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. BMC Biol. 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. BMC Biol. 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