Search | Genome Research

Your search for returned 6,373 results

LETTER

Genomic copy number and expression variation within the C57BL/6J inbred mouse strain

Dawn E. Watkins-Chow
William J. Pavan

First Published November 21, 2007

LETTER

Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA

Yulia Korshunova
Rebecca K. Maloney
Nathan Lakey
Robert W. Citek
Blaire Bacher
Arief Budiman Jared M. Ordway
... [+2 authors] ...,
W. Richard McCombie
Jorge Leon
Jeffrey A. Jeddeloh
John D. McPherson

First Published November 21, 2007

LETTER

Features of 5′-splice-site efficiency derived from disease-causing mutations and comparative genomics

Xavier Roca
Andrew J. Olson
Atmakuri R. Rao
Espen Enerly
Vessela N. Kristensen
Anne-Lise Børresen-Dale
Brage S. Andresen
Adrian R. Krainer
Ravi Sachidanandam

First Published November 21, 2007

LETTER

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

Schraga Schwartz
João Silva
David Burstein
Tal Pupko
Eduardo Eyras
Gil Ast

First Published November 21, 2007

LETTER

Universal patterns of purifying selection at noncoding positions in bacteria

Nacho Molina
Erik van Nimwegen

First Published November 21, 2007

ARTICLE

A code for transcription initiation in mammalian genomes

Martin C. Frith
Eivind Valen
Anders Krogh
Yoshihide Hayashizaki
Piero Carninci
Albin Sandelin

First Published November 21, 2007

LETTER

A nuclear matrix attachment site in the 4q35 locus has an enhancer-blocking activity in vivo: Implications for the facio-scapulo-humeral dystrophy

Andrei Petrov
Jeanne Allinne
Iryna Pirozhkova
Dalila Laoudj
Marc Lipinski
Yegor S. Vassetzky

First Published November 21, 2007

LETTER

Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation" > Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation

Guo-Qing Tang
E. Stuart Maxwell

First Published November 21, 2007

LETTER

Tribolium castaneum" > Genomics, transcriptomics, and peptidomics of neuropeptides and protein hormones in the red flour beetle Tribolium castaneum

Bin Li
Reinhard Predel
Susanne Neupert
Frank Hauser
Yoshiaki Tanaka
Giuseppe Cazzamali Michael Williamson Yasuyuki Arakane Peter Verleyen
... [+4 authors] ...,
Liliane Schoofs
Joachim Schachtner
Cornelis J.P. Grimmelikhuijzen
Yoonseong Park

First Published November 19, 2007

LETTER

Genomic architecture and inheritance of human ribosomal RNA gene clusters

Dawn M. Stults
Michael W. Killen
Heather H. Pierce
Andrew J. Pierce

First Published November 19, 2007

LETTER

Genome-wide patterns of gene flow across a house mouse hybrid zone

Katherine C. Teeter
Bret A. Payseur
Leslie W. Harris
Margaret A. Bakewell
Lisa M. Thibodeau
Janelle E. O’Brien
... [+1 authors] ...,
James G. Krenz
Maria A. Sans-Fuentes
Michael W. Nachman
Priscilla K. Tucker

First Published November 19, 2007

RESOURCE

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

Brandi L. Cantarel
Ian Korf
Sofia M.C. Robb
Genis Parra
Eric Ross
Barry Moore
Carson Holt
Alejandro Sánchez Alvarado
Mark Yandell

First Published November 19, 2007

LETTER

A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast

Devin R. Scannell
Kenneth H. Wolfe

First Published November 19, 2007

RESOURCE

A second-generation combined linkage–physical map of the human genome

Tara C. Matise
Fang Chen
Wenwei Chen
Francisco M. De La Vega
Mark Hansen
Chunsheng He Fiona C.L. Hyland Giulia C. Kennedy Xiangyang Kong
... [+4 authors] ...,
Sarah S. Murray
Janet S. Ziegle
William C.L. Stewart
Steven Buyske

First Published November 7, 2007

Methods

Targeted discovery of novel human exons by comparative genomics

Adam Siepel
Mark Diekhans
Broňa Brejová
Laura Langton
Michael Stevens
Charles L.G. Comstock Colleen Davis Brent Ewing Shelly Oommen Christopher Lau Hung-Chun Yu Jianfeng Li Bruce A. Roe Phil Green
... [+9 authors] ...,
Daniela S. Gerhard
Gary Temple
David Haussler
Michael R. Brent

First Published November 7, 2007

LETTER

Significant gene content variation characterizes the genomes of inbred mouse strains

Gene Cutler
Lisa A. Marshall
Ni Chin
Helene Baribault
Paul D. Kassner

First Published November 7, 2007

LETTER

Drosophila melanogaster genome" > Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome

Peter Andolfatto

First Published November 7, 2007

Methods

Examining protein–protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system

Bernhard Suter
Michael J. Fetchko
Ralph Imhof
Christopher I. Graham
Ingrid Stoffel-Studer
Caroline Zbinden Maanasa Raghavan Lianet Lopez Lucija Beneti Jacqueline Hort Jeffrey Fillingham
... [+6 authors] ...,
Jack F. Greenblatt
Guri Giaever
Corey Nislow
Igor Stagljar

First Published November 7, 2007

LETTER

Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines

Kee-Pyo Kim
Alexandra Thurston
Christine Mummery
Dorien Ward-van Oostwaard
Helen Priddle
Cinzia Allegrucci
Chris Denning
Lorraine Young

First Published November 7, 2007

12 | Genomes/Methods

Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes

Pouya Kheradpour
Alexander Stark
Sushmita Roy
Manolis Kellis

First Published November 7, 2007

12 | Genomes/Letter

Genome-scale analysis of positionally relocated genes

Arjun Bhutkar
Susan M. Russo
Temple F. Smith
William M. Gelbart

First Published November 7, 2007

12 | Genomes/Letter

Drosophila melanogaster using 12 fly genomes" > Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes

Michael F. Lin
Joseph W. Carlson
Madeline A. Crosby
Beverley B. Matthews
Charles Yu
Soo Park Kenneth H. Wan Andrew J. Schroeder L. Sian Gramates Susan E. St. Pierre Margaret Roark Kenneth L. Wiley Rob J. Kulathinal Peili Zhang Kyl V. Myrick
... [+10 authors] ...,
Jerry V. Antone
Susan E. Celniker
William M. Gelbart
Manolis Kellis

First Published November 7, 2007

12 | Genomes/Letter

Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

J. Graham Ruby
Alexander Stark
Wendy K. Johnston
Manolis Kellis
David P. Bartel
Eric C. Lai

First Published November 7, 2007

12 | Genomes/Letter

Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Alexander Stark
Pouya Kheradpour
Leopold Parts
Julius Brennecke
Emily Hodges
Gregory J. Hannon
Manolis Kellis

First Published November 7, 2007

12 | Genomes/Letter

Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase" > Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase

Alfredo Villasante
José P. Abad
Rosario Planelló
María Méndez-Lago
Susan E. Celniker
Beatriz de Pablos

First Published November 7, 2007

12 | Genomes/Letter

Drosophila species" > Sequence variation within the rRNA gene loci of 12 Drosophila species

Deborah E. Stage
Thomas H. Eickbush

First Published November 7, 2007

12 | Genomes/Letter

Drosophila genomes" > Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes

Andreas Heger
Chris P. Ponting

First Published November 7, 2007

12 | Genomes/Methods

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

Matthew D. Rasmussen
Manolis Kellis

First Published November 7, 2007

12 | Genomes/Letter

Genomic regulatory blocks underlie extensive microsynteny conservation in insects

Pär G. Engström
Shannan J. Ho Sui
Øyvind Drivenes
Thomas S. Becker
Boris Lenhard

First Published November 7, 2007

RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Webb Miller
Kate Rosenbloom
Ross C. Hardison
Minmei Hou
James Taylor
Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
... [+17 authors] ...,
Eric S. Lander
Adam Siepel
David Haussler
W. James Kent

First Published November 5, 2007

RESOURCE

Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi

Michael J. Cornell
Intikhab Alam
Darren M. Soanes
Han Min Wong
Cornelia Hedeler
Norman W. Paton
... [+1 authors] ...,
Magnus Rattray
Simon J. Hubbard
Nicholas J. Talbot
Stephen G. Oliver

First Published November 5, 2007

RESOURCE

Initial sequence and comparative analysis of the cat genome

Joan U. Pontius
James C. Mullikin
Douglas R. Smith
Kerstin Lindblad-Toh
Sante Gnerre
Michele Clamp Jean Chang Robert Stephens Beena Neelam Natalia Volfovsky Alejandro A. Schäffer Richa Agarwala Kristina Narfström William J. Murphy Urs Giger Alfred L. Roca Agostinho Antunes Marilyn Menotti-Raymond Naoya Yuhki Jill Pecon-Slattery
... [+15 authors] ...,
Warren E. Johnson
Guillaume Bourque
Glenn Tesler
Stephen J. O’Brien

First Published November 1, 2007

COMMENTARY

2× genomes—Does depth matter?

Phil Green

First Published November 1, 2007

LETTER

Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus

Christiane Robbins
Jada Benn Torres
Stanley Hooker
Carolina Bonilla
Wenndy Hernandez
Angela Candreva
Chiledum Ahaghotu
Rick Kittles
John Carpten

First Published October 31, 2007

RESOURCE

Sequence-based estimation of minisatellite and microsatellite repeat variability

Matthieu Legendre
Nathalie Pochet
Theodore Pak
Kevin J. Verstrepen

First Published October 31, 2007

LETTER

Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases

Marius K. Lemberg
Matthew Freeman

First Published October 15, 2007

LETTER

Arabidopsis gene network based on the graphical Gaussian model" > An Arabidopsis gene network based on the graphical Gaussian model

Shisong Ma
Qingqiu Gong
Hans J. Bohnert

First Published October 5, 2007

Methods

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

Kai Wang
Mingyao Li
Dexter Hadley
Rui Liu
Joseph Glessner
Struan F.A. Grant
Hakon Hakonarson
Maja Bucan

First Published October 5, 2007

LETTER

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Laurie Gordon
Shan Yang
Mary Tran-Gyamfi
Dan Baggott
Mari Christensen
Aaron Hamilton Richard Crooijmans
... [+2 authors] ...,
Martien Groenen
Susan Lucas
Ivan Ovcharenko
Lisa Stubbs

First Published October 5, 2007

ARTICLE

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

Heidi G. Parker
Anna V. Kukekova
Dayna T. Akey
Orly Goldstein
Ewen F. Kirkness
Kathleen C. Baysac
... [+1 authors] ...,
Dana S. Mosher
Gustavo D. Aguirre
Gregory M. Acland
Elaine A. Ostrander

First Published October 4, 2007

LETTER

Rickettsia massiliae genome" > Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

Guillaume Blanc
Hiroyuki Ogata
Catherine Robert
Stéphane Audic
Jean-Michel Claverie
Didier Raoult

First Published October 4, 2007

ARTICLE

A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

Xiaoqin Xu
Mark Bieda
Victor X. Jin
Alina Rabinovich
Mathew J. Oberley
Roland Green
Peggy J. Farnham

First Published October 1, 2007

RESOURCE

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

Juliane C. Dohm
Claudio Lottaz
Tatiana Borodina
Heinz Himmelbauer

First Published October 1, 2007

LETTER

Altered adenosine-to-inosine RNA editing in human cancer

Nurit Paz
Erez Y. Levanon
Ninette Amariglio
Amy B. Heimberger
Zvi Ram
Shlomi Constantini Zohar S. Barbash Konstantin Adamsky Michal Safran Avi Hirschberg Meir Krupsky Issachar Ben-Dov Simona Cazacu
... [+8 authors] ...,
Tom Mikkelsen
Chaya Brodie
Eli Eisenberg
Gideon Rechavi

First Published October 1, 2007

ARTICLE

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

Minglei Wang
Liudmila S. Yafremava
Derek Caetano-Anollés
Jay E. Mittenthal
Gustavo Caetano-Anollés

First Published October 1, 2007

LETTER

Systematic condition-dependent annotation of metabolic genes

Tomer Shlomi
Markus Herrgard
Vasiliy Portnoy
Efrat Naim
Bernhard Ø. Palsson
Roded Sharan
Eytan Ruppin

First Published September 25, 2007

RESOURCE

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

Robert Lyle
Paola Prandini
Kazutoyo Osoegawa
Boudewijn ten Hallers
Sean Humphray
Baoli Zhu Eduardo Eyras Robert Castelo Christine P. Bird Sarantos Gagos Carol Scott Antony Cox Samuel Deutsch Catherine Ucla Marc Cruts Sophie Dahoun Xinwei She Frederique Bena Sheng-Yue Wang Christine Van Broeckhoven Evan E. Eichler Roderic Guigo
... [+17 authors] ...,
Jane Rogers
Pieter J. de Jong
Alexandre Reymond
Stylianos E. Antonarakis

First Published September 25, 2007

LETTER

Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates

Chris Wallace
Richard J. Dobson
Patricia B. Munroe
Mark J. Caulfield

First Published September 25, 2007

LETTER

Moraxella catarrhalis" > The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis

Thierry Wirth
Giovanna Morelli
Barica Kusecek
Alex van Belkum
Cindy van der Schee
Axel Meyer
Mark Achtman

First Published September 25, 2007

Methods

Prediction of individual genetic risk to disease from genome-wide association studies

Naomi R. Wray
Michael E. Goddard
Peter M. Visscher

First Published September 4, 2007

ARTICLE

The anatomy of microbial cell state transitions in response to oxygen

Amy K. Schmid
David J. Reiss
Amardeep Kaur
Min Pan
Nichole King
Phu T. Van
Laura Hohmann
Daniel B. Martin
Nitin S. Baliga

First Published September 4, 2007

LETTER

Causes for the intriguing presence of tRNAs in phages

Marc Bailly-Bechet
Massimo Vergassola
Eduardo Rocha

First Published September 4, 2007

LETTER

C. elegans noncoding transcriptome with a whole-genome tiling microarray" > Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray

Housheng He
Jie Wang
Tao Liu
X. Shirley Liu
Tiantian Li
Yunfei Wang Zuwei Qian Haixia Zheng Xiaopeng Zhu Tao Wu Baochen Shi
... [+6 authors] ...,
Wei Deng
Wei Zhou
Geir Skogerbø
Runsheng Chen

First Published September 4, 2007

LETTER

The evolution of genome compression and genomic novelty in RNA viruses

Robert Belshaw
Oliver G. Pybus
Andrew Rambaut

First Published September 4, 2007

LETTER

Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion

Timothy R. Dreszer
Gregory D. Wall
David Haussler
Katherine S. Pollard

First Published September 4, 2007

Methods

High-throughput methylation profiling by MCA coupled to CpG island microarray

Marcos R.H. Estécio
Pearlly S. Yan
Ashraf E.K. Ibrahim
Carmen S. Tellez
Lanlan Shen
Tim H.-M. Huang
Jean-Pierre J. Issa

First Published September 4, 2007

LETTER

Computational identification and functional validation of regulatory motifs in cartilage-expressed genes

Sherri R. Davies
Li-Wei Chang
Debabrata Patra
Xiaoyun Xing
Karen Posey
Jacqueline Hecht
Gary D. Stormo
Linda J. Sandell

First Published September 4, 2007

Methods

A systems biology approach for pathway level analysis

Sorin Draghici
Purvesh Khatri
Adi Laurentiu Tarca
Kashyap Amin
Arina Done
Calin Voichita
Constantin Georgescu
Roberto Romero

First Published September 4, 2007

LETTER

Functional conservation of Rel binding sites in drosophilid genomes

Richard R. Copley
Maxim Totrov
Jane Linnell
Simon Field
Jiannis Ragoussis
Irina A. Udalova

First Published September 4, 2007

LETTER

Drosophila melanogaster" > A model of segmental duplication formation in Drosophila melanogaster

Anna-Sophie Fiston-Lavier
Dominique Anxolabehere
Hadi Quesneville

First Published August 28, 2007

LETTER

A novel olfactory receptor gene family in teleost fish

Luis R. Saraiva
Sigrun I. Korsching

First Published August 23, 2007

LETTER

Chromosomal rearrangement interferes with meiotic X chromosome inactivation

David Homolka
Robert Ivanek
Jana Capkova
Petr Jansa
Jiri Forejt

First Published August 23, 2007

LETTER

Caenorhabditis elegans operons" > Identification and analysis of internal promoters in Caenorhabditis elegans operons

Peiming Huang
Erin D. Pleasance
Jason S. Maydan
Rebecca Hunt-Newbury
Nigel J. O’Neil
Allan Mah
... [+1 authors] ...,
David L. Baillie
Marco A. Marra
Donald G. Moerman
Steven J.M. Jones

First Published August 21, 2007

Methods

A new approach to estimate parameters of speciation models with application to apes

Celine Becquet
Molly Przeworski

First Published August 21, 2007

LETTER

Direct linkage of mitochondrial genome variation to risk factors for type 2 diabetes in conplastic strains

Michal Pravenec
Masaya Hyakukoku
Josef Houstek
Vaclav Zidek
Vladimir Landa
Petr Mlejnek Ivan Miksik Kristyna Dudová-Mothejzikova Petr Pecina Marek Vrbacký Zdenek Drahota Alena Vojtiskova Tomas Mracek Ludmila Kazdova Olena Oliyarnyk Jiaming Wang
... [+11 authors] ...,
Christopher Ho
Nathan Qi
Ken Sugimoto
Theodore Kurtz

First Published August 10, 2007

LETTER

A multidimensional analysis of genes mutated in breast and colorectal cancers

Jimmy Lin
Christine M. Gan
Xiaosong Zhang
Siân Jones
Tobias Sjöblom
Laura D. Wood D. Williams Parsons Nickolas Papadopoulos
... [+3 authors] ...,
Kenneth W. Kinzler
Bert Vogelstein
Giovanni Parmigiani
Victor E. Velculescu

First Published August 10, 2007

LETTER

Domain-wide regulation of gene expression in the human genome

Hinco J. Gierman
Mireille H.G. Indemans
Jan Koster
Sandra Goetze
Jurgen Seppen
Dirk Geerts
Roel van Driel
Rogier Versteeg

First Published August 10, 2007

Methods

Conrad: Gene prediction using conditional random fields

David DeCaprio
Jade P. Vinson
Matthew D. Pearson
Philip Montgomery
Matthew Doherty
James E. Galagan

First Published August 9, 2007

Methods

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

Nitin Gupta
Stephen Tanner
Navdeep Jaitly
Joshua N. Adkins
Mary Lipton
Robert Edwards Margaret Romine
... [+2 authors] ...,
Andrei Osterman
Vineet Bafna
Richard D. Smith
Pavel A. Pevzner

First Published August 9, 2007

PERSPECTIVE

Raising the estimate of functional human sequences

Michael Pheasant
John S. Mattick

First Published August 9, 2007

LETTER

Human gene organization driven by the coordination of replication and transcription

Maxime Huvet
Samuel Nicolay
Marie Touchon
Benjamin Audit
Yves d'Aubenton-Carafa
Alain Arneodo
Claude Thermes

First Published August 3, 2007

Methods

Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development

Daniel B. McClatchy
Lujian Liao
Sung Kyu Park
John D. Venable
John R. Yates

First Published August 3, 2007

LETTER

Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution

Graham R. Bignell
Thomas Santarius
Jessica C.M. Pole
Adam P. Butler
Janet Perry
Erin Pleasance Chris Greenman Andrew Menzies Sheila Taylor Sarah Edkins Peter Campbell Michael Quail Bob Plumb Lucy Matthews Kirsten McLay Paul A.W. Edwards
... [+11 authors] ...,
Jane Rogers
Richard Wooster
P. Andrew Futreal
Michael R. Stratton

First Published August 3, 2007

LETTER

Escherichia coli" > Genes under positive selection in Escherichia coli

Lise Petersen
Jonathan P. Bollback
Matt Dimmic
Melissa Hubisz
Rasmus Nielsen

First Published August 3, 2007

LETTER

A periodic pattern of SNPs in the human genome

Bo Eskerod Madsen
Palle Villesen
Carsten Wiuf

First Published August 2, 2007

Methods

Heritability of alternative splicing in the human genome

Tony Kwan
David Benovoy
Christel Dias
Scott Gurd
David Serre
Harry Zuzan Tyson A. Clark Anthony Schweitzer Michelle K. Staples Hui Wang
... [+5 authors] ...,
John E. Blume
Thomas J. Hudson
Rob Sladek
Jacek Majewski

First Published August 1, 2007

ERRATUM

Errata

First Published August 1, 2007

ARTICLE

Gene copy number variation spanning 60 million years of human and primate evolution

Laura Dumas
Young H. Kim
Anis Karimpour-Fard
Michael Cox
Janet Hopkins
Jonathan R. Pollack
James M. Sikela

First Published July 31, 2007

LETTER

VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure" > Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure

Lucio Marcello
J. David Barry

First Published July 25, 2007

LETTER

Unique genes in giant viruses: Regular substitution pattern and anomalously short size

Hiroyuki Ogata
Jean-Michel Claverie

First Published July 25, 2007

ARTICLE

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

Yoichiro Nakatani
Hiroyuki Takeda
Yuji Kohara
Shinichi Morishita

First Published July 25, 2007

Methods

Calling cards for DNA-binding proteins

Haoyi Wang
Mark Johnston
Robi David Mitra

First Published July 10, 2007

Methods

Recombination rate estimation in the presence of hotspots

Adam Auton
Gil McVean

First Published July 10, 2007

LETTER

Mycobacterium leprae: The dynamics of gene loss and genome reduction" > Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction

Laura Gómez-Valero
Eduardo P.C. Rocha
Amparo Latorre
Francisco J. Silva

First Published July 10, 2007

LETTER

Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)

Maren Krull
Mirjan Petrusma
Wojciech Makalowski
Jürgen Brosius
Jürgen Schmitz

First Published July 10, 2007

ARTICLE

A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids

Daria V. Babushok
Kazuhiko Ohshima
Eric M. Ostertag
Xinsheng Chen
Yanfeng Wang
Prabhat K. Mandal
Norihiro Okada
Charles S. Abrams
Haig H. Kazazian

First Published July 10, 2007

RESOURCE

Drosophila melanogaster" > Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster

Ming Zhan
Haruyoshi Yamaza
Yu Sun
Jason Sinclair
Huai Li
Sige Zou

First Published July 10, 2007

LETTER

Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere

Lee H. Wong
Kate H. Brettingham-Moore
Lyn Chan
Julie M. Quach
Melissa A. Anderson
Emma L. Northrop Ross Hannan
... [+2 authors] ...,
Richard Saffery
Margaret L. Shaw
Evan Williams
K.H. Andy Choo

First Published July 10, 2007

LETTER

Nucleosome positioning signals in genomic DNA

Heather E. Peckham
Robert E. Thurman
Yutao Fu
John A. Stamatoyannopoulos
William Stafford Noble
Kevin Struhl
Zhiping Weng

First Published July 9, 2007

LETTER

trans-acting factors" > Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

Daryi Wang
Huang-Mo Sung
Tzi-Yuan Wang
Chih-Jen Huang
Peggy Yang
Tiffany Chang Yang-Chao Wang Da-Lun Tseng
... [+3 authors] ...,
Jen-Pey Wu
Tso-Ching Lee
Ming-Che Shih
Wen-Hsiung Li

First Published July 5, 2007

RESOURCE

Detecting genetic variation in microarray expression data

Jennifer A. Greenhall
Matthew A. Zapala
Mario Cáceres
Ondrej Libiger
Carrolee Barlow
Nicholas J. Schork
David J. Lockhart

First Published July 3, 2007

PERSPECTIVE

Promoting transcriptome diversity

Robert L. Strausberg
Samuel Levy

First Published July 2, 2007

Methods

Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance

Chunlin Wang
Yumi Mitsuya
Baback Gharizadeh
Mostafa Ronaghi
Robert W. Shafer

First Published June 28, 2007

LETTER

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Zhengdong D. Zhang
Alberto Paccanaro
Yutao Fu
Sherman Weissman
Zhiping Weng
Joseph Chang
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

LETTER

Structured RNAs in the ENCODE selected regions of the human genome

Stefan Washietl
Jakob S. Pedersen
Jan O. Korbel
Claudia Stocsits
Andreas R. Gruber
Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Reiche Andrea Tanzer Catherine Ucla Carine Wyss Stylianos E. Antonarakis France Denoeud Julien Lagarde Jorg Drenkow Philipp Kapranov Thomas R. Gingeras Roderic Guigó Michael Snyder
... [+15 authors] ...,
Mark B. Gerstein
Alexandre Reymond
Ivo L. Hofacker
Peter F. Stadler

First Published June 13, 2007

RESOURCE

Construction of a genome-scale structural map at single-nucleotide resolution

Jason A. Greenbaum
Bo Pang
Thomas D. Tullius

First Published June 13, 2007

LETTER

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

Yijun Ruan
Hong Sain Ooi
Siew Woh Choo
Kuo Ping Chiu
Xiao Dong Zhao
K.G. Srinivasan Fei Yao Chiou Yu Choo Jun Liu Pramila Ariyaratne Wilson G.W. Bin Vladimir A. Kuznetsov Atif Shahab
... [+8 authors] ...,
Wing-Kin Sung
Guillaume Bourque
Nallasivam Palanisamy
Chia-Lin Wei

First Published June 13, 2007

RESOURCE

The ENCODEdb portal: Simplified access to ENCODE Consortium data

Laura L. Elnitski
Prachi Shah
R. Travis Moreland
Lowell Umayam
Tyra G. Wolfsberg
Andreas D. Baxevanis

First Published June 13, 2007

LETTER

cis-regulatory elements using comparative genomics: Some lessons from ENCODE data" > Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

David C. King
James Taylor
Ying Zhang
Yong Cheng
Heather A. Lawson
Joel Martin
Francesca Chiaromonte
Webb Miller
Ross C. Hardison

First Published June 13, 2007

LETTER

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

Victor X. Jin
Henriette O’Geen
Sushma Iyengar
Roland Green
Peggy J. Farnham

First Published June 13, 2007

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