Volume 19, Issue 10 | October 2009

Commentary
- - Darwinian alchemy: Human genes from noncoding DNA
    Adam Siepel
    First Published October 1, 2009
Article
- - Comparative genomics of protoploid Saccharomycetaceae
    Jean-Luc Souciet
    Bernard Dujon
    Claude Gaillardin
    Mark Johnston
    Philippe V. Baret
    Paul Cliften David J. Sherman Jean Weissenbach Eric Westhof Patrick Wincker Claire Jubin Julie Poulain Valérie Barbe Béatrice Ségurens François Artiguenave Véronique Anthouard Benoit Vacherie Marie-Eve Val Robert S. Fulton Patrick Minx Richard Wilson Pascal Durrens Géraldine Jean Christian Marck Tiphaine Martin Macha Nikolski Thomas Rolland Marie-Line Seret Serge Casarégola Laurence Despons Cécile Fairhead Gilles Fischer Ingrid Lafontaine Véronique Leh Marc Lemaire Jacky de Montigny Cécile Neuvéglise Agnès Thierry Isabelle Blanc-Lenfle Claudine Bleykasten Julie Diffels Emilie Fritsch Lionel Frangeul Adrien Goëffon Nicolas Jauniaux Rym Kachouri-Lafond Célia Payen Serge Potier Lenka Pribylova Christophe Ozanne
    ...[+45 authors]...,
    Guy-Franck Richard
    Christine Sacerdot
    Marie-Laure Straub
    Emmanuel Talla
    First Published June 12, 2009
Letter
- - Unusual composition of a yeast chromosome arm is associated with its delayed replication
    Célia Payen
    Gilles Fischer
    Christian Marck
    Caroline Proux
    David James Sherman
    Jean-Yves Coppée
    Mark Johnston
    Bernard Dujon
    Cécile Neuvéglise
    First Published July 10, 2009
  - Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    Thomas J. Sharpton
    Jason E. Stajich
    Steven D. Rounsley
    Malcolm J. Gardner
    Jennifer R. Wortman
    Vinita S. Jordar Rama Maiti Chinnappa D. Kodira Daniel E. Neafsey Qiandong Zeng Chiung-Yu Hung Cody McMahan Anna Muszewska Marcin Grynberg M. Alejandra Mandel Ellen M. Kellner Bridget M. Barker John N. Galgiani Marc J. Orbach Theo N. Kirkland
    ...[+15 authors]...,
    Garry T. Cole
    Matthew R. Henn
    Bruce W. Birren
    John W. Taylor
    First Published August 28, 2009
  - Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    Stefan Enroth
    Alvaro Rada-Iglesias
    Claes Wadelius
    Jan Komorowski
    First Published August 17, 2009
  - Chromatin poises miRNA- and protein-coding genes for expression
    Artem Barski
    Raja Jothi
    Suresh Cuddapah
    Kairong Cui
    Tae-Young Roh
    Dustin E. Schones
    Keji Zhao
    First Published August 27, 2009
  - Recent de novo origin of human protein-coding genes
    David G. Knowles
    Aoife McLysaght
    First Published September 2, 2009
  - Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability
    Yong-Yi Shen
    Peng Shi
    Yan-Bo Sun
    Ya-Ping Zhang
    First Published July 17, 2009
  - Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis
    Javier Armisen
    Michael J. Gilchrist
    Anna Wilczynska
    Nancy Standart
    Eric A. Miska
    First Published July 23, 2009
  - Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
    Nelson C. Lau
    Nicolas Robine
    Raquel Martin
    Wei-Jen Chung
    Yuzo Niki
    Eugene Berezikov
    Eric C. Lai
    First Published June 18, 2009
  - Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
    Monica A. Grobei
    Ermir Qeli
    Erich Brunner
    Hubert Rehrauer
    Runxuan Zhang
    Bernd Roschitzki
    Konrad Basler
    Christian H. Ahrens
    Ueli Grossniklaus
    First Published June 22, 2009
  - Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria
    Hidekazu Nakazawa
    Atsushi Arakaki
    Sachiko Narita-Yamada
    Isao Yashiro
    Koji Jinno
    Natsuko Aoki Ai Tsuruyama Yoshiko Okamura
    ...[+3 authors]...,
    Satoshi Tanikawa
    Nobuyuki Fujita
    Haruko Takeyama
    Tadashi Matsunaga
    First Published August 12, 2009
  - Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
    Tadasuke Ooka
    Yoshitoshi Ogura
    Md Asadulghani
    Makoto Ohnishi
    Keisuke Nakayama
    Jun Terajima
    Haruo Watanabe
    Tetsuya Hayashi
    First Published June 29, 2009
Methods
- - Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
    J. Douglas Freeman
    René L. Warren
    John R. Webb
    Brad H. Nelson
    Robert A. Holt
    First Published June 18, 2009
  - Next-generation tag sequencing for cancer gene expression profiling
    A. Sorana Morrissy
    Ryan D. Morin
    Allen Delaney
    Thomas Zeng
    Helen McDonald
    Steven Jones
    Yongjun Zhao
    Martin Hirst
    Marco A. Marra
    First Published June 18, 2009
  - Quantitative phenotyping via deep barcode sequencing
    Andrew M. Smith
    Lawrence E. Heisler
    Joseph Mellor
    Fiona Kaper
    Michael J. Thompson
    Mark Chee
    Frederick P. Roth
    Guri Giaever
    Corey Nislow
    First Published July 21, 2009
  - Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
    Mathias Stiller
    Michael Knapp
    Udo Stenzel
    Michael Hofreiter
    Matthias Meyer
    First Published July 27, 2009
  - Genome-wide comparisons of variation in linkage disequilibrium
    Yik Y. Teo
    Andrew E. Fry
    Kanishka Bhattacharya
    Kerrin S. Small
    Dominic P. Kwiatkowski
    Taane G. Clark
    First Published June 18, 2009
  - The human protein coevolution network
    Elisabeth R.M. Tillier
    Robert L. Charlebois
    First Published August 20, 2009
  - Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
    Christoph Kaleta
    Luís Filipe de Figueiredo
    Stefan Schuster
    First Published June 18, 2009
Resource
- - BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing
    Wei-Chun Kao
    Kristian Stevens
    Yun S. Song
    First Published August 6, 2009
  - GenGIS: A geospatial information system for genomic data
    Donovan H. Parks
    Michael Porter
    Sylvia Churcher
    Suwen Wang
    Christian Blouin
    Jacqueline Whalley
    Stephen Brooks
    Robert G. Beiko
    First Published July 27, 2009
  - Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network
    Gabriel Markson
    Christina Kiel
    Russell Hyde
    Stephanie Brown
    Panagoula Charalabous
    Anja Bremm Jennifer Semple Jonathan Woodsmith Simon Duley Kourosh Salehi-Ashtiani Marc Vidal
    ...[+6 authors]...,
    David Komander
    Luis Serrano
    Paul Lehner
    Christopher M. Sanderson
    First Published June 23, 2009
  - Evidence-based gene predictions in plant genomes
    Chengzhi Liang
    Long Mao
    Doreen Ware
    Lincoln Stein
    First Published June 18, 2009

Table of Contents

Volume 19, Issue 10 | October 2009

Commentary

Darwinian alchemy: Human genes from noncoding DNA

Article

Comparative genomics of protoploid Saccharomycetaceae

Letter

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

Nucleosomes are well positioned in exons and carry characteristic histone modifications

Chromatin poises miRNA- and protein-coding genes for expression

Recent de novo origin of human protein-coding genes

Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability

Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis

Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria

Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes

Methods

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

Next-generation tag sequencing for cancer gene expression profiling

Quantitative phenotyping via deep barcode sequencing

Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

Genome-wide comparisons of variation in linkage disequilibrium

The human protein coevolution network

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

Resource

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

GenGIS: A geospatial information system for genomic data

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Evidence-based gene predictions in plant genomes

Table of Contents

Volume 19, Issue 10 | October 2009

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Commentary

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Letter

Methods

Resource