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Table of Contents: May 2008

COVER

Image Credit:
Issue Image
The genetic effects of growth rate in chicken domestication

More than a century after the foundation of genetics as a scientific field, researchers are still developing a general theory for how genes can control traits. Recent advances in the conceptualization and formalization of this theory have provided new insights into the estimation of genetic effects and the genetics of evolutionary processes. This image illustrates the use of chicken growth rate to analyze the genetics of domestication (see Álvarez-Castro et al., doi:10.1371/journal.pgen.1000062).

Image Credit: Ernesto González Torterolo and Ignacio Castro (Náchok)

Special Report

Zebrafish VEGF Receptors: A Guideline to Nomenclature

Jeroen Bussmann, Nathan Lawson, Leonard Zon, Stefan Schulte-Merker , Zebrafish Nomenclature Committee

Review

Research Articles

The Inexorable Spread of a Newly Arisen Neo-Y Chromosome

Paris Veltsos, Irene Keller, Richard A. Nichols

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

Adam R. Boyko, Scott H. Williamson, Amit R. Indap, Jeremiah D. Degenhardt, Ryan D. Hernandez, Kirk E. Lohmueller, Mark D. Adams, Steffen Schmidt, John J. Sninsky, Shamil R. Sunyaev, Thomas J. White, Rasmus Nielsen, Andrew G. Clark, Carlos D. Bustamante

Specificity of the STAT4 Genetic Association for Severe Disease Manifestations of Systemic Lupus Erythematosus

Kimberly E. Taylor, Elaine F. Remmers, Annette T. Lee, Ward A. Ortmann, Robert M. Plenge, Chao Tian, Sharon A. Chung, Joanne Nititham, Geoffrey Hom, Amy H. Kao, F. Yesim Demirci, M. Ilyas Kamboh, Michelle Petri, Susan Manzi, Daniel L. Kastner, Michael F. Seldin, Peter K. Gregersen, Timothy W. Behrens, Lindsey A. Criswell

Systematic Identification of Genes that Regulate Neuronal Wiring in the Drosophila Visual System

Jürg Berger, Kirsten-André Senti, Gabriele Senti, Timothy P. Newsome, Bengt Åsling, Barry J. Dickson, Takashi Suzuki

Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40T

Ronald M. Weiner, Larry E. Taylor II, Bernard Henrissat, Loren Hauser, Miriam Land, Pedro M. Coutinho, Corinne Rancurel, Elizabeth H. Saunders, Atkinson G. Longmire, Haitao Zhang, Edward A. Bayer, Harry J. Gilbert, Frank Larimer, Igor B. Zhulin, Nathan A. Ekborg, Raphael Lamed, Paul M. Richardson, Ilya Borovok, Steven Hutcheson

ATM Promotes the Obligate XY Crossover and both Crossover Control and Chromosome Axis Integrity on Autosomes

Marco Barchi, Ignasi Roig, Monica Di Giacomo, Dirk G. de Rooij, Scott Keeney, Maria Jasin

Inferring Human Colonization History Using a Copying Model

Garrett Hellenthal, Adam Auton, Daniel Falush

Targeted Deficiency of the Transcriptional Activator Hnf1α Alters Subnuclear Positioning of Its Genomic Targets

Reini F. Luco, Miguel A. Maestro, Nicolas Sadoni, Daniele Zink, Jorge Ferrer

BRCA1 and BRCA2 Missense Variants of High and Low Clinical Significance Influence Lymphoblastoid Cell Line Post-Irradiation Gene Expression

Nic Waddell, Anette Ten Haaf, Anna Marsh, Julie Johnson, Logan C. Walker, kConFab Investigators, Milena Gongora, Melissa Brown, Piyush Grover, Mark Girolami, Sean Grimmond, Georgia Chenevix-Trench, Amanda B. Spurdle

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer

Kevin A. Kwei, Murali D. Bashyam, Jessica Kao, Raman Ratheesh, Edumakanti C. Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon-La Choi, Sreejata Chatterjee, Collins A. Karikari, Keyan Salari, Pei Wang, Tina Hernandez-Boussard, Gowrishankar Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack

HOXA13 Is Essential for Placental Vascular Patterning and Labyrinth Endothelial Specification

Carley A. E. Shaut, Douglas R. Keene, Lise K. Sorensen, Dean Y. Li, H. Scott Stadler

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

Jiali Han, Peter Kraft, Hongmei Nan, Qun Guo, Constance Chen, Abrar Qureshi, Susan E. Hankinson, Frank B. Hu, David L. Duffy, Zhen Zhen Zhao, Nicholas G. Martin, Grant W. Montgomery, Nicholas K. Hayward, Gilles Thomas, Robert N. Hoover, Stephen Chanock, David J. Hunter

Demographic History of European Populations of Arabidopsis thaliana

Olivier François, Michael G. B. Blum, Mattias Jakobsson, Noah A. Rosenberg

A Genetic Screen for Dihydropyridine (DHP)-Resistant Worms Reveals New Residues Required for DHP-Blockage of Mammalian Calcium Channels

Trevor C. Y. Kwok, Kwokyin Hui, Wojciech Kostelecki, Nicole Ricker, Guillermo Selman, Zhong-Ping Feng, Peter John Roy

An Inducible and Reversible Mouse Genetic Rescue System

Hongkui Zeng, Kyoji Horie, Linda Madisen, Maria N. Pavlova, Galina Gragerova, Alex D. Rohde, Brian A. Schimpf, Yuqiong Liang, Ethan Ojala, Farah Kramer, Patricia Roth, Olga Slobodskaya, Io Dolka, Eileen A. Southon, Lino Tessarollo, Karin E. Bornfeldt, Alexander Gragerov, George N. Pavlakis, George A. Gaitanaris

Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators

Chunlei Wu, David L. Delano, Nico Mitro, Stephen V. Su, Jeff Janes, Phillip McClurg, Serge Batalov, Genevieve L. Welch, Jie Zhang, Anthony P. Orth, John R. Walker, Richard J. Glynne, Michael P. Cooke, Joseph S. Takahashi, Kazuhiro Shimomura, Akira Kohsaka, Joseph Bass, Enrique Saez, Tim Wiltshire, Andrew I. Su

A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

David Melzer, John R. B. Perry, Dena Hernandez, Anna-Maria Corsi, Kara Stevens, Ian Rafferty, Fulvio Lauretani, Anna Murray, J. Raphael Gibbs, Giuseppe Paolisso, Sajjad Rafiq, Javier Simon-Sanchez, Hana Lango, Sonja Scholz, Michael N. Weedon, Sampath Arepalli, Neil Rice, Nicole Washecka, Alison Hurst, Angela Britton, William Henley, Joyce van de Leemput, Rongling Li, Anne B. Newman, Greg Tranah, Tamara Harris, Vijay Panicker, Colin Dayan, Amanda Bennett, Mark I. McCarthy, Aimo Ruokonen, Marjo-Riitta Jarvelin, Jack Guralnik, Stefania Bandinelli, Timothy M. Frayling, Andrew Singleton, Luigi Ferrucci

How To Perform Meaningful Estimates of Genetic Effects

José M. Álvarez-Castro, Arnaud Le Rouzic, Örjan Carlborg

SU(VAR)3-7 Links Heterochromatin and Dosage Compensation in Drosophila

Anne Spierer, Flora Begeot, Pierre Spierer, Marion Delattre