2008

Original Research Papers

Aulehla A, Wiegraebe W, Baubet V, Wahl MB, Deng C, Taketo M, Lewandoski M, Pourquie O. A β-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, Pourquie O. Mutations in the MESP2 Gene Cause Spondylothoracic Dysostosis/Jarcho-Levin Syndrome. Am J Hum Genet. 2008;82:1334-1341. Abstract 

Dequeant ML, Ahnert S, Edelsbrunner H, Fink TMA, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie 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, Pourquie 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, Ozbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquie 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, Song X, 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 MJC, 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. BMC Genomics. 2008;9:188. Abstract

Li X, Magenheimer BS, Xia S, Johnson T, Wallace DP, Calvet JP, Li R. A tumor necrosis factor-α-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, Bradford WD, 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.

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

Sanso M, Gogol M, Ayte J, Seidel C, Hidalgo E. The Transcription Factors Pcr1 and Atf1 Have Distinct Roles in Stress- and Sty1-Dependent Gene Regulation. Eukaryot Cell. 2008;7:826-35. 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.

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

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. 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

Tümpel S, Cambronero F, Sims C, Krumlauf R, Wiedemann LM. Gene Networks in Development and Evolution Special Feature Sackler Colloquium: 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 X, Baumann P. Chromosome Fusions following Telomere Loss Are Mediated by Single-Strand Annealing. Mol Cell. 2008;31:463-473. 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

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 or Chapters

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

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

Benazeraf B, Pourquie O. One step beyond: cell intercalation during primitive streak formation. Curr Biol. 2008;18:R119-R121. Abstract  

Bhattacharyya S, Kulesa PM, Fraser SE. Vital Labeling of Embryonic Cells Using Fluorescent Dyes and Proteins. Avian Embryology. 2nd Edition; 2008;87:187-210.

Dequeant ML, Pourquie 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.

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. 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, Pourquie O. Manipulation and electroporation of the avian segmental plate and somites in vitro. Methods in Cell Biology: Avian Embryology; 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, Pourquie O. Pattern formation and developmental mechanisms. Curr Opin Genet Dev. 2008;18:285-394. 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. Cohesinopathies: One ring, many obligations. Mutat Res. 2008;647:103-111. Abstract

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

Mehrotra S, Hawley RS, McKim KS. Synapsis, Double Strand Breaks, and Domains of Crossover Control in Drosophila Females. In: R Engel, 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. Scientist reacts to Vatican bioethics paper [published online ahead of print December 24 2008]. National Catholic Reporter. 2008.

Ozbudak EM, Pourquie 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, Li L, He X. Current View: Intestinal Stem Cells & 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. Cold Spring Harbor Protocols. 2008;4975. Abstract

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. 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. StemBook ed: The Stem Cell Research Community; 2008. doi/103824/stembook.1.23.1. Available at: http://www.stembook.org. Accessed September 30, 2008.

Zhu D, Dequeant 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; 2008:27-50.

Book

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