| | Other Issues: previous | next | latest | archivePerspective Order and Disorder during Escherichia coli Divergence Heather Hendrickson PMCID: PMC2621348 Converging on the Origins of Axonal Ion Channel Clustering Matthew N. Rasband PMCID: PMC2613034 CCL3L Copy Number Variation and the Co-Evolution of Primate and Viral Genomes German Gornalusse, Srinivas Mummidi, Weijing He, Guido Silvestri, Mike Bamshad, and Sunil K. Ahuja PMCID: PMC2628739 Review A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation P. J. Hastings, Grzegorz Ira, and James R. Lupski PMCID: PMC2621351 Research Articles Neuropeptide Y Gene Polymorphisms Confer Risk of Early-Onset Atherosclerosis Svati H. Shah, Neil J. Freedman, Lisheng Zhang, David R. Crosslin, David H. Stone, Carol Haynes, Jessica Johnson, Sarah Nelson, Liyong Wang, Jessica J. Connelly, Michael Muehlbauer, Geoffrey S. Ginsburg, David C. Crossman, Christopher J. H. Jones, Jeffery Vance, Michael H. Sketch, Jr, Christopher B. Granger, Christopher B. Newgard, Simon G. Gregory, Pascal J. Goldschmidt-Clermont, William E. Kraus, and Elizabeth R. Hauser PMCID: PMC2602734 A Genome-Wide Association Study Identifies Novel and Functionally Related Susceptibility Loci for Kawasaki Disease David Burgner, Sonia Davila, Willemijn B. Breunis, Sarah B. Ng, Yi Li, Carine Bonnard, Ling Ling, Victoria J. Wright, Anbupalam Thalamuthu, Miranda Odam, Chisato Shimizu, Jane C. Burns, Michael Levin, Taco W. Kuijpers, Martin L. Hibberd, and International Kawasaki Disease Genetics Consortium PMCID: PMC2607021 Regulation of Small RNA Accumulation in the Maize Shoot Apex Fabio T. S. Nogueira, Daniel H. Chitwood, Shahinez Madi, Kazuhiro Ohtsu, Patrick S. Schnable, Michael J. Scanlon, and Marja C. P. Timmermans PMCID: PMC2602737 Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae Laura A. Kavanaugh and Fred S. Dietrich PMCID: PMC2603021 IL2RA Genetic Heterogeneity in Multiple Sclerosis and Type 1 Diabetes Susceptibility and Soluble Interleukin-2 Receptor Production Lisa M. Maier, Christopher E. Lowe, Jason Cooper, Kate Downes, David E. Anderson, Christopher Severson, Pamela M. Clark, Brian Healy, Neil Walker, Cristin Aubin, Jorge R. Oksenberg, Stephen L. Hauser, Alistair Compston, Stephen Sawcer, The International Multiple Sclerosis Genetics Consortium, Philip L. De Jager, Linda S. Wicker, John A. Todd, and David A. Hafler PMCID: PMC2602853 Instability of Plastid DNA in the Nuclear Genome Anna E. Sheppard and Jeremy N. Timmis PMCID: PMC2602989 ATR and Chk1 Suppress a Caspase-3–Dependent Apoptotic Response Following DNA Replication Stress Katie Myers, Mary E. Gagou, Pedro Zuazua-Villar, Rene Rodriguez, and Mark Meuth PMCID: PMC2607051 Adaptive Evolution in Zinc Finger Transcription Factors Ryan O. Emerson and James H. Thomas PMCID: PMC2604467 A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus Joshua B. Gross, Richard Borowsky, and Clifford J. Tabin PMCID: PMC2603666 Arabidopsis CULLIN3 Genes Regulate Primary Root Growth and Patterning by Ethylene-Dependent and -Independent Mechanisms Alexis Thomann, Esther Lechner, Maureen Hansen, Eva Dumbliauskas, Yves Parmentier, Joe Kieber, Ben Scheres, and Pascal Genschik PMCID: PMC2607017 Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak? Zhi Wang and Jianzhi Zhang PMCID: PMC2605560 Evolution of Regulatory Sequences in 12 Drosophila Species Jaebum Kim, Xin He, and Saurabh Sinha PMCID: PMC2607023 Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci Giacomo Manenti, Antonella Galvan, Angela Pettinicchio, Gaia Trincucci, Elena Spada, Anna Zolin, Silvano Milani, Anna Gonzalez-Neira, and Tommaso A. Dragani PMCID: PMC2614123 A cis-Acting Diversification Activator Both Necessary and Sufficient for AID-Mediated Hypermutation Artem Blagodatski, Vera Batrak, Sabine Schmidl, Ulrike Schoetz, Randolph B. Caldwell, Hiroshi Arakawa, and Jean-Marie Buerstedde PMCID: PMC2607555 Gγ1, a Downstream Target for the hmgcr-Isoprenoid Biosynthetic Pathway, Is Required for Releasing the Hedgehog Ligand and Directing Germ Cell Migration Girish Deshpande, Anuradha Godishala, and Paul Schedl PMCID: PMC2607556 Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon Xiang Zhang, Irwin Leav, Monica P. Revelo, Ranjan Deka, Mario Medvedovic, Zhong Jiang, and Shuk-Mei Ho PMCID: PMC2613032 Pervasive Hitchhiking at Coding and Regulatory Sites in Humans James J. Cai, J. Michael Macpherson, Guy Sella, and Dmitri A. Petrov PMCID: PMC2613029 Genome-Wide Association Study of Plasma Polyunsaturated Fatty Acids in the InCHIANTI Study Toshiko Tanaka, Jian Shen, Gonçalo R. Abecasis, Aliaksei Kisialiou, Jose M. Ordovas, Jack M. Guralnik, Andrew Singleton, Stefania Bandinelli, Antonio Cherubini, Donna Arnett, Michael Y. Tsai, and Luigi Ferrucci PMCID: PMC2613033 Yeast Genetic Analysis Reveals the Involvement of Chromatin Reassembly Factors in Repressing HIV-1 Basal Transcription Manuela Vanti, Edurne Gallastegui, Iñaki Respaldiza, Alfonso Rodríguez-Gil, Fernando Gómez-Herreros, Silvia Jimeno-González, Albert Jordan, and Sebastián Chávez PMCID: PMC2613532 Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs Meiying Fang, Greger Larson, Helena Soares Ribeiro, Ning Li, and Leif Andersson PMCID: PMC2613536 Genetic Differences between the Determinants of Lipid Profile Phenotypes in African and European Americans: The Jackson Heart Study Rahul C. Deo, David Reich, Arti Tandon, Ermeg Akylbekova, Nick Patterson, Alicja Waliszewska, Sekar Kathiresan, Daniel Sarpong, Herman A. Taylor, Jr., and James G. Wilson PMCID: PMC2613537 Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool Agnar Helgason, Carles Lalueza-Fox, Shyamali Ghosh, Sigrún Sigurðardóttir, Maria Lourdes Sampietro, Elena Gigli, Adam Baker, Jaume Bertranpetit, Lilja Árnadóttir, Unnur Þorsteinsdottir, and Kári Stefánsson PMCID: PMC2613751 Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P. C. Rocha, and Erick Denamur PMCID: PMC2617782 TraR, a Homolog of a RNAP Secondary Channel Interactor, Modulates Transcription Matthew D. Blankschien, Katarzyna Potrykus, Elicia Grace, Abha Choudhary, Daniel Vinella, Michael Cashel, and Christophe Herman PMCID: PMC2613031 Copy Number Variation of CCL3-like Genes Affects Rate of Progression to Simian-AIDS in Rhesus Macaques (Macaca mulatta) Jeremiah D. Degenhardt, Paola de Candia, Adrien Chabot, Stuart Schwartz, Les Henderson, Binhua Ling, Meredith Hunter, Zhaoshi Jiang, Robert E. Palermo, Michael Katze, Evan E. Eichler, Mario Ventura, Jeffrey Rogers, Preston Marx, Yoav Gilad, and Carlos D. Bustamante PMCID: PMC2621346 Natural Variation in an ABC Transporter Gene Associated with Seed Size Evolution in Tomato Species Cintia Hotta Orsi and Steven D. Tanksley PMCID: PMC2617763 Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes Stacie E. Hughes, William D. Gilliland, Jeffrey L. Cotitta, Satomi Takeo, Kim A. Collins, and R. Scott Hawley PMCID: PMC2615114 Multiple Chromosomal Rearrangements Structured the Ancestral Vertebrate Hox-Bearing Protochromosomes Vincent J. Lynch and Günter P. Wagner PMCID: PMC2622764 An ALS-Linked Mutant SOD1 Produces a Locomotor Defect Associated with Aggregation and Synaptic Dysfunction When Expressed in Neurons of Caenorhabditis elegans Jiou Wang, George W. Farr, David H. Hall, Fei Li, Krystyna Furtak, Lars Dreier, and Arthur L. Horwich PMCID: PMC2621352 Integrating Computational Biology and Forward Genetics in Drosophila Stein Aerts, Sven Vilain, Shu Hu, Leon-Charles Tranchevent, Roland Barriot, Jiekun Yan, Yves Moreau, Bassem A. Hassan, and Xiao-Jiang Quan PMCID: PMC2628282 Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3 Elise A. Kikis, Yoshito Oka, Matthew E. Hudson, Akira Nagatani, and Peter H. Quail PMCID: PMC2621353 A Systematic Approach to Mapping Recessive Disease Genes in Individuals from Outbred Populations Friedhelm Hildebrandt, Saskia F. Heeringa, Franz Rüschendorf, Massimo Attanasio, Gudrun Nürnberg, Christian Becker, Dominik Seelow, Norbert Huebner, Gil Chernin, Christopher N. Vlangos, Weibin Zhou, John F. O'Toole, Bethan E. Hoskins, Matthias T. F. Wolf, Bernward G. Hinkes, Hassan Chaib, Shazia Ashraf, Susan J. Allen, Virginia Vega-Warner, Eric Wise, Heather M. Harville, Robert H. Lyons, Joseph Washburn, James MacDonald, Peter Nürnberg, and Edgar A. Otto PMCID: PMC2621355 LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin Anderly C. Chueh, Emma L. Northrop, Kate H. Brettingham-Moore, K. H. Andy Choo, and Lee H. Wong PMCID: PMC2625447 DETORQUEO, QUIRKY, and ZERZAUST Represent Novel Components Involved in Organ Development Mediated by the Receptor-Like Kinase STRUBBELIG in Arabidopsis thaliana Lynette Fulton, Martine Batoux, Prasad Vaddepalli, Ram Kishor Yadav, Wolfgang Busch, Stig U. Andersen, Sangho Jeong, Jan U. Lohmann, and Kay Schneitz PMCID: PMC2628281 Genetic Evidence for Single-Strand Lesions Initiating Nbs1-Dependent Homologous Recombination in Diversification of Ig V in Chicken B Lymphocytes Makoto Nakahara, Eiichiro Sonoda, Kuniharu Nojima, Julian E. Sale, Katsuya Takenaka, Koji Kikuchi, Yoshihito Taniguchi, Kyoko Nakamura, Yoshiki Sumitomo, Ronan T. Bree, Noel F. Lowndes, and Shunichi Takeda PMCID: PMC2625440 Short Telomeres Initiate Telomere Recombination in Primary and Tumor Cells Tammy A. Morrish and Carol W. Greider PMCID: PMC2627939 Learning a Prior on Regulatory Potential from eQTL Data Su-In Lee, Aimée M. Dudley, David Drubin, Pamela A. Silver, Nevan J. Krogan, Dana Pe'er, and Daphne Koller PMCID: PMC2627940 Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene David Reich, Michael A. Nalls, W. H. Linda Kao, Ermeg L. Akylbekova, Arti Tandon, Nick Patterson, James Mullikin, Wen-Chi Hsueh, Ching-Yu Cheng, Josef Coresh, Eric Boerwinkle, Man Li, Alicja Waliszewska, Julie Neubauer, Rongling Li, Tennille S. Leak, Lynette Ekunwe, Joe C. Files, Cheryl L. Hardy, Joseph M. Zmuda, Herman A. Taylor, Elad Ziv, Tamara B. Harris, and James G. Wilson PMCID: PMC2628742 |
