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. BMC Bioinf. 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. Cold Spring Harbor Symposium 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