kinase get free? Cell Cycle.2008;7:698-701. Abstract

Stark DA, Kasemeier-Kulesa JC, Kulesa PM. Photoactivation cell labeling for cell tracing in avian development. CSH Protocols.2008;doi10.1101/pdb.prot4975.

Suganuma T, Pattenden SG, Workman JL. Diverse functions of WD40 repeat proteins in histone recognition. Genes Dev.2008;22:1265-1268. Abstract

Suganuma T, Workman JL. Crosstalk among histone modifications. Cell.2008;135:604-607. Abstract

Vilhais-Neto GC, Pourquié O. Retinoic acid [published correction appears in Curr Biol. 2008;18:550-552]. Curr Biol.2008;18:R191-192. Abstract

Washburn M. Coupled multidimensional chromatography and tandem mass spectrometry systems for complex peptide mixture analysis. In: SA Cohen, and MR Schure, eds. Multidimensional Liquid Chromatography: Theory and Applications in Industrial Chemistry and the Life Sciences. Hoboken, N.J.: Wiley-Interscience; 2008;11:243-259. Table of Contents

Weake VM, Workman JL. Clearing the way for unpaused polymerases. Cell.2008;134:16-18. Abstract

Weake VM, Workman JL. Histone ubiquitination: triggering gene activity. Mol Cell.2008;29:653-663. Abstract

Wedlich-Soldner R, Li R. Yeast and fungal morphogenesis from an evolutionary perspective. Semin Cell Dev Biol.2008;19:224-233. Abstract

Xie T. Germline stem cell niches. In: H Lin, and P Donahoe, eds. StemBook: The Stem Cell Research Community; 2008;doi/103824/stembook.1.23.1. Available at: http://www.stembook.org. Accessed September 30, 2008.

Zhu D, Dequéant ML, Li H. Comparative analysis of clustering methods for microarray data. In: F Emmert-Streib, and M Dehmer, eds. Analysis of Microarray Data: A Network-Based Approach. Weinheim: Wiley-VCH Verlag GmbH & Co; 2008;2:27-50.

Book

Dehmer M, Emmert-Streib F, eds. Analysis of Microarray Data: A Network-Based Approach. Weinheim, Wiley-VCH Verlag GMBH & Co. KgaA. 2008.

2007

Original Research Papers

Bae NS, Baumann P. A RAP1/TRF2 Complex Inhibits Nonhomologous End-Joining at Human Telomeric DNA Ends. Mol Cell.2007;26:323-334. Abstract

Banks CA, Kong SE, Spahr H, Florens L, Martin-Brown S, Washburn MP, Conaway JW, Mushegian A, Conaway RC. Identification and Characterization of a Schizosaccharomyces pombe RNA Polymerase II Elongation Factor with Similarity to the Metazoan Transcription Factor ELL. J Biol Chem.2007;282:5761-5769. Abstract

Bausch C, Noone S, Henry JM, Gaudenz K, Sanderson B, Seidel C, Gerton JL. Transcription alters chromosomal locations of cohesin in Saccharomyces cerevisiae. Mol Cell Biol.2007;27:8522-8532. Abstract

Bleuming SA, He XC, Kodach LL, Hardwick JC, Koopman FA, Ten Kate FJ, van Deventer SJ, Hommes DW, Peppelenbosch MP, Offerhaus GJ, Li L, van den Brink GR. Bone morphogenetic protein signaling suppresses tumorigenesis at gastric epithelial transition zones in mice. Cancer Res.2007;67:8149-8155. Abstract

Bupp JM, Martin AE, Stensrud ES, Jaspersen SL. Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3. J Cell Biol. 2007;179:845-854. Abstract

Cai Y, Jin J, Yao T, Gottschalk AJ, Swanson SK, Wu S, Shi Y, Washburn MP, Florens L, Conaway RC, Conaway JW. YY1 functions with INO80 to activate transcription. Nat Struct Mol Biol.2007;14:872-874. Abstract

Camahort R, Li B, Florens L, Swanson SK, Washburn MP, Gerton JL. Scm3 is essential to recruit the histone h3 variant cse4 to centromeres and to maintain a functional kinetochore. Mol Cell.2007;26:853-865. Abstract

Chen X, Wurtmann EJ, Van Batavia J, Zybailov B, Washburn MP, Wolin SL. An orthologue of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans. Genes Dev.2007;21:1328-1339.

Collins KA, Camahort R, Seidel C, Gerton JL, Biggins S. The Overexpression of a Saccharomyces cerevisiae Centromeric Histone H3 Variant Mutant Protein Leads to a Defect in Kinetochore Biorientation. Genetics.2007;175:513-525. Abstract

Deng M, Suraneni P, Schultz RM, Li R. The Ran GTPase Mediates Chromatin Signaling to Control Cortical Polarity during Polar Body Extrusion in Mouse Oocytes. Dev Cell.2007;12:301-308. Abstract

Eissenberg JC, Lee MG, Schneider J, Ilvarsonn A, Shiekhattar R, Shilatifard A. The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat Struct Mol Biol.2007;14:344-346. Abstract

Emmert-Streib F. The chronic fatigue syndrome: a comparative pathway analysis. J Comput Biol.2007;14:961-972. Abstract

Emmert-Streib F, Mushegian A. A topological algorithm for identification of structural domains of proteins. BMCBioinf.2007;8:237. Abstract

Emmert-Streib F, Dehmer M. Topological mappings between graphs, trees and generalized trees. Appl Math Comput.2007;186:1326-1333. Abstract

Gilliland WD, Hughes SE, Cotitta JL, Takeo S, Xiang Y, Hawley RS. The Multiple Roles of Mps1 in Drosophila Female Meiosis. PLoS Genet.2007;3:e113. Abstract

Glazko G, Makarenkov V, Liu J, Mushegian A. Evolutionary history of bacteriophages with double-stranded DNA genomes. Biol Direct.2007;2:36. Abstract

Goldbeter A, Gonze D, Pourquie O. Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signaling. Dev Dyn.2007;236:1495-1508. Abstract

Gutierrez JL, Chandy M, Carrozza MJ, Workman JL. Activation domains drive nucleosome eviction by SWI/SNF. Embo J.2007;26:730-740. Abstract

He XC, Yin T, Grindley JC, Tian Q, Sato T, Tao WA, Dirisina R, Porter-Westpfahl KS, Hembree M, Johnson T, Wiedemann LM, Barrett TA, Hood L, Wu H, Li L. PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet.2007;39:189-198. Abstract

Hendrix MJ, Seftor EA, Seftor RE, Kasemeier-Kulesa J, Kulesa PM, Postovit LM. Reprogramming metastatic tumour cells with embryonic microenvironments. Nat Rev Cancer.2007;7:246-255. Abstract

Hrecka K, Gierszewska M, Srivastava S, Kozaczkiewicz L, Swanson SK, Florens L, Washburn MP, Skowronski J. Lentiviral Vpr usurps Cul4-DDB1[VprBP] E3 ubiquitin ligase to modulate cell cycle. Proc Natl Acad Sci U S A.2007;104:11778-11783. Abstract

Iimura T, Yang X, Weijer CJ, Pourquie O. Dual mode of paraxial mesoderm formation during chick gastrulation. Proc Natl Acad Sci U S A.2007;104:2744-2749. Abstract

Jeffress JK, Page SL, Royer SK, Belden ED, Blumenstiel JP, Anderson LK, Hawley RS. The Formation of the Central Element of the Synaptonemal Complex May Occur by Multiple Mechanisms: The Roles of the N- and C-Terminal Domains of the Drosophila C(3)G Protein in Mediating Synapsis and Recombination. Genetics.2007;177:2445-2456. Genetics.2007;177:2445-2456. Abstract

Jin Z, Xie T. Dcr-1 Maintains Drosophila Ovarian Stem Cells. Curr Biol.2007;17:1-6. Abstract

Kasemeier-Kulesa JC, Lefcort F, Kulesa PM. Sagittal Explant Culture for 3D Confocal Time-Lapse Analysis of Chick Peripheral Nervous System Formation. CSH Protocols.2007;doi:10.1101/pdb.prot4791. Abstract

Kulesa PM, Kasemeier-Kulesa JC. Construction of a Heated Incubation Chamber around a Microscope Stage for Time-Lapse Imaging. CSH Protocols.2007;doi:10.1101/pdb.prot4792. Abstract

Lake CM, Teeter K, Page SL, Nielsen R, Hawley RS. A Genetic Analysis of the Drosophila mcm5 Gene Defines a Domain Specifically Required for Meiotic Recombination. Genetics.2007;176:2151-2163. Abstract

Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI. MSL Complex Is Attracted to Genes Marked by H3K36 Trimethylation Using a Sequence-Independent Mechanism. Mol Cell.2007;28:121-133. Abstract

Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A. Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Cell.2007;131:1084-1096. Abstract

Li B, Gogol M, Carey M, Lee D, Seidel C, Workman JL. Combined Action of PHD and Chromo Domains Directs the Rpd3S HDAC to Transcribed Chromatin. Science.2007;316:1050-1054. Abstract

Li B, Gogol M, Carey M, Pattenden SG, Seidel C, Workman JL. Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription. Genes Dev.2007;21:1422-1430. Abstract

Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS, DeCaprio JA. Evolutionarily Conserved Multisubunit RBL2/p130 and E2F4 Protein Complex Represses Human Cell Cycle-Dependent Genes in Quiescence. Mol Cell.2007;26:539-551.Abstract

McLennan R, Kulesa PM. In vivo analysis reveals a critical role for neuropilin-1 in cranial neural crest cell migration in chick. Dev Biol.2007;301:227-239. Abstract

Marco E, Wedlich-Soldner R, Li R, Altschuler SJ, Wu LF. Endocytosis Optimizes the Dynamic Localization of Membrane Proteins that Regulate Cortical Polarity. Cell.2007;129:411-422. Abstract

Page SL, Nielsen RJ, Teeter K, Lake CM, Ong S, Wright KR, Dean KL, Agne D, Gilliland WD, Hawley RS. A Germline Clone Screen for Meiotic Mutants in Drosophila melanogaster. Fly.2007;1:172-181.

Pan L, Chen S, Weng C, Call G, Zhu D, Tang H, Zhang N, Xie T. Stem Cell Aging Is Controlled Both Intrinsically and Extrinsically in the Drosophila Ovary. Cell Stem Cell.2007;1:458-469.

Rinon A, Lazar S, Marshall H, Buchmann-Moller S, Neufeld A, Elhanany-Tamir H, Taketo MM, Sommer L, Krumlauf R, Tzahor E. Cranial neural crest cells regulate head muscle patterning and differentiation during vertebrate embryogenesis. Development.2007;134:3065-3075. Abstract

Rupp PA, Kulesa PM. High-resolution, intravital 4D confocal time-lapse imaging in avian embryos using a teflon culture chamber design. CSH Protocols.2007;doi:10.1101/pdb.prot4790. Abstract

Rupp PA, Kulesa PM. A role for RhoA in the two-phase migratory pattern of post-otic neural crest cells. Dev Biol.2007;311:159-171. Abstract

Salamat-Miller N, Fang J, Seidel CW, Assenov Y, Albrecht M, Middaugh CR. A Network-based Analysis of Polyanion-binding Proteins Utilizing Human Protein Arrays. J Biol Chem.2007;282:10153-10163. Abstract

Sandell LL, Sanderson BW, Moiseyev G, Johnson T, Mushegian A, Young K, Rey JP, Ma JX, Staehling-Hampton K, Trainor PA. RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. Genes Dev.2007;21:1113-1124. Abstract

Skaar JR, Florens L, Tsutsumi T, Arai T, Tron A, Swanson SK, Washburn MP, DeCaprio JA. PARC and CUL7 form atypical Cullin RING ligase complexes. Cancer Res.2007;67:2007-2014. Abstract

Slaughter BD, Schwartz JW, Li R. Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging. Proc Natl Acad Sci U S A.2007;104:20320-20325. Abstract

Song X, Call GB, Kirilly D, Xie T. Notch signaling controls germline stem cell niche formation in the Drosophila ovary. Development.2007;134:1071-1080. Abstract

Stark DA, Kulesa PM. An In Vivo Comparison of Photoactivatable Fluorescent Proteins in an Avian Embryo Model Dev Dyn.2007;236:1583-1594. Abstract

Tümpel S, Cambronero F, Ferretti E, Blasi F, Wiedemann LM, Krumlauf R. Expression of Hoxa2 in rhombomere 4 is regulated by a conserved cross-regulatory mechanism dependent upon Hoxb1. Dev Biol.2007;302:646-660. Abstract

Wahl MB, Deng C, Lewandoski M, Pourquie O. FGF signaling acts upstream of the NOTCH and WNT signaling pathways to control segmentation clock oscillations in mouse somitogenesis. Development.2007;134:4033-4041. Abstract

Wood A, Shukla A, Schneider J, Lee JS, Stanton JD, Dzuiba T, Swanson SK, Florens L, Washburn MP, Wyrick J, Bhaumik SR, Shilatifard A. Ctk Complex-Mediated Regulation of Histone Methylation by COMPASS. Mol Cell Biol.2007;27:709-720. Abstract

Xhemalce B, Riising EM, Baumann P, Dejean A, Arcangioli B, Seeler JS. Role of SUMO in the dynamics of telomere maintenance in fission yeast. Proc Natl Acad Sci U S A.2007;104:893-898. Abstract

Xiang Y, Takeo S, Florens L, Hughes SE, Huo LJ, Gilliland WD, Swanson SK, Teeter K, Schwartz JW, Washburn MP, Jaspersen SL, Hawley RS. The Inhibition of Polo Kinase by Matrimony Maintains G2 Arrest in the Meiotic Cell Cycle. PLoS Biol.2007;5:2831-2846. Abstract

Yuan CC, Zhao X, Florens L, Swanson SK, Washburn MP, Hernandez N. CHD8 Associates with Human Staf and Contributes to Efficient U6 RNA Polymerase III Transcription. Mol Cell Biol.2007;27:8729-8738. Abstract

Zhu D, Hero AO, III. Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. J Comput Biol.2007;14:1311-1326. Abstract

Zhu D, Li Y, Li H. Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. Bioinformatics.2007;23:2298-2305. Abstract

Zybailov BL, Florens L, Washburn MP. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst.2007;3:354-360. Abstract

Reviews, Commentaries or Chapters

Allis CD, Berger SL, Cote J, Dent S, Jenuwien T, Kouzarides T, Pillus L, Reinberg D, Shi Y, Shiekhattar R, Shilatifard A, Workman J, Zhang Y. New nomenclature for chromatin-modifying enzymes. Cell.2007;131:633-636. Abstract

Bhaumik SR, Smith E, Shilatifard A. Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol.2007;14:1008-1016. Abstract

Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional Separations-Based Shotgun Proteomics. Chem Rev.2007;107:3654-3686. Abstract

Gerton JL. Enhancing togetherness: kinetochores and cohesion. Genes Dev.2007;21:238-241. Abstract

Gibson MC. Bicoid by the Numbers: Quantifying a Morphogen Gradient. Cell.2007;130:14-16. Abstract

Gilmore JM, Washburn MP. Deciphering the combinatorial histone code. Nat Methods.2007;4:480-481. Abstract

Hawley RS. Meiosis in living color: Fluorescence-based tetrad analysis in Arabidopsis. Proc Natl Acad Sci U S A.2007;104:3673-3674. Abstract

Hawley RS, Warburton D. Scrambling Eggs in Plastic Bottles. PLoS Genet.2007;3:e6. Abstract

Iimura T, Pourquie O. Hox genes in time and space during vertebrate body formation. Dev Growth Differ.2007;49:265-275. Abstract

Kirilly D, Xie T. The Drosophila ovary: an active stem cell community. Cell Res.2007;17:15-25. Abstract

Kulesa PM, Schnell S, Rudloff S, Baker RE, Maini PK. From Segment to Somite: Segmentation to Epithelialization Analyzed Within Quantitative Frameworks. Dev Dyn.2007;236:1392-1402. Abstract

Kusch T, Workman JL. Histone Variants and Complexes Involved in Their Exchange. Chromatin and Disease: Subcellular Biochemistry. New York: Springer 2007;41:91-110. Abstract

Lee KK, Workman JL. Histone acetyltransferase complexes: one size doesn't fit all. Nat Rev Mol Cell Biol.2007;8:284-295. Abstract

Li B, Carey M, Workman JL. The Role of Chromatin During Transcription. Cell.2007;128:707-719. Abstract

Li L. Does 'Immortal DNA strand' exist in 'immortal' stem cells? Cell Res.2007;17:834-835. Abstract

Li R. Cytokinesis in development and disease: variations on a common theme. Cell Mol Life Sci. 2007;64:3044-3058. Abstract

Mosley AL, Washburn M. Application of Shotgun Proteomics to Transcriptional Regulatory Pathways. In: DS Sem, Ed. Spectral Techniques in Proteomics. Boca Raton: CRC Press; 2007:207-222. Table of Contents

Perry JM, Li L. Disrupting the Stem Cell Niche: Good Seeds in Bad Soil. Cell.2007;129:1045-1047. Abstract

Pourquie O. Building the Spine: The Vertebrate Segmentation Clock. ColdSpring HarborSymposium on Quantitative Biology: Clocks and Rhythms Symposium 2007;72:445-449.

Pourquie O. Editorial on Segmentation Focus. Dev Dyn.2007;236:1377-1378. Abstract

Rancati G, Li R. Polarized Cell Growth: Double Grip by CDK1. Curr Biol.2007;17:R600-R603. Abstract

Scoville DH, He XC, Lee G, Sato T, Barrett TA, Li L. Intestinal Stem Cells in Physiologic Regeneration and Disease. Principles of Developmental Genetics. Burlington, MA: Elsevier Academic Press; 2007:1004-1022.

Smith S, Neaves W, Teitelbaum S. Adult Versus Embryonic Stem Cells: Treatments. Science.2007;316:1422-1423. Abstract

Smith E, Shilatifard A. The A, B, Gs of silencing. Genes Dev.2007;21:1141-1144. Abstract

Turnpenny PD, Alman B, Cornier AS, Giampietro PF, Offiah A, Tassy O, Pourquie O, Kusumi K, Dunwoodie S. Abnormal Vertebral Segmentation and the Notch Signaling Pathway in Man. Dev Dyn.2007;236:1456-1474. Abstract

Xie T, Li L. Stem cells and their niche: an inseparable relationship. Development.2007;134:2001-2006. Abstract

Zhu D, Hero AO, III. Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. J Comput Biol.2007;14:1311-1326. Abstract

Books

Mushegian AR. Foundations of Comparative Genomics. Amsterdam: Academic Press; 2007. Bibliographic Record

2006

Original Research Papers

Araki Y, Lau CK, Maekawa H, Jaspersen SL, Giddings TH, Jr., Schiebel E, Winey M. The Saccharomyces cerevisiae Spindle Pole Body (SPB) Component Nbp1p Is Required for SPB Membrane Insertion and Interacts with the Integral Membrane Proteins Ndc1p and Mps2p. Mol Biol Cell.2006;17:1959-1970. Abstract

Balagopalan L, Chen MH, Geisbrecht ER, Abmayr SM. The CDM superfamily protein MBC directs myoblast fusion through a mechanism that requires phosphatidylinositol 3,4,5-triphosphate binding but is independent of direct interaction with DCrk. Mol Cell Biol.2006;26:9442-9455. Abstract

Bradham CA, Foltz KR, Beane WS, Arnone MI, Rizzo F, Coffman JA, Mushegian A, Goel M, Morales J, Geneviere AM, Lapraz F, Robertson AJ, Kelkar H, Loza-Coll M, Townley IK, Raisch M, Roux MM, Lepage T, Gache C, McClay DR, Manning G. The sea urchin kinome: A first look. Dev Biol.2006;300:180-193. Abstract

Cai Y, Jin J, Gottschalk AJ, Yao T, Conaway JW, Conaway RC. Purification and assay of the human INO80 and SRCAP chromatin remodeling complexes. Methods.2006;40:312-317. Abstract

Carey M, Li B, Workman JL. RSC Exploits Histone Acetylation to Abrogate the Nucleosomal Block to RNA Polymerase II Elongation. Mol Cell.2006;24:481-487. Abstract

Chandy M, Gutierrez JL, Prochasson P, Workman JL. SWI/SNF Displaces SAGA-Acetylated Nucleosomes. Eukaryot Cell.2006;5:1738-1747. Abstract

Dale JK, Malapert P, Chal J, Vilhais-Neto G, Maroto M, Johnson T, Jayasinghe S, Trainor P, Herrmann B, Pourquie O. Oscillations of the snail genes in the presomitic mesoderm coordinate segmental patterning and morphogenesis in vertebrate somitogenesis. Dev Cell.2006;10:355-366. Abstract

Dehmer M, Emmert-Streib F, Kilian J. A similarity measure for graphs with low computational complexity. Applied Mathematics and Computation.2006;182:447-459. Abstract

Dequeant ML, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, Pourquie O. A complex oscillating network of signaling genes underlines the mouse segmentation clock. Science.2006;314:1595-1598. Abstract

Dixon J, Jones NC, Sandell LL, Jayasinghe SM, Crane J, Rey JP, Dixon MJ, Trainor PA. Tcof1/Treacle is required for neural crest cell formation and proliferation deficiencies that cause craniofacial abnormalities. Proc Natl Acad Sci U S A.2006;103:13403-13408. Abstract

Ellies DL, Viviano B, McCarthy J, Rey JP, Itasaki N, Saunders S, Krumlauf R. Bone Density Ligand, Sclerostin, Directly Interacts With LRP5 but Not LRP5(G171V) to Modulate Wnt Activity. J Bone Miner Res.2006;21:1738-1749. Abstract

Emmert-Streib F. Algorithmic computation of knot polynomials of secondary structure elements of proteins. J Comput Biol.2006;13:1503-1512. Abstract

Emran F, Florens L, Ma B, Swanson SK, Washburn MP, Hernandez N. A role for Yin Yang-1 (YY1) in the assembly of snRNA transcription complexes. Gene.2006;377:96-108. Abstract

Glazko G, Coleman M, Mushegian A. Similarity searches in genome-wide numerical data sets. Biol Direct.2006;1:13. Abstract

Glazko G, Babenko VN, Koonin EV, Rogozin IB. Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection. Biol Direct.2006;1:4. Abstract

Glynn EF, Chen J, Mushegian AR. Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics.2006;22:310-316. Abstract

Goel M, Mushegian A. Intermediary metabolism in sea urchin: The first inferences from the genome sequence. Dev Biol.2006;300:282-292. Abstract

Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Anderson S, Yates JR, 3rd, Washburn MP, Abmayr SM, Workman JL. Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila. Mol Cell Biol.2006;26:871-882. Abstract

Guelman S, Suganuma T, Florens L, Weake V, Swanson SK, Washburn MP, Abmayr SM, Workman JL. The Essential Gene wda Encodes a WD40 Repeat Subunit of Drosophila SAGA Required for Histone H3 Acetylation. Mol Cell Biol.2006;26:7178-7189. Abstract

Henry JM, Camahort R, Rice DA, Florens L, Swanson SK, Washburn MP, Gerton J. MND1/HOP2 facilitates Dmc1-dependent interhomolog crossover formation in meiosis of budding yeast. Mol Cell Biol.2006;26:2913-2923. Abstract

Hu K, Johnson J, Florens L, Fraunholz M, Suravajjala S, Dilullo C, Yates J, Roos DS, Murray JM. Cytoskeletal Components of an Invasion Machine-The Apical Complex of Toxoplasma gondii. PLoS Pathog.2006;2:e13. Abstract

Iimura T, Pourquie O. Collinear activation of Hoxb genes during gastrulation is linked to mesoderm cell ingression. Nature.2006;442:568-571. Abstract

Jaspersen SL, Martin AE, Glazko G, Giddings TH, Jr., Morgan G, Mushegian A, Winey M. The Sad1-UNC-84 homology domain in Mps3 interacts with Mps2 to connect the spindle pole body with the nuclear envelope. J Cell Biol.2006;174:665-675. Abstract

Jayasinghe SM, Wunderlich J, McKee A, Newkirk H, Pope S, Zhang J, Staehling-Hampton K, Li L, Haug JS. Sterile and disposable fluidic subsystem suitable for clinical high speed fluorescence-activated cell sorting. Cytometry B Clin Cytom.2006;70:344-354. Abstract

Kasemeier-Kulesa JC, Bradley R, Pasquale EB, Lefcort F, Kulesa PM. Eph/ephrins and N-cadherin coordinate to control the pattern of sympathetic ganglia. Development.2006;133:4839-4847.Abstract

Kulesa PM, Kasemeier-Kulesa JC, Teddy JM, Margaryan NV, Seftor EA, Seftor RE, Hendrix MJ. Reprogramming metastatic melanoma cells to assume a neural crest cell-like phenotype in an embryonic microenvironment. Proc Natl Acad Sci U S A.2006;103:3752-3757. Abstract

Lister IM, Tolliday NJ, Li R. Characterization of the minimum domain required for targeting budding yeast myosin II to the site of cell division. BMCBiol.2006;4:19. Abstract

Liu J, Glazko G, Mushegian A. Protein repertoire of double-stranded DNA bacteriophages. Virus Res.2006;117:68-80. Abstract

Mieczkowski PA, Dominska M, Buck MJ, Gerton JL, Lieb JD, Petes TD. Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae. Mol Cell Biol.2006;26:1014-1027. Abstract
Naryshkina T, Liu J, Florens L, Swanson SK, Pavlov AR, Pavlova NV, Inman R, Minakhin L, Kozyavkin SA, Washburn M, Mushegian A, Severinov K. Thermus thermophilus Bacteriophage varphiYS40 Genome and Proteomic Characterization of Virions. J Mol Biol.2006;364:667-677. Abstract
Palframan WJ, Meehl JB, Jaspersen SL, Winey M, Murray AW. Anaphase inactivation of the spindle checkpoint. Science.2006;313:680-684. Abstract
Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A.2006;103:18928-18933. Abstract
Rai R, Mushegian A, Makarova K, Kashina A. Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases. EMBO Rep.2006;7:800-805. Abstract
Robertson AJ, Dickey-Sims C, Ransick A, Rupp DE, McCarthy JJ, Coffman JA. CBFbeta is a facultative Runx partner in the sea urchin embryo. BMCBiol.2006;4:4.Abstract

Ruhl DD, Jin J, Cai Y, Swanson S, Florens L, Washburn MP, Conaway RC, Conaway JW, Chrivia JC. Purification of a human SRCAP complex that remodels chromatin by incorporating the histone variant H2A.Z into nNucleosomes. Biochemistry (Mosc).2006;45:5671-5677.Abstract

Salamat-Miller N, Fang J, Seidel CW, Smalter AM, Assenov Y, Albrecht M, Middaugh CR. A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. Mol Cell Proteomics.2006;5:2263-2278. Abstract
Shia WJ, Li B, Workman JL. SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae. Genes Dev.2006;20:2507-2512. Abstract

The Sea Urchin Genome Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science.2006;314:941-952. Abstract

Tümpel S, Cambronero F, Wiedemann LM, Krumlauf R. Evolution of cis elements in the differential expression of two Hoxa2 coparalogous genes in pufferfish (Takifugu rubripes). Proc Natl Acad Sci U S A.2006;103:5419-5424. Abstract
Xiang Y, Hawley RS. The Mechanism of Secondary Nondisjunction in Drosophila melanogaster Females. Genetics.2006;174:67-78.Abstract

Yao T, Song L, Xu W, Demartino GN, Florens L, Swanson SK, Washburn MP, Conaway RC, Conaway JW, Cohen RE. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol.2006;8:994-1002. Abstract

Zhang J, Grindley JC, Yin T, Jayasinghe S, He XC, Ross JT, Haug JS, Rupp D, Porter-Westpfahl KS, Wiedemann LM, Wu H, Li L. PTEN maintains haematopoietic stem cells and acts in lineage choice and leukaemia prevention. Nature.2006;441:519-522.Cover, News & Views., Abstract, and corrected Sup-Fig.4.

Zhang J, He XC, Tong WG, Johnson T, Wiedemann LM, Mishina Y, Feng JQ, Li L. Bone morphogenetic protein signaling inhibits hair follicle anagen induction by restricting epithelial stem/progenitor cell activation and expansion. Stem Cells.2006;24:2826-2839. Abstract
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res.2006;5:2339-2347. Abstract

Reviews, Commentaries or Chapters

Abmayr SM, Kocherlakota KS. Muscle morphogenesis: the process of embryonic myoblast fusion. In: H Sink, ed. Muscle Development in Drosophila. Georgetown, Tex. New York, N.Y.: Landes Bioscience/Eurekah.com ;Springer Science+Business Media; 2006:p.1-12. Table of Contents

Atkinson B, Shapiro L, Crist W, Slocum P, Drees B, Willsie S, Neaves W. Vote YES on the Missouri stem cell research and cures initiative. Mo Med.2006;103:498-499. Abstract
Aulehla A, Pourquie O. On periodicity and directionality of somitogenesis. Anat Embryol. 2006;211 Suppl 7:3-8. Abstract

Baumann P. Are mouse telomeres going to pot? Cell.2006;126:33-36. Abstract

Crane JF, Trainor PA. Neural Crest Stem and Progenitor Cells. Annu Rev Cell Dev Biol.2006;22:267-286. Abstract

Ellies DL, Krumlauf R. Bone formation: the nuclear matrix reloaded. Cell.2006;125:840-842. Abstract

Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, Workman JL, Washburn MP. Analyzing Chromatin Remodeling Complexes Using Shotgun Proteomics and Normalized Spectral Abundance Factors. Methods.2006;40:303-311. Abstract

Florens L, Washburn MP. Proteomic Analysis by Multidimensional Protein Identification Technology. Methods in Molecular Biology: New and Emerging Proteomics Techniques. Totowa, NJ: Humana Press Inc.; 2006;328:159-175.

Hawley RS. Epilogue. In: M Ashburner, ed. Won For All: How The Drosophila Genome Was Sequenced. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2006. 75-90. Table of Contents

Hawley RS, Gilliland WD. Sometimes the result is not the answer: the truths and the lies that come from using the complementation test. Genetics.2006;174:5-15. Abstract

Inoue T, Correia K, Krumlauf R. Electroporation of living embryos. Book Chapter 6, In Cell Biology: A Laboratory Handbook. 3rd Ed. Amsterdam ; Boston: Elsevier Academic; 2006:35-41.

Jin Z, Xie T. Germline specification: small things have a big role. Curr Biol.2006;16:R966-967. Abstract

Karpen GH, Hawley RS. Epigenetic Regulation of Chromosome Inheritance. In: DC Allis, T Jenuwein, and D Reinberg, eds. Epigenetics. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2006:265-289. Table of Contents

Li L, Neaves WB. Normal stem cells and cancer stem cells: the niche matters. Cancer Res.2006;66:4553-4557. Abstract

Li Z, Li L. Understanding hematopoietic stem-cell microenvironments. Trends Biochem Sci.2006;31:589-595. Abstract

Litvin O, Tiunova A, Connell-Alberts Y, Panchin Y, Baranova A. What is hidden in the pannexin treasure trove: the sneak peek and the guesswork. J Cell Mol Med.2006;10:613-634. Abstract

Neaves W, Onder R. Stem cell research: the debate continues. Mo Med.2006;103:202-204. Abstract

Neaves WB. Biomedical research in Missouri: great promise & imminent peril. Mo Med.2006;103:10-15. Abstract

Neaves WB. Cell Clump isn't a person. The Kansas City Star. Kansas City, MO; 2006;March 24:B6.

Nolte C, Krumlauf R. Expression of Hox Genes in the Nervous System of Vertebrates. In: S Papageorgiou, ed. Hox Gene Expression. Austin, TX: Landes Bioscience & Springer; 2006;Epub Open Access:14-41.

Paoletti A, Washburn MP. Quantitation in Proteomic Experiments Utilizing Mass Spectrometry. In: SE Harding, ed. Biotechnology and Genetic Engineering Reviews. Andover, United Kingdom: Intercept Ltd; 2006;22:1-19.

Ross J, Li L. Recent advances in understanding extrinsic control of hematopoietic stem cell fate. Curr Opin Hematol.2006;13:237-242. Abstract

Sandell LL, Trainor PA. Neural crest cell plasticity. size matters.In: Neural Crest Induction and Differentiation. New York, N.Y. Georgetown, Tex.: Springer Science+Business Media Landes Bioscience/Eurekah.com; 2006;589:78-95. Abstract

Sauer B. Cre/loxP Strategies. In:D Ganten, and K Ruckpaul, eds. Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. Berlin ; New York: Springer; 2006;2:2090.

Shia WJ, Pattenden SG, Workman JL. Histone H4 lysine 16 acetylation breaks the genome's silence. Genome Biol.2006;7:217. Abstract

Slaughter B, Li R. Toward a molecular interpretation of the surface stress theory for yeast morphogenesis. Curr Opin Cell Biol.2006;18:47-53. Abstract

Smith S, Neaves W, Teitelbaum S. Adult stem cell treatments for diseases? Science.2006;313:439. Abstract

Svejstrup JQ, Conaway RC, Conaway JW. RNA Polymerase II: A "Nobel" Enzyme Demystified. Mol Cell.2006;24:637-642. Abstract

Walker M, Trainor P. Craniofacial malformations: intrinsic vs extrinsic neural crest cell defects in Treacher Collins and 22q11 deletion syndromes. Clin Genet.2006;69:471-479. Abstract

White-Grindley E, Si K. RISC-y Memories. Cell.2006;124:23-26. Abstract

Workman JL. Nucleosome displacement in transcription. Genes Dev.2006;20:2009-2017. Abstract

Yin T, Li L. The stem cell niches in bone. J Clin Invest.2006;116:1195-1201. Abstract

2005

Original Research Papers

Alder MN, Rogozin IB, Iyer LM, Glazko GV, Cooper MD, Pancer Z. Diversity and function of adaptive immune receptors in a jawless vertebrate. Science.2005;310:1970-1973. Abstract

Anderson LK, Royer SM, Page SL, McKim KS, Lai A, Lilly MA, Hawley RS. Juxtaposition of C(2)M and the transverse filament protein C(3)G within the central region of Drosophila synaptonemal complex. Proc Natl Acad Sci U S A.2005;102:4482-4487. Abstract

Brandman O, Ferrell JE, Jr., Li R, Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science.2005;310:496-498. Abstract

Bunch JT, Bae NS, Leonardi J, Baumann P. Distinct requirements for pot1 in limiting telomere length and maintaining chromosome stability. Mol Cell Biol.2005;25:5567-5578. Abstract

Cai Y, Jin J, Florens L, Swanson SK, Kusch T, Li B, Workman JL, Washburn MP, Conaway RC, Conaway JW. The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J Biol Chem.2005:13665-13670.Abstract

Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta.2005;1731:77-87; discussion 75-76. Abstract

Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell.2005;123:581-592. Abstract

Chen EI, Florens L, Axelrod FT, Monosov E, Barbas CF, 3rd, Yates JR, 3rd, Felding-Habermann B, Smith JW. Maspin alters the carcinoma proteome. FASEB J.2005;19:1123-1124. Abstract

Cui W, Sproul LR, Gustafson SM, Matthies HJ, Gilbert SP, Hawley RS. Drosophila nod protein binds preferentially to the plus ends of microtubules and promotes microtubule polymerization in vitro. Mol Biol Cell.2005;16:5400-5409. Abstract

Cui W, Hawley RS. The HhH(2)/NDD Domain of the Drosophila Nod Chromokinesin-Like Protein Is Required for Binding to Chromosomes in the Oocyte Nucleus. Genetics.2005.Abstract

Delfini MC, Dubrulle J, Malapert P, Chal J, Pourquie O. Control of the segmentation process by graded MAPK/ERK activation in the chick embryo. Proc Natl Acad Sci U S A.2005;102:11343-11348.Abstract

Dickey-Sims C, Robertson AJ, Rupp DE, McCarthy JJ, Coffman JA. Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo. BMCBiol.2005;3:18. Abstract

Egile C, Rouiller I, Xu XP, Volkmann N, Li R, Hanein D. Mechanism of Filament Nucleation and Branch Stability Revealed by the Structure of the Arp2/3 Complex at Actin Branch Junctions. PLoS Biol.2005;3:e383.Abstract

Ercan S, Reese JC, Workman JL, Simpson RT. Yeast recombination enhancer is stimulated by transcription activation. Mol Cell Biol.2005;25:7976-7987.Abstract

Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, Wright AP. Mechanism of transcription factor recruitment by acidic activators. J Biol Chem.2005. Abstract

Ferretti E, Cambronero F, Tumpel S, Longobardi E, Wiedemann LM, Blasi F, Krumlauf R. Hoxb1 Enhancer and Control of Rhombomere 4 Expression: Complex Interplay between PREP1-PBX1-HOXB1 Binding Sites. Mol Cell Biol.2005;25:8541-8552. Abstract

Gilliland WD, Wayson S, Hawley RS. The Meiotic Defects of Mutants in the Drosophila mps1 Gene Reveal A Critical Role of Mps1 in the Segregation of Achiasmate Homologs. Curr Biol.2005;15:672-677. Abstract

Glazko G, Gordon A, Mushegian A. The choice of optimal distance measure in genome-wide datasets. Bioinformatics.2005;21:iii3-iii11. Abstract

Gong WJ, McKim KS, Hawley RS. All Paired Up with No Place to Go: Pairing, Synapsis, and DSB Formation in a Balancer Heterozygote. PLoS Genet.2005;1:e67. Abstract

Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR, 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science.2005;307:82-86. Abstract

Heuze ML, Guibal FC, Banks CA, Conaway JW, Conaway RC, Cayre YE, Benecke A, Lutz PG. ASB2 Is an Elongin BC-interacting Protein That Can Assemble with Cullin 5 and Rbx1 to Reconstitute an E3 Ubiquitin Ligase Complex. J Biol Chem.2005;280:5468-5474. Abstract

Hilgers V, Pourquie O, Dubrulle J. In vivo analysis of mRNA stability using the Tet-Off system in the chicken embryo. Dev Biol.2005;284:292-300. Abstract

Huang JK, Phillips GR, Roth AD, Pedraza L, Shan W, Belkaid W, Mi S, Fex-Svenningsen A, Florens L, Yates JR, 3rd, Colman DR. Glial membranes at the node of Ranvier prevent neurite outgrowth. Science.2005;310:1813-1817. Abstract

Jin J, Cai Y, Yao T, Gottschalk AJ, Florens L, Swanson SK, Gutierrez JL, Coleman MK, Workman JL, Mushegian A, Washburn MP, Conaway RC, Conaway JW. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J Biol Chem.2005;280:41207-41212. Abstract

Kasemeier-Kulesa JC, Kulesa PM, Lefcort F. Imaging neural crest cell dynamics during formation of dorsal root ganglia and sympathetic ganglia. Development.2005;132:235-245. Abstract

Kirilly D, Spana EP, Perrimon N, Padgett RW, Xie T. BMP Signaling Is Required for Controlling Somatic Stem Cell Self-Renewal in the Drosophila Ovary. Dev Cell.2005;9:651-662. Abstract

Kong SE, Banks CA, Shilatifard A, Conaway JW, Conaway RC. ELL-associated factors 1 and 2 are positive regulators of RNA polymerase II elongation factor ELL. Proc Natl Acad Sci U S A.2005;102:10094-10098. Abstract

Kozbial PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMCStruct Biol.2005;5:19. Abstract

Kulesa PM, Lu CC, Fraser SE. Time-Lapse Analysis Reveals a Series of Events by Which Cranial Neural Crest Cells Reroute around Physical Barriers. Brain Behav Evol.2005;66:255-265. Abstract

Lee D, Ezhkova E, Li B, Pattenden SG, Tansey WP, Workman JL. The Proteasome Regulatory Particle Alters the SAGA Coactivator to Enhance Its Interactions with Transcriptional Activators. Cell.2005;123:423-436.

Lee KK, Florens L, Swanson SK, Washburn MP, Workman JL. The deubiquitylation activity of Ubp8 is dependent upo n Sgf11 and its association with the SAGA complex. Mol Cell Biol.2005;25:1173-1182. Abstract

Li B, Pattenden SG, Lee D, Gutierrez J, Chen J, Seidel C, Gerton J, Workman JL. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A.2005. Abstract

Maroto M, Dale JK, Dequeant ML, Petit AC, Pourquie O. Synchronised cycling gene oscillations in presomitic mesoderm cells require cell-cell contact. Int J Dev Biol.2005;49:309-315. Abstract

Minakhin L, Semenova E, Liu J, Vasilov A, Severinova E, Gabisonia T, Inman R, Mushegian A, Severinov K. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J Mol Biol.2005;354:1-15. Abstract

Mushegian A. Protein content of minimal and ancestral ribosome. RNA.2005;11:1400-1406. Abstract

Page SL, Hawley RS. The Drosophila Meiotic Mutant mei-352 Is an Allele of klp3A and Reveals a Role for a Kinesin-like Protein in Crossover Distribution. Genetics.2005;170:1797-1807. Abstract

Pourquie O. Segmentation and somitogeneisis in vertebrates. McGraw-Hill Yearbook of Science & Technology 2005. New York ; London: McGraw-Hill; 2004:432.*

Prochasson P, Florens L, Swanson SK, Washburn MP, Workman JL. The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev.2005;19:2534-2539. Abstract

Ren J, Shi M, Liu R, Yang QH, Johnson T, Skarnes WC, Du C. The Birc6 (Bruce) gene regulates p53 and the mitochondrial pathway of apoptosis and is essential for mouse embryonic development. Proc Natl Acad Sci U S A.2005;102:565-570. Abstract

Ruan C, Workman JL, Simpson RT. The DNA repair protein yKu80 regulates the function of recombination enhancer during yeast mating type switching. Mol Cell Biol.2005;25:8476-8485. Abstract

Schneider J, Wood A, Lee JS, Schuster R, Dueker J, Maguire C, Swanson SK, Florens L, Washburn MP, Shilatifard A. Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol Cell.2005;19:849-856. Abstract

Serpente P, Tumpel S, Ghyselinck NB, Niederreither K, Wiedemann LM, Dolle P, Chambon P, Krumlauf R, Gould AP. Direct crossregulation between retinoic acid receptor {beta} and Hox genes during hindbrain segmentation. Development.2005;132:503-513. Abstract

Shia WJ, Osada S, Florens L, Swanson SK, Washburn MP, Workman JL. Characterization of the yeast trimeric-SAS acetyltransferase complex. J Biol Chem.2005;280:11987-11994. Abstract

Stark DA, Kulesa PM. Photoactivatable green fluorescent protein as a single-cell marker in living embryos. Dev Dyn.2005;233:983-992. Abstract

Stewart PL, Makabi M, Lang J, Dickey-Sims C, Robertson AJ, Coffman JA, Suprenant KA. Sea urchin vault structure, composition, and differential localization during development. BMCDev Biol.2005;5:3. Abstract

Teddy JM, Lansford R, Kulesa PM. Four-Color, 4D Time-Lapse Confocal Imaging of Chick Embryos. Biotechniques.2005;39:703-710. Abstract

Thummel R, Burket CT, Brewer JL, Sarras MP, Jr., Li L, Perry M, McDermott JP, Sauer B, Hyde DR, Godwin AR. Cre-mediated site-specific recombination in zebrafish embryos. Dev Dyn.2005;233:1366-1377. Abstract

Tian Q, He XC, Hood L, Li L. Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta. Cell Cycle.2005;4:215-216.Abstract

Trainor PA. Specification of neural crest cell formation and migration in mouse embryos. Semin Cell Dev Biol.2005;16:683-693. Abstract

Trujillo KM, Bunch JT, Baumann P. Extended DNA binding site in Pot1 broadens sequence specificity to allow recognition of heterogeneous fission yeast telomeres. J Biol Chem.2005;280:9119-9128. Abstract

Tsuchida T, Berlin WK, Sauer B. Dual chromogenic reporter gene detection in mammalian cells with lacZ and arabinofuranosidase. Biotechniques.2004;37:896-897. Abstract *

Vermot J, Pourquie O. Retinoic acid coordinates somitogenesis and left-right patterning in vertebrate embryos. Nature.2005;435:215-220. Abstract

Xi R, Doan C, Liu D, Xie T. Pelota controls self-renewal of germline stem cells by repressing a Bam-independent differentiation pathway. Development.2005;132:5365-5374. Abstract

Xi R, Kirilly D, Xie T. Molecular mechanisms controlling germline and somatic stem cells: similarities and differences. Curr Opin Genet Dev.2005;15:381-387. Abstract

Xi R, Xie T. Stem cell self-renewal controlled by chromatin remodeling factors. Science.2005;310:1487-1489. Abstract

Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem.2005;77:6218-6224. Abstract

Reviews, Commentaries and Chapters

Abmayr SM, Balagopalan L, Galletta BJ, Hong S-J. Myogenesis and Muscle Development. In: L Gilbert, I K., and S Gill, eds. Comprehensive Molecular Insect Science. 1st ed. San Diego, CA: Pergamon; Elsevier LTD; ^©2005;2:p. 1-45. Table of Contents

Baumann P. Taking control of G-quadruplexes. Nat Struct Mol Biol.2005;12:832-833. Abstract

Coffman JA. On reductionism, organicism, somatic mutations and cancer. Bioessays.2005;27:459. Abstract

Conaway JW, Florens L, Sato S, Tomomori-Sato C, Parmely TJ, Yao T, Swanson SK, Banks CAS, Washburn MP, Conaway RC. The Mammalian Mediator Complex. FEBS Lett.2005;579:904-908. Abstract

Conaway RC, Sato S, Tomomori-Sato C, Yao T, Conaway JW. The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem Sci.2005;30:250-255. Abstract

Danforth WH, Neaves WB. Using words carefully. Science.2005;309:1815-1816. Abstract

Dequeant ML, Pourquie O. Chicken genome: new tools and concepts. Dev Dyn.2005;232:883-886. Abstract

Gerton J. Chromosome cohesion: a cycle of holding together and falling apart. PLoS Biol.2005;3:e94. Abstract

Gerton JL, Hawley RS. Homologous chromosome interactions in meiosis: diversity amidst conservation. Nat Rev Genet.2005;6:477-487. Abstract

Gilliland WD, Hawley RS. Cohesin and the maternal age effect. Cell.2005;123:371-373. Abstract

Glazko GV, Koonin EV, Rogozin IB. Molecular dating: ape bones agree with chicken entrails. Trends Genet.2005;21:89-92. Abstract

He XC, Li L. Reply to Re-examination of P-PTEN staining patterns in the intestinal crypt. Nat Genet.2005;37:1017-1018. Abstract

He XC, Zhang J, Li L. Cellular and molecular regulation of hematopoietic and intestinal stem cell behavior. Book Chapter forAnn Rev Cell Dev Biol; In: Stem Cell Biology: Development and Plasticity; 2005;1049:28-38. Abstract

Jin J, Cai Y, Li B, Conaway RC, Workman JL, Conaway JW, Kusch T. In and out: histone variant exchange in chromatin. Trends Biochem Sci.2005;30:680-687. Abstract

Jones NC, Trainor PA. Role of morphogens in neural crest cell determination. J Neurobiol.2005;64:388-404.Abstract

Koonin EV, Rogozin IB, Glazko GV. p53 gain-of-function: tumor biology and bioinformatics come together. Cell Cycle.2005;4:686-688. Abstract

Krull CE, McLennan R, O'Connell S, Chen Y, Trainor PA. In Vivo Electroporation during Embryogenesis In: R Yuste, and A Konnerth, eds. Imaging in Neuroscience and Development: A Llaboratory Manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2005:79-94. Table of Contents

Lake CM, Hawley RS. A new target for POLO in meiotic centromere cohesion. Dev Cell.2005;8:5-7. Abstract

Li B, Ruan C, Workman JL. Histones: should I stay or should I go? Genome Biol.2005;6:306. Abstract

Li L. Finding the Hematopoietic Stem Cell Niche in Placenta. Dev Cell.2005;8:297-304. Abstract

Li L, Xie T. Stem Cell Niche: Structure and Function. Annu Rev Cell Dev Biol.2005;17:605-631. Abstract

Neaves WB. The ends and means of stem cell research. Practical Bioethics.2005;1:3-5.

Neaves WB. Stem cells from somatic cell nuclear transfer: research to unlock the body's potential for self-repair. Mo Med.2005;102:14-17. Abstract

Noden DM, Trainor PA. Relations and interactions between cranial mesoderm and neural crest populations. J Anat.2005;207:575-601. Abstract

Pattenden SG, Chandy MJ, Gutierrez JL, Workman JL. Chromatin dynamics rule the genome. Genome Biol.2005;6:355. Abstract

Pourquie O. Signal transduction: a new canon. Nature.2005;433:208-209. Abstract

Rosa-Molinar E, Krumlauf RK, Pritz MB. Hindbrain development and evolution: past, present, and future. Brain Behav Evol.2005;66:219-221. Abstract **

Stark D, Kulesa P. In vivo marking of single cells in chick embryos using photoactivation of GFP. Current Protocols in Cell Biology.2005; Supplement 28:12.18.1-12.18.11.
Swanson SK, Washburn MP. The continuing evolution of shotgun proteomics. Drug Discov Today.2005;10:719-725.Abstract

Trainor PA. Specification and patterning of neural crest cells during craniofacial development. Brain Behav Evol.2005;66:266-280. Abstract
Wong MD, Jin Z, Xie T. Molecular Mechanisms of Germline Stem Cell Regulation. Annu Rev Genet.2005:173-195.Abstract

Xie T, Kawase E, Kirilly D, Wong MD. Intimate relationships with their neighbors: Tales of stem cells in Drosophila reproductive systems. Dev Dyn.2005;232:775-790. Abstract

Zhang J, Li L. BMP signaling and stem cell regulation. Dev Biol.2005;284:1-11. Abstract

Zybailov B, Washburn MP. Mass Spectrometry-based Methods of Proteome Analysis. Encyclopedia of molecular cell biology and molecular medicine. 2nd ed. Weinheim: Wiley-VCH Verlag; 2005;8:1-43. Table of Contents and Cover

Books

Richards JE, Hawley RS. The Human Genome: A User's Guide. 2nd Ed. San Diego, Calif.: Elsevier Academic Press; 2005. TOC

* This article was published in 2004 and not included in the 2004 SIMR Publications Book.

** Publisher error. Correct reference: Rosa-Molinar E, Krumlauf R, Pritz MB. Hindbrain development and evolution: past, present, and future. Brain Behav Evol. 2005;66:219-221.

2004

Original Research Papers

Chen J, He X, Li L. Identifying the Patterns of Hematopoietic Stem Cells Gene Expressions Using Clustering Methods. Journal of Data Science.2004;2:297-309.

Coffman JA, Dickey-Sims C, Haug JS, McCarthy JJ, Robertson AJ. Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene. BMC Biol.2004;2:6. Abstract

Coffman JA, McCarthy J, Dickey-Sims C, Robertson A. Oral-aboral axis specification in the sea urchin embryo. II. Mitochondrial distribution and redox state contribute to establishing polarity in strongylocentrotus purpuratus. Dev Biol.2004;273:160-171. Abstract

Dubrulle J, Pourquie O. fgf8 mRNA decay establishes a gradient that couples axial elongation to patterning in the vertebrate embryo. Nature. 2004;427:419-422. Abstract

Galletta BJ, Chakravarti M, Banerjee R, Abmayr SM. SNS: adhesive properties, localization requirements and ectodomain dependence in S2 cells and embryonic myoblasts. Mech Dev.2004;121:1455-1468. Abstract

Gensheimer M, Mushegian A. Chalcone isomerase family and fold: no longer unique to plants. Protein Sci. 2004;13:540-544. Abstract

Gerber M, Eissenberg JC, Kong S, Tenney K, Conaway JW, Conaway RC, Shilatifard A. In vivo requirement of the RNA polymerase II elongation factor elongin A for proper gene expression and development. Mol Cell Biol.2004;24:9911-9919. Abstract

Glazko GV, Koonin EV, Rogozin IB. Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection. Biochim Biophys Acta.2004;1679:95-106. Abstract

Glazko GV, Mushegian AR. Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol.2004;5:R32. Abstract

Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-Wide Mapping of the Cohesin Complex in the Yeast Saccharomyces cerevisiae. PLoS Biol.2004;2:E259. Abstract

He XC, Zhang J, Tong WG, Tawfik O, Ross J, Scoville DH, Tian Q, Zeng X, He X, Wiedemann LM, Mishina Y, Li L. BMP signaling inhibits intestinal stem cell self-renewal through suppression of Wnt-beta-catenin signaling. Nat Genet.2004;36:1117-1121. Abstract, The comments regarding this paper News and Views.

Kawase E, Wong MD, Ding BC, Xie T. Gbb/Bmp signaling is essential for maintaining germline stem cells and for repressing bam transcription in the Drosophila testis. Development. 2004;131:1365-1375. Abstract

Kulesa PM. Developmental imaging: Insights into the avian embryo. Birth Defects Res Part C Embryo Today.2004;72:260-266. Abstract

Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates Iii JR, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science.2004;306:2084-2087. Abstract

Kusumi K, Mimoto MS, Covello KL, Beddington RS, Krumlauf R, Dunwoodie SL. Dll3 pudgy mutation differentially disrupts dynamic expression of somite genes. Genesis.2004;39:115-121. Abstract

Laurencon A, Orme CM, Peters HK, Boulton CL, Vladar EK, Langley SA, Bakis EP, Harris DT, Harris NJ, Wayson SM, Hawley RS, Burtis KC. A large-scale screen for mutagen-sensitive Loci in Drosophila. Genetics.2004;167:217-231. Abstract

Lee KK, Prochasson P, Florens L, Swanson SK, Washburn MP, Workman JL. Proteomic analysis of chromatin-modifying complexes in Saccharomyces cerevisiae identifies novel subunits. Biochem Soc Trans.2004;32:899-903. Abstract

Liu J, Mushegian A. Displacements of Prohead Protease Genes in the Late Operons of Double-Stranded-DNA Bacteriophages. J Bacteriol.2004;186:4369-4375. Abstract

Lo AC, Fung MK, Au CL, Chan TS, Sauer B, Chung SS, Chung SK. Transgenic mice over-expressing endothelin-1 in testis transactivated by a Cre/loxP system showed decreased testicular capillary blood flow. Transgenic Res.2004;13:119-134. Abstract

McDermott J, Zhao Y, Sauer B. A simple polymerase chain reaction screen for homologous targeting in embryonic stem cells. Anal Biochem.2004;332:401-403. Abstract

Melko OM, Mushegian AR. Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes. Bioinformatics. 2004;20:67-74. Abstract

Mercurio S, Latinkic B, Itasaki N, Krumlauf R, Smith JC. Connective-tissue growth factor modulates WNT signalling and interacts with the WNT receptor complex. Development.2004;131:2137-2147. Abstract

Petyuk V, McDermott J, Cook M, Sauer B. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis. J Biol Chem.2004;279:37040-37048. Abstract

Powles N, Marshall H, Economou A, Chiang C, Murakami A, Dickson C, Krumlauf R, Maconochie M. Regulatory analysis of the mouse Fgf3 gene: control of embryonic expression patterns and dependence upon sonic hedgehog (Shh) signalling. Dev Dyn.2004;230:44-56. Abstract

Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA. Global Position and Recruitment of HATs and HDACs in the Yeast Genome. Mol Cell.2004;16:199-209. Abstract

Robertson AJ, Howard JT, Dominski Z, Schnackenberg BJ, Sumerel JL, McCarthy JJ, Coffman JA, Marzluff WF. The sea urchin stem-loop-binding protein: a maternally expressed protein that probably functions in expression of multiple classes of histone mRNA. Nucleic Acids Res.2004;32:811-818. Abstract

Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC. A set of consensus Mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell.2004;14:685-691. Abstract

Sauer B, McDermott J. DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages. Nucleic Acids Res.2004;32:6086-6095. Abstract

Song X, Wong MD, Kawase E, Xi R, Ding BC, McCarthy JJ, Xie T. Bmp signals from niche cells directly repress transcription of a differentiation-promoting gene, bag of marbles, in germline stem cells in the Drosophila ovary. Development. 2004;131:1353-1364. Abstract

Teddy JM, Kulesa PM. In vivo evidence for short- and long-range cell communication in cranial neural crest cells. Development.2004;131:6141-6151. Abstract

Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L. Proteomic analysis identifies that 14-3-3{zeta} interacts with {beta}-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A.2004. Abstract

Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L,Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW. A Mammalian Mediator Subunit that Shares Properties with Saccharomyces cerevisiae Mediator Subunit Cse2. J Biol Chem. 2004;279:5846-5851. Abstract

Weber SA, Gerton JL, Polancic JE, DeRisi JL, Koshland D, Megee PC. The Kinetochore Is an Enhancer of Pericentric Cohesin Binding. PLoS Biol; 2004;2:E260. Abstract.

Wiederkehr C, Basavaraj R, Sarrauste de Menthiere C, Hermida L, Koch R, Schlecht U, Amon A, Brachat S, Breitenbach M, Briza P, Caburet S, Cherry M, Davis R, Deutschbauer A, Dickinson HG, Dumitrescu T, Fellous M, Goldman A, Grootegoed JA, Hawley R, Ishii R, Jegou B, Kaufman RJ, Klein F, Lamb N, Maro B, Nasmyth K, Nicolas A, Orr-Weaver T, Philippsen P, Pineau C, Rabitsch KP, Reinke V, Roest H, Saunders W, Schroder M, Schedl T, Siep M, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Esposito RE, Primig M. GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res.2004;32 Database issue:D560-567. Abstract

Yan Q, Kamura T, Cai Y, Jin J, Ivan M, Mushegian A, Conaway RC, Conaway JW. Identification of elongin C and Skp1 sequences that determine cullin selection. J Biol Chem.2004. Abstract

Yang QH, Du C. Smac/DIABLO selectively reduces the levels of c-IAP1 and c-IAP2 but not that of XIAP and livin in HeLa cells. J Biol Chem.2004;279:16963-16970. Abstract

Reviews, Commentaries and Chapters

Abmayr SM, Kocherlakota K. Muscle morphogenesis: the process of embryonic myoblast fusion. In: H Sink, ed. Drosophila Muscle Development: Eurekah.com; 2004.

Coffman JA. Cell cycle development. Dev Cell. 2004;6:321-327. Abstract

Coffman JA, Yuh CH. Identification of sequence-specific DNA binding proteins. Methods Cell Biol.2004;74:653-675. Abstract

Conaway JW, Conaway RC. RNA Polymerase II and Basal Transcription Factors in Eukaryotes. Encyclopedia of biological chemistry. 1st ed. Amsterdam ; Boston: Elsevier; 2004;3:763-765. Abstract

Conaway JW, Conaway RC. Von Hippel-Lindau (VHL) Protein. Encyclopedia of biological chemistry. 1st ed. Amsterdam ; Boston: Elsevier; 2004;4:416-418. Abstract

Dubrulle J, Pourquie O. Coupling segmentation to axis formation. Development.2004;131:5783-5793. Abstract

Ercan S, Carrozza MJ, Workman JL. Global nucleosome distribution and the regulation of transcription in yeast. Genome Biol.2004;5:243. Abstract

Jones NC, Trainor P. The therapeutic potential of stem cells in the treatment of craniofacial abnormalities. Expert Opin Biol Ther.2004;4:645-657. Abstract

Kasemeier J, Lefcort F, Fraser SE, Kulesa P. A novel sagittal slice explant technique for time-lapse imaging of the formation of the chick periperal nervous system. In: R Yuste, and A Konnerth, eds. Imaging in neuroscience and development : a laboratory manual. New York: Oxford: Cold Spring Harbor Laboratory Press; Lavis Marketing; 2004:700 p.

Kulesa P, Ellies DL, Trainor PA. Comparative analysis of neural crest cell death, migration, and function during vertebrate embryogenesis. Dev Dyn. 2004;229:14-29. Abstract

Kulesa P, Fraser SE. In Ovo Imaging of Avian Embryogenesis. In: R Yuste, and A Konnerth, eds. Imaging in neuroscience and development : a laboratory manual. New York: Oxford: Cold Spring Harbor Laboratory Press; Lavis Marketing; 2004:700 p.

Melton KR, Iulianella A, Trainor PA. Gene expression and regulation of hindbrain and spinal cord development. Front Biosci. 2004;9:117-138. Abstract

Mushegian A. Evolution and function of processosome, the complex that assembles ribosomes in eukaryotes: clues from comparative sequence analysis. Practical bioinformatics. Berlin ; New York: Springer; 2004;15:xvii, 265 p.

Page SL, Hawley RS. The genetics and molecular biology of the synaptonemal complex. Annu Rev Cell Dev Biol.2004;20:525-558. Abstract

Pourquie O. The chick embryo: a leading model in somitogenesis studies. Mech Dev.2004;121:1069-1079. Abstract

Trainor PA. Developmental biology is "cruzing". Dev Cell.2004;7:481-486. Abstract

Trainor PA, Bronner-Fraser M, Krumlauf R. Neural Crest Cells. In: RP Lanza, ed. Book Chapter for 2 vol. work, The Handbook of Stem Cells. Boston, MA: Elsevier Academic; 2004:2 v.

Washburn MP. Utilisation of proteomics datasets generated via multidimensional protein identification technology (MudPIT). Brief Funct Genomic Proteomic.2004;3:280-286.Abstract

Workman JL, Abmayr SM. Histone H3 variants and modifications on transcribed genes. Proc Natl Acad Sci U S A. 2004;101:1429-1430. Abstract

Books

Ashburner M, Hawley RS, Golic KG. Drosophila : A Laboratory Handbook, 2nd Edition: Cold Springs Harbor Press; 2004.

2003

Original Research Papers

Adams LD, Choi L, Xian HQ, Yang A, Sauer B, Wei L, Gottlieb DI. Double lox targeting for neural cell transgenesis. Brain Res Mol Brain Res. 2003;110:220-233.

AkashiK, He X, Chen J, Iwasaki H, Niu C, Steenhard B, Zhang J, Haug J, Li L. Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood. 2003;101:383-389.

CaiY, Jin J, Tomomori-Sato C, Sato S, Sorokina I, Parmely TJ, Conaway RC, Conaway JW. Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. J Biol Chem. 22003;278:42733-42736.

Conaway RC, Kong SE, Conaway JW. TFIIS and GreB. Two like-minded transcription elongation factors with sticky fingers. Cell. 2003;114:272-274.

Dale JK, Maroto M, Dequeant ML, Malapert P, McGrew M, Pourquie O. Periodic notch inhibition by lunaticfFringe underlies the chick segmentation clock. Nature. 2003;421:275-278.

GavalasA, Ruhrberg C, Livet J, Henderson CE, Krumlauf R. Neuronal defects in the hindbrain of Hoxa1, Hoxb1 and Hoxb2 mutants reflect regulatory interactions among these Hox genes. Development. 2003;130:5663-5679.

Gong WJ, Golic KG. Ends-out, or replacement, gene targeting in Drosophila. Proc Natl Acad Sci USA.2993;100:2556-2561.

ItasakiN, Jones CM, Mercurio S, Rowe A, Domingos PM, Smith JC, Krumlauf R. Wise, a context-dependent activator and inhibitor of Wnt signalling. Development. 2003;130:4295-4305.

IulianellaA, Vanden Heuvel G, Trainor P. Dynamic expression of murine Cux2 in craniofacial, limb, urogenital and neuronal primordia. Gene Expr Patterns. 2003;3:571-577.

IvinsS, Pemberton K, Guidez F, Howell L, Krumlauf R, Zelent A. Regulation of Hoxb2 by APL-associated PLZF protein. Oncogene. 2003;22:3685-3697

Kramer J, Hawley RS. The spindle-associated transmembrane protein axs identifies a new family of transmembrane proteins in eukaryotes. Cell Cycle. 2003;2:174-176.

Kramer J, Hawley RS. The spindle-associated transmembrane protein Axs identifies a membranous structure ensheathing the meiotic spindle. Nat Cell Biol. 2003;5: 261-263.

KuznetsovaAV, Meller J, Schnell PO, Nash JA, Ignacak ML, Sanchez Y, Conaway JW, Conaway RC, Czyzyk-Krzeska MF. von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination. Proc Natl Acad Sci USA. 2003;100:2706-2711.

LaurenconA, Purdy A, Sekelsky J, Hawley RS, Su TT. Phenotypic analysis of separation-of-function alleles of MEI-41, Drosophila ATM/ATR. Genetics. 2003;164:589-601.

Le Y, Gagneten S, Larson T, Santha E, Dobi A, Agoston Dv D, Sauer B. Far-upstream elements are dispensable for tissue-specific proenkephalin expression using a Cre-mediated knock-in strategy. J Neurochem. 2003;84:689-697.

Lin F, Cordes K, Li L, Hood L, Couser WG, Shankland SJ, Igarashi P. Hematopoietic stem cells contribute to the regeneration of renal tubules after renal ischemia-reperfusion injury in mice. J Am Soc Nephrol. 2003;14:1188-1199.

Liu J, Mushegian A. Three monophyletic superfamilies account for the majority of the known glycosyltransferases. Protein Sci. 2003;12:1418-1431.

Maynard MA, Qi H, Chung J, Lee EH, Kondo Y, Hara S, Conaway RC, Conaway JW, Ohh M. Multiple splice variants of the human HIF-3 alpha locus are targets of the von Hippel-Lindau E3 ubiquitin ligase complex. J Biol Chem. 2003;278:11032-11040.

PattynA, Vallstedt A, Dias JM, Samad OA, Krumlauf R, Rijli FM, Brunet JF, Ericson J. Coordinated temporal and spatial control of motor neuron and serotonergic neuron generation from a common pool of CNS progenitors. Genes Dev. 2003; 17:729-737.

Rennert J, Coffman JA, Mushegian AR, Robertson AJ. The evolution of runx genes I. A comparative study of sequences from phylogenetically diverse model organisms. BMC Evol Biol. 2003;3:4.

Sato S, Tomomori-Sato C, Banks CA, Sorokina I, Parmely TJ, Kong SE, Jin J, Cai Y, Lane WS, Brower CS, Conaway RC, Conaway JW. Identification of mammalian Mediator subunits with similarities to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. J Biol Chem. 2003;278:15123-15127.

Song X, Xie T. wingless signaling regulates the maintenance of ovarian somatic stem cells in Drosophila. Development. 2003;130:3259-3268.

Yang QH, Church-Hajduk R, Ren J, Newton ML, Du C. Omi/HtrA2 catalytic cleavage of inhibitor of apoptosis (IAP) irreversibly inactivates IAPs and facilitates caspase activity in apoptosis. Genes Dev. 2003;17:1487-1496.

YuzendovaJ, Nechaev S, Berlin J, Rogulja D, Kuznedelov K, Inman R, Mushegian A, Severinov K. Genome of Xanthomonas oryzae Bacteriophage Xp10: An odd T-Odd Phage. J Mol Biol. 2003;330:735-748.

Zhang J, Niu C, Ye L, Huang H, He X, Tong WG, Ross J, Haug J, Johnson T, Feng JQ, Harri S, Wiedemann LM, Mishina Y, Li L. Identification of the haematopoietic stem cell niche and control of the niche size. Nature. 2003;425:836-841

Zhu CH, Xie T. Clonal expansion of ovarian germline stem cells during niche formation in Drosophila. Development. 2003;130:2579-2588.

Reviews, Commentaries and Chapters

Burt D, Pourquie O. Genetics. Chicken genome--science nuggets to come soon. Science. 2003;300:1669.

Coffman JA. Runx transcription factors and the developmental balance between cell proliferation and differentiation. Cell Biol Int. 2003;27:315-324.

Dale JK, Maroto M. A Hes1-based oscillator in cultured cells and its potential implications for the segmentation clock. Bioessays. 2003;25:200-203.

DubrulleJ, Pourquie O. Welcome to syndetome. A new somitic compartment. Dev Cell. 2003;4:611-612.

Hawley RS. Human meiosis: model organisms address the maternal age effect. CurrBiol. 2003;13:R305-R307.

Hawley RS. The human Y chromosome: rumors of its death have been greatly exaggerated. Cell. 2003;113:825-828.

IulianellaA, Melton KR, Trainor PA. Somitogenesis: breaking new boundaries. Neuron. 2003;40:11-14.

Page SL, Hawley RS. Chromosome choreography: the meiotic ballet. Science. 2003;301:785-789.

PfendlerKC, Kawase E. The potential of stem cells. ObstetGynecol Surv. 2003;58:197-208.

Pourquie O. The segmentation clock : converting embryonic time into spatial pattern. Science. 2003;301:328-330.

Pourquie O. Vertebrate somitogenesis: a novel paradigm for animal segmentation? IntJ Dev Biol. 2003;47:in press.

Pourquie O, Goldbeter A. Segmentation clock: insights from computational models. CurrBiol. 2003;13:R632-R634.

ShilatifardA, Conaway RC, Conaway JW. The RNA polymerase II elongation complex. Ann Rev Biochem. 2003;72:693-715.

StainierDY, Pourquie O. Entrails, heart, brain, limbs, and lymphatics- a recipe for success? Dev Cell. 2003;5:193-196.

Trainor PA. Making headway: the roles of hox genes and neural crest cells in craniofacial development. ScientificWorldJournal. 2003;3:240-264.

Trainor P. Development. The bills of qucks and duails. Science. 2003;299:523-524.

Trainor P, Nieto MA. Jawsfest: new perspectives on neural crest lineages and morphogenesis. Development. 2003;130:5059-5063.

van Veen E, Hawley RS. Meiosis: when even two is a crowd. CurrBiol. 2003;13:R831-R833.

Washburn MP. Soft landing for protein chips. Nat Biotech. 2003;21:1156-1157.

Books

Hawley RS. Advanced Genetic Analysis: Finding Meaning in the Genome. New York, NY: Blackwell Science; 2003.

2002

Original Research Papers

Bel-Vialar, S., Itasaki, N., & Krumlauf, R. (2002). Initiating Hox gene expression: in the early chick neural tube differential sensitivity to FGF and RA signaling subdivides the HoxB genes in two distinct groups. Development, 129(22), 5103-5115.

Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., Conaway, R. C.(2002). Mammalian mediator subunit mMED8 is an Elongin BC-interacting protein that can assemble with Cul2 and Rbx1 to reconstitute a ubiquitin ligase. Proc Natl Acad Sci U S A, 99(16), 10353-10358.

Deshmukh, M., Du, C., Wang, X., & Johnson, E. M., Jr. (2002). Exogenous smac induces competence and permits caspase activation in sympathetic neurons. Journal of Neuroscience, 22(18), 8018-8027.

Golden, T. A., Schauer, S. E., Lang, J. D., Pien, S., Mushegian, A. R., Grossniklaus, U., Meinke, D. W., Ray, A.(2002). Short Integuments1/suspensor1/carpel Factory, a Dicer Homolog, Is a Maternal Effect Gene Required for Embryo Development in Arabidopsis. Plant Physiol, 130(2), 808-822.

Ivan, M., Haberberger, T., Gervasi, D. C., Michelson, K. S., Gunzler, V., Kondo, K., Yang, H., Sorokina, I., Conaway, R. C., Conaway, J. W., Kaelin, W. G., Jr.(2002). Biochemical purification and pharmacological inhibition of a mammalian prolyl hydroxylase acting on hypoxia-inducible factor. Proc Natl Acad Sci U S A, 99(21), 13459-13464.

Kamura, T., Brower, C. S., Conaway, R. C., & Conaway, J. W. (2002). A molecular basis for stabilization of the von Hippel-Lindau (VHL) tumor suppressor protein by components of the VHL ubiquitin ligase. J Biol Chem, 277(33), 30388-30393.

Leong, K. G., Hu, X., Li, L., Noseda, M., Larrivee, B., Hull, C., Hood, L., Wong, F., Karsan, A.(2002). Activated Notch4 Inhibits Angiogenesis: Role of beta1-Integrin Activation. Mol Cell Biol, 22(8), 2830-2841.

Li, S., Zhao, Y., He, X., Kim, T. H., Kuharsky, D. K., Rabinowich, H., Chen, J., Du, C., Yin, X. M.(2002). Relief of extrinsic pathway inhibition by the Bid-dependent mitochondrial release of Smac in Fas-mediated hepatocyte apoptosis. J Biol Chem, 277(30), 26912-26920.

Maggert, K. A., & Golic, K. G. (2002). The Y Chromosome of Drosophila melanogaster Exhibits Chromosome-Wide Imprinting. Genetics, 162(3), 1245-1258.

Manzanares, M., Nardelli, J., Gilardi-Hebenstreit, P., Marshall, H., Giudicelli, F., Martinez-Pastor, M. T., Krumlauf, R., Charnay, P.(2002). Krox20 and kreisler co-operate in the transcriptional control of segmental expression of Hoxb3 in the developing hindbrain. Embo J, 21(3), 365-376.

Mushegian, A. (2002). Refining structural and functional predictions for secretasome components by comparative sequence analysis. Proteins, 47(1), 69-74.

Ning, X. H., Chen, S. H., Xu, C. S., Li, L., Yao, L. Y., Qian, K., Krueger, J. J., Hyyti, O. M., Portman, M. A.(2002). Hypothermic protection of the ischemic heart via alterations in apoptotic pathways as assessed by gene array analysis. J Appl Physiol, 92(5), 2200-2207.

Park, I. K., He, Y., Lin, F., Laerum, O. D., Tian, Q., Bumgarner, R., Klug, C. A., Li, K., Kuhr, C., Doyle, M. J., Xie, T., Schummer, M., Sun, Y., Goldsmith, A., Clarke, M. F., Weissman, I. L., Hood, L., Li, L.(2002). Differential gene expression profiling of adult murine hematopoietic stem cells. Blood, 99(2), 488-498.

Robertson, A. J., Dickey, C. E., McCarthy, J. J., & Coffman, J. A. (2002). The expression of SpRunt during sea urchin embryogenesis. Mech Dev, 117(1-2), 327-330.

Rong, Y. S., Titen, S. W., Xie, H. B., Golic, M. M., Bastiani, M., Bandyopadhyay, P., Olivera, B. M., Brodsky, M., Rubin, G. M., Golic, K. G.(2002). Targeted mutagenesis by homologous recombination in D. melanogaster. Genes Dev, 16(12), 1568-1581.

Rufer, A., Neuenschwander, P., & Sauer, B. (2002). Analysis of Cre-loxP interaction by surface plasmon resonance: Influence of spermidine on cooperativity. Anal Biochem, 308(1), 90-99.

Rufer, A. W., & Sauer, B. (2002). Non-contact positions impose site selectivity on Cre recombinase. Nucleic Acids Res, 30(13), 2764-2771.

Schulte, C. E., von Lindern, M., Steinlein, P., Beug, H., & Wiedemann, L. M. (2002). MLL-ENL cooperates with SCF to transform primary avian multipotent cells. Embo J, 21(16), 4297-4306.

Song, X., & Xie, T. (2002). DE-cadherin-mediated cell adhesion is essential for maintaining somatic stem cells in the Drosophila ovary. Proc Natl Acad Sci U S A, 99(23), 14813-14818.

Song, X., Zhu, C. H., Doan, C., & Xie, T. (2002). Germline stem cells anchored by adherens junctions in the Drosophila ovary niches. Science, 296(5574), 1855-1857.

Theil, T., Ariza-McNaughton, L., Manzanares, M., Brodie, J., Krumlauf, R., & Wilkinson, D. G. (2002). Requirement for downregulation of kreisler during late patterning of the hindbrain. Development, 129(6), 1477-1485.

Trainor, P. A., Ariza-McNaughton, L., & Krumlauf, R. (2002). Role of the isthmus and FGFs in resolving the paradox of neural crest plasticity and prepatterning. Science, 295(5558), 1288-1291.

Trainor, P. A., Sobieszczuk, D., Wilkinson, D., & Krumlauf, R. (2002). Signalling between the hindbrain and paraxial tissues dictates neural crest migration pathways. Development, 129(2), 433-442.

Tumpel, S., Maconochie, M., Wiedemann, L. M., & Krumlauf, R. (2002). Conservation and Diversity in the cis-Regulatory Networks That Integrate Information Controlling Expression of Hoxa2 in Hindbrain and Cranial Neural Crest Cells in Vertebrates. Dev Biol, 246(1), 45-56.

Zheng, N., Schulman, B. A., Song, L., Miller, J. J., Jeffrey, P. D., Wang, P., Chu, C., Koepp, D. M., Elledge, S. J., Pagano, M., Conaway, R. C., Conaway, J. W., Harper, J. W., Pavletich, N. P.(2002). Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Nature, 416(6882), 703-709.

Reviews, Commentaries & Chapters

Ariza-McNaughton, L., & Krumlauf, R. (2002). Non-radioactive in situ hybridization: simplified procedures for use in whole-mounts of mouse and chick embryos. In Int Rev Neurobiol (Vol. 47, pp. 239-250).

Champion, M. D., & Hawley, R. S. (2002). Playing for half the deck: the molecular biology of meiosis. Nat Cell Biol, 4 Suppl, s50-56.

Conaway, J. W., & Conaway, R. C. (2002). RNA Polymerases. InWiley Encyclopedia of Molecular Medicine (pp. 2840-2843): John Wiley & Sons, Inc.

Conaway, R. C., Brower, C. S., & Conaway, J. W. (2002). Emerging roles of ubiquitin in transcription regulation. Science, 296(5571), 1254-1258.

Conaway, R. C., & Conaway, J. W. (2002). The von Hippel-Lindau tumor suppressor complex and regulation of hypoxia-inducible transcription. Adv Cancer Res, 85, 1-12.

Dubrulle, J., & Pourquie, O. (2002). From head to tail: links between the segmentation clock and antero-posterior patterning of the embryo. Curr Opin Genet Dev, 12(5), 519-523.

Hawley, R. S. (2002). Meiosis: how male flies do meiosis. Curr Biol, 12(19), R660-662.

Kamura, T., Conaway, J. W., & Conaway, R. C. (2002). Roles of SCF and VHL ubiquitin ligases in regulation of cell growth. Prog Mol Subcell Biol, 29, 1-15.

Krumlauf, R. (2002). Spring forward and fall back. Dynamics in formation of somite boundaries. Dev Cell, 3(5), 605-606.

Neaves, W. B. (2002). Leaping beyond the genome -- what lies ahead?, CAP Today, 16, 54-64.

Pourquie, O. (2002). Vertebrate segmentation: lunatic transcriptional regulation. Curr Biol, 12(20), R699-701.

Sauer, B. (2002). Cre/lox: One More Step in the Taming of the Genome. Endocrine, 19(3), 221-228.

Trainor, P. (2002). Mouse development comes of age. Nat Cell Biol, 4(9), E219.

Trainor, P., & Krumlauf, R. (2002). Development. Riding the crest of the Wnt signaling wave. Science, 297(5582), 781-783.

2001

Original Research Papers

Coffman, J. A., & Davidson, E. H. (2001). Oral-aboral axis specification in the sea urchin embryo. I. Axis entrainment by respiratory asymmetry. Dev Biol, 230(1), 18-28.

Di Rocco, G., Gavalas, A., Popperl, H., Krumlauf, R., Mavilio, F., & Zappavigna, V. (2001). The recruitment of SOX/OCT complexes and the differential activity of HOXA1 and HOXB1 modulate the Hoxb1 auto-regulatory enhancer function. J Biol Chem, 276(23), 20506-20515.

Iyer, L. M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A. R., Zhulin, I. B., Koonin, E. V.(2001). Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol, 2(12), RESEARCH0051.

Johnson, L., Staub, C., Neaves, W. B., & Yanagimachi, R. (2001). Live human germ cells in the context of their spermatogenic stages. Hum Reprod, 16(8), 1575-1582.

Kwan, C. T., Tsang, S. L., Krumlauf, R., & Sham, M. H. (2001). Regulatory analysis of the mouse Hoxb3 gene: multiple elements work in concert to direct temporal and spatial patterns of expression. Dev Biol, 232(1), 176-190.

Manzanares, M., Bel-Vialar, S., Ariza-McNaughton, L., Ferretti, E., Marshall, H., Maconochie, M. M., Blasi, F., Krumlauf, R.(2001). Independent regulation of initiation and maintenance phases of Hoxa3 expression in the vertebrate hindbrain involve auto- and cross- regulatory mechanisms. Development, 128(18), 3595-3607.

Querido, E., Blanchette, P., Yan, Q., Kamura, T., Morrison, M., Boivin, D., Kaelin, W. G., Conaway, R. C., Conaway, J. W., Branton, P. E.(2001). Degradation of p53 by adenovirus E4orf6 and E1B55K proteins occurs via a novel mechanism involving a Cullin-containing complex. Genes Dev, 15(23), 3104-3117.

Reviews, Commentaries & Chapters

Gavalas, A., & Krumlauf, R. (2001). Hox Genes. In S. Brenner & J. Miller (Eds.), Encyclopedia of Genetics (pp. 978-979): Academic Press.

Hawley, R. S. (2001). Altered nuclear transport and the most selfish of genes. Dev Cell, 1(3), 311-313.

Inoue, T., & Krumlauf, R. (2001). An impulse to the brain--using in vivo electroporation. Nat Neurosci, 4 Suppl, 1156-1158.

Krull, C. E., & Krumlauf, R. (2001). Building from the bottom up. Nat Cell Biol, 3(6), E138-139.

Mushegian, A., & Medzhitov, R. (2001). Evolutionary perspective on innate immune recognition. J Cell Biol, 155(5), 705-710.

Neaves, W. B. (2001). Medicine in the Postgenome Era. Mo Med, 98(9), 461-464.

Trainor, P., Bel-Vialar, S., Itasaki, N., & Krumlauf, R. (2001). Novel roles for head mesoderm and somites in patterning the vertebrate neural tube. In E. J. Sanders (Ed.), The Origin and Fate of Somites (pp. 30-47): IOS Press.

Trainor, P. A., & Krumlauf, R. (2001). Hox genes, neural crest cells and branchial arch patterning. Curr Opin Cell Biol, 13(6), 698-705.

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