2008

Original Research Papers

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

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.

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

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

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

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. 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. 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. 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

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

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

Reviews, Commentaries or Chapters

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 ed; 2008;87:187-210.

Dequeant ML, Pourquie O. Segmental patterning of the vertebrate embryonic axis. Nat Rev Genet. 2007;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.

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

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

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. Frontiers in Bioscience. 2008;May 1:4657-4666.

Nagpal R, Patel A, Gibson MC. Problems and Paradigms: Epithelial Topology. BioEssays. 2008;30:260-266. 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.

Shilatifard A. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol. 2008. Abstract

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

Vilhais-Neto GC, Pourquie O. Retinoic Acid. Curr Biol. 2008;18:R191-192. 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

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.