Comparative analysis of the vaginal microbiome in health and disease

Bryan A White, Andres M Gomez, Mengfei Ho, Margret Berg Miller, Susan M Thomas, Carl J Yeoman, Suleyman Yildirim, Douglas J Creedon, Tony L Goldberg, Steven R Leigh, Karen E Nelson, Rebecca M Stumpf, Brenda A Wilson

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M Madan Babu, Siddhartha Basu, Yulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H Putnam, Christopher M West, William F Loomis, Rex L Chisholm, Gad Shaulsky, Joan E Strassmann, David C Queller, Adam Kuspa, Igor V Grigoriev

Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins

Tanja Scherrer, Christian Femmer, Ralph Schiess, Ruedi Aebersold, André P Gerber

Metatranscriptomics of the human gut microbiome

Thomas Sichertz Pontén

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

Christian M Zmasek, Adam Godzik

RNA-Seq methods for imperfect samples: development, evaluation and applications

Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet, Aaron Berlin, Sarah Young, Gad Getz, Aviv Regev, Chad Nusbaum, Andreas Gnirke, Joshua Z Levin

High recombination rates and hotspots in a Plasmodium falciparum genetic cross

Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin

There is a sanity clause

Gregory A Petsko

The tubby family proteins

Saikat Mukhopadhyay, Peter K Jackson

Grand network convergence

Joel S Bader

Comparative genomic analysis of mouse and human mammary tumors

Charles M Perou

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

France Denoeud, Micha？l Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne Da Silva, Marie Diogon, Eric Viscogliosi, Céline Brochier-Armanet, Arnaud Couloux, Julie Poulain, Béatrice Segurens, Véronique Anthouard, Catherine Texier, Nicolas Blot, Philippe Poirier, Geok Choo Ng, Kevin SW Tan, Fran？ois Artiguenave, Olivier Jaillon, Jean-Marc Aury, Frédéric Delbac, Patrick Wincker, Christian P Vivarès, Hicham El Alaoui

The mouse genetics toolkit: revealing function and mechanism

Louise van der Weyden, Jacqueline K White, David J Adams, Darren W Logan

A Drosophila model for the role of epigenetics in brain function and development

Roman M Stilling, André Fischer

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von D？hren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber

The cullin protein family

Antonio Sarikas, Thomas Hartmann, Zhen-Qiang Pan

Hybrid selection for sequencing pathogen genomes from clinical samples

Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell, Daria Van Tyne, Carsten Russ, Rachel Daniels, Kayla G Barnes, James Bochicchio, Daouda Ndiaye, Papa D Sene, Dyann F Wirth, Chad Nusbaum, Sarah K Volkman, Bruce W Birren, Andreas Gnirke, Daniel E Neafsey

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord

Integrating diverse genomic data using gene sets

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani

Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii

Elizabeth P Murchison, David J Adams

Nothing to do and all day to do it in

Gregory A Petsko

Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes

Katherine R Smith, Catherine J Bromhead, Michael S Hildebrand, A Eliot Shearer, Paul J Lockhart, Hossein Najmabadi, Richard J Leventer, George McGillivray, David J Amor, Richard J Smith, Melanie Bahlo

A comparative analysis of exome capture

Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie

Bacterial epidemiology and biology - lessons from genome sequencing

Julian Parkhill, Brendan W Wren

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark

Mapping meiotic breaks: Spo11 oligonucleotides precisely mark the spots

Patty Hwang, Neil Hunter

The rhomboid protease family: a decade of progress on function and mechanism

Sinisa Urban, Seth W Dickey

How hemp got high

Naomi Attar

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein

Opening sequence: computational genomics in the era of high-throughput sequencing

Emily V Chambers, Alida S Kindt, Colin AM Semple

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack

Computational biology: plus c'est la même chose, plus ？a change

Curtis Huttenhower

The real cost of sequencing: higher than you think!

Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang

Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism

Peter Meister, Sonia Schott, Cécile Bedet, Yu Xiao, Sabine Rohner, Selena Bodennec, Bruno Hudry, Laurent Molin, Florence Solari, Susan M Gasser, Francesca Palladino

Abstract not submitted for online publication

Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

Joshua Akey

Correction: Closing gaps in the human genome using sequencing by synthesis

Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz

Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease

Fereshteh Fani, Philippe Leprohon, Danielle Légaré, Marc Ouellette

Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Mogens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani

Exome sequencing: the expert view

Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu

Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia

Atsushi Takata, Maiko Kato, Masayuki Nakamura, Takeo Yoshikawa, Shigenobu Kanba, Akira Sano, Tadafumi Kato

Mutation discovery in mice by whole exome sequencing

Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D'Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Donahue, Jeffrey Jeddeloh, Jay Shendure, Laura G Reinholdt

Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard

Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy

Michal Ozery-Flato, Chaim Linhart, Luba Trakhtenbrot, Shai Izraeli, Ron Shamir

Transcriptomics in a high throughput world

Chad Nusbaum