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Methods

Identification of higher-order functional domains in the human ENCODE regions

Robert E. Thurman
Nathan Day
William S. Noble
John A. Stamatoyannopoulos

First Published June 13, 2007

ARTICLE

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

Alvaro Rada-Iglesias
Stefan Enroth
Adam Ameur
Christoph M. Koch
Gayle K. Clelland
Patricia Respuela-Alonso Sarah Wilcox Oliver M. Dovey Peter D. Ellis
... [+4 authors] ...,
Cordelia F. Langford
Ian Dunham
Jan Komorowski
Claes Wadelius

First Published June 13, 2007

LETTER

Transcription factor binding and modified histones in human bidirectional promoters

Jane M. Lin
Patrick J. Collins
Nathan D. Trinklein
Yutao Fu
Hualin Xi
Richard M. Myers
Zhiping Weng

First Published June 13, 2007

Methods

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Ghia M. Euskirchen
Joel S. Rozowsky
Chia-Lin Wei
Wah Heng Lee
Zhengdong D. Zhang
Stephen Hartman Olof Emanuelsson Viktor Stolc
... [+3 authors] ...,
Sherman Weissman
Mark B. Gerstein
Yijun Ruan
Michael Snyder

First Published June 13, 2007

RESOURCE

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Daniel Blankenberg
James Taylor
Ian Schenck
Jianbin He
Yi Zhang
Matthew Ghent Narayanan Veeraraghavan Istvan Albert
... [+3 authors] ...,
Webb Miller
Kateryna D. Makova
Ross C. Hardison
Anton Nekrutenko

First Published June 13, 2007

Methods

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

Akshay A. Bhinge
Jonghwan Kim
Ghia M. Euskirchen
Michael Snyder
Vishwanath R. Iyer

First Published June 13, 2007

ARTICLE

The landscape of histone modifications across 1% of the human genome in five human cell lines

Christoph M. Koch
Robert M. Andrews
Paul Flicek
Shane C. Dillon
Ulaş Karaöz
Gayle K. Clelland Sarah Wilcox David M. Beare Joanna C. Fowler Phillippe Couttet Keith D. James Gregory C. Lefebvre Alexander W. Bruce Oliver M. Dovey Peter D. Ellis Pawandeep Dhami Cordelia F. Langford Zhiping Weng
... [+13 authors] ...,
Ewan Birney
Nigel P. Carter
David Vetrie
Ian Dunham

First Published June 13, 2007

LETTER

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Deyou Zheng
Adam Frankish
Robert Baertsch
Philipp Kapranov
Alexandre Reymond
Siew Woh Choo Yontao Lu France Denoeud Stylianos E. Antonarakis Michael Snyder Yijun Ruan Chia-Lin Wei
... [+7 authors] ...,
Thomas R. Gingeras
Roderic Guigó
Jennifer Harrow
Mark B. Gerstein

First Published June 13, 2007

Methods

Detection of DNA structural motifs in functional genomic elements

Jason A. Greenbaum
Stephen C.J. Parker
Thomas D. Tullius

First Published June 13, 2007

ARTICLE

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

Joel S. Rozowsky
Daniel Newburger
Fred Sayward
Jiaqian Wu
Greg Jordan
Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
... [+6 authors] ...,
Sherman Weissman
Perry Miller
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

LETTER

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas

Neerja Karnani
Christopher Taylor
Ankit Malhotra
Anindya Dutta

First Published June 13, 2007

ARTICLE

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

Nathan D. Trinklein
Ulaş Karaöz
Jiaqian Wu
Anason Halees
Shelley Force Aldred
Patrick J. Collins Deyou Zheng Zhengdong D. Zhang
... [+3 authors] ...,
Mark B. Gerstein
Michael Snyder
Richard M. Myers
Zhiping Weng

First Published June 13, 2007

ARTICLE

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

France Denoeud
Philipp Kapranov
Catherine Ucla
Adam Frankish
Robert Castelo
Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte N. Henrichsen Nancy Holroyd Mark C. Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard M. Myers Jane Rogers Tim Hubbard Jennifer Harrow
... [+17 authors] ...,
Roderic Guigó
Thomas R. Gingeras
Stylianos E. Antonarakis
Alexandre Reymond

First Published June 13, 2007

ARTICLE

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott H. Margulies
Gregory M. Cooper
George Asimenos
Daryl J. Thomas
Colin N. Dewey
Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
... [+68 authors] ...,
Webb Miller
Lior Pachter
Eric D. Green
Arend Sidow

First Published June 13, 2007

Methods

Independent and complementary methods for large-scale structural analysis of mammalian chromatin

Jonathan H. Dennis
Hua-Ying Fan
Sheila M. Reynolds
Guocheng Yuan
James C. Meldrim
Daniel J. Richter
... [+1 authors] ...,
Daniel G. Peterson
Oliver J. Rando
William S. Noble
Robert E. Kingston

First Published June 13, 2007

LETTER

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

Hualin Xi
Yong Yu
Yutao Fu
Jonathan Foley
Anason Halees
Zhiping Weng

First Published June 13, 2007

COMMENTARY

ENCODE: More genomic empowerment

George M. Weinstock

First Published June 13, 2007

PERSPECTIVE

What is a gene, post-ENCODE? History and updated definition

Mark B. Gerstein
Can Bruce
Joel S. Rozowsky
Deyou Zheng
Jiang Du
Jan O. Korbel
... [+1 authors] ...,
Olof Emanuelsson
Zhengdong D. Zhang
Sherman Weissman
Michael Snyder

First Published June 13, 2007

PERSPECTIVE

Origin of phenotypes: Genes and transcripts

Thomas R. Gingeras

First Published June 13, 2007

RESOURCE

RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins

Noel G. Faux
Gavin A. Huttley
Khalid Mahmood
Geoffrey I. Webb
Maria Garcia de la Banda
James C. Whisstock

First Published June 13, 2007

LETTER

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Katsuki Tsuritani
Takuma Irie
Riu Yamashita
Yuta Sakakibara
Hiroyuki Wakaguri
Akinori Kanai
... [+1 authors] ...,
Junko Mizushima-Sugano
Sumio Sugano
Kenta Nakai
Yutaka Suzuki

First Published June 13, 2007

Methods

Ciona intestinalis and comparative analysis with Ciona savignyi" > Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi

Jong Hyun Kim
Michael S. Waterman
Lei M. Li

First Published June 13, 2007

LETTER

copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families" > Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families

Thomas Wicker
Beat Keller

First Published June 7, 2007

LETTER

Differing patterns of selection in alternative and constitutive splice sites

Kavita Garg
Phil Green

First Published June 7, 2007

LETTER

HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

Gary P. Wang
Angela Ciuffi
Jeremy Leipzig
Charles C. Berry
Frederic D. Bushman

First Published June 1, 2007

Methods

Accurate quantitation of allele-specific expression patterns by analysis of DNA melting

Sangkyun Jeong
Yoonsoo Hahn
Qi Rong
Karl Pfeifer

First Published June 1, 2007

LETTER

A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells

Guglielmo Roma
Gilda Cobellis
Pamela Claudiani
Francesco Maione
Pedro Cruz
Gaetano Tripoli
Marco Sardiello
Ivana Peluso
Elia Stupka

First Published May 31, 2007

LETTER

A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing

Rodger B. Voelker
J. Andrew Berglund

First Published May 24, 2007

RESOURCE

Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB)

Jinghui Zhang
Richard P. Finney
William Rowe
Michael Edmonson
Sei Hoon Yang
Tatiana Dracheva
Jin Jen
Jeffery P. Struewing
Kenneth H. Buetow

First Published May 24, 2007

LETTER

Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes" > Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

Mohammed Sebaihia
Michael W. Peck
Nigel P. Minton
Nicholas R. Thomson
Matthew T.G. Holden
Wilfrid J. Mitchell Andrew T. Carter Stephen D. Bentley David R. Mason Lisa Crossman Catherine J. Paul Alasdair Ivens Marjon H.J. Wells-Bennik Ian J. Davis Ana M. Cerdeño-Tárraga Carol Churcher Michael A. Quail Tracey Chillingworth Theresa Feltwell Audrey Fraser Ian Goodhead Zahra Hance Kay Jagels Natasha Larke Mark Maddison Sharon Moule Karen Mungall Halina Norbertczak Ester Rabbinowitsch Mandy Sanders
... [+25 authors] ...,
Mark Simmonds
Brian White
Sally Whithead
Julian Parkhill

First Published May 22, 2007

LETTER

C. elegans core neuronal protein–DNA interaction network" > Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network

Vanessa Vermeirssen
M. Inmaculada Barrasa
César A. Hidalgo
Jenny Aurielle B. Babon
Reynaldo Sequerra
Lynn Doucette-Stamm
Albert-László Barabási
Albertha J.M. Walhout

First Published May 18, 2007

LETTER

Three distinct modes of intron dynamics in the evolution of eukaryotes

Liran Carmel
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published May 10, 2007

LETTER

Evolutionarily conserved genes preferentially accumulate introns

Liran Carmel
Igor B. Rogozin
Yuri I. Wolf
Eugene V. Koonin

First Published May 10, 2007

LETTER

Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes" > An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Leo Goodstadt
Andreas Heger
Caleb Webber
Chris P. Ponting

First Published May 10, 2007

LETTER

Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system

Katherine Belov
Claire E. Sanderson
Janine E. Deakin
Emily S.W. Wong
Daniel Assange
Kaighin A. McColl Alex Gout Bernard de Bono
... [+3 authors] ...,
Alexander D. Barrow
Terence P. Speed
John Trowsdale
Anthony T. Papenfuss

First Published May 10, 2007

LETTER

Monodelphis domestica" > Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

Andrew J. Gentles
Matthew J. Wakefield
Oleksiy Kohany
Wanjun Gu
Mark A. Batzer
David D. Pollock
Jerzy Jurka

First Published May 10, 2007

LETTER

CpG methylation is targeted to transcription units in an invertebrate genome

Miho M. Suzuki
Alastair R.W. Kerr
Dina De Sousa
Adrian Bird

First Published April 9, 2007

LETTER

The mode and tempo of genome size evolution in eukaryotes

Matthew J. Oliver
Dmitri Petrov
David Ackerly
Paul Falkowski
Oscar M. Schofield

First Published April 9, 2007

RESOURCE

PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data

Ken Chen
Michael D. McLellan
Li Ding
Michael C. Wendl
Yumi Kasai
Richard K. Wilson
Elaine R. Mardis

First Published April 6, 2007

LETTER

Rapid evolution of an X-linked microRNA cluster in primates

Rui Zhang
Yi Peng
Wen Wang
Bing Su

First Published April 6, 2007

LETTER

Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1)

Satoshi Mikawa
Takeya Morozumi
Shin-Ichi Shimanuki
Takeshi Hayashi
Hirohide Uenishi
Michiko Domukai
Naohiko Okumura
Takashi Awata

First Published April 6, 2007

Methods

Caenorhabditis elegans: Toward a knockout for every gene" > Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene

Edwin Cuppen
Eelke Gort
Esther Hazendonk
Josine Mudde
José van de Belt
Isaäc J. Nijman
Victor Guryev
Ronald H.A. Plasterk

First Published April 6, 2007

LETTER

Fast-X on the Z: Rapid evolution of sex-linked genes in birds

Judith E. Mank
Erik Axelsson
Hans Ellegren

First Published April 6, 2007

ARTICLE

Darc) as a BMD QTL gene" > Identification of mouse Duffy Antigen Receptor for Chemokines (Darc) as a BMD QTL gene

Bouchra Edderkaoui
David J. Baylink
Wesley G. Beamer
Jon E. Wergedal
Ryan Porte
Asok Chaudhuri
Subburaman Mohan

First Published April 6, 2007

LETTER

trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase" > Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase

José L. Garcia-Perez
Aurélien J. Doucet
Alain Bucheton
John V. Moran
Nicolas Gilbert

First Published April 6, 2007

Methods

PLP2 promoter polymorphism enriched in patients with X-linked mental retardation" > X chromosome cDNA microarray screening identifies a functional PLP2 promoter polymorphism enriched in patients with X-linked mental retardation

Lilei Zhang
Chunfa Jie
Cassandra Obie
Fatima Abidi
Charles E. Schwartz
Roger E. Stevenson
David Valle
Tao Wang

First Published April 6, 2007

LETTER

Arabidopsis thaliana genome are transcribed and/or under purifying selection" > A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection

Kousuke Hanada
Xu Zhang
Justin O. Borevitz
Wen-Hsiung Li
Shin-Han Shiu

First Published March 29, 2007

ARTICLE

Min 2 (Mom2) locus: Embryonic lethality of a mutation in the Atp5a1 gene suggests a novel mechanism of polyp suppression" > The modifier of Min 2 (Mom2) locus: Embryonic lethality of a mutation in the Atp5a1 gene suggests a novel mechanism of polyp suppression

Amy A. Baran
Karen A. Silverman
Joseph Zeskand
Revati Koratkar
Ashley Palmer
Kristen McCullen
... [+1 authors] ...,
Walter J. Curran
Tina Bocker Edmonston
Linda D. Siracusa
Arthur M. Buchberg

First Published March 26, 2007

ARTICLE

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

Hiroshi Kikuta
Mary Laplante
Pavla Navratilova
Anna Z. Komisarczuk
Pär G. Engström
David Fredman Altuna Akalin Mario Caccamo Ian Sealy Kerstin Howe Julien Ghislain Guillaume Pezeron Philippe Mourrain Staale Ellingsen Andrew C. Oates Christine Thisse Bernard Thisse Isabelle Foucher
... [+13 authors] ...,
Birgit Adolf
Andrea Geling
Boris Lenhard
Thomas S. Becker

First Published March 26, 2007

ARTICLE

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

Jasmina Ponjavic
Chris P. Ponting
Gerton Lunter

First Published March 26, 2007

PERSPECTIVE

Evolution and multilevel optimization of the genetic code

Tobias Bollenbach
Kalin Vetsigian
Roy Kishony

First Published March 9, 2007

LETTER

A palindrome-driven complex rearrangement of 22q11.2 and 8q24.1 elucidated using novel technologies

Anthony L. Gotter
Manjunath A. Nimmakayalu
G. Reza Jalali
April M. Hacker
Jacob Vorstman
Danielle Conforto Duffy
Livija Medne
Beverly S. Emanuel

First Published March 9, 2007

LETTER

Candida albicans" > Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans

Quinn M. Mitrovich
Brian B. Tuch
Christine Guthrie
Alexander D. Johnson

First Published March 9, 2007

Methods

Genome-wide identification of spliced introns using a tiling microarray

Zhihong Zhang
Jay R. Hesselberth
Stanley Fields

First Published March 9, 2007

Methods

Recent human effective population size estimated from linkage disequilibrium

Albert Tenesa
Pau Navarro
Ben J. Hayes
David L. Duffy
Geraldine M. Clarke
Mike E. Goddard
Peter M. Visscher

First Published March 9, 2007

LETTER

Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms

Tamim H. Shaikh
Ronald J. O’Connor
Mary Ella Pierpont
James McGrath
April M. Hacker
Manjunath Nimmakayalu
Elizabeth Geiger
Beverly S. Emanuel
Sulagna C. Saitta

First Published March 9, 2007

LETTER

The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage

John K. Pace
Cédric Feschotte

First Published March 5, 2007

RESOURCE

E. coli by combining improved genome context methods: Comparison with high-throughput experimental data" > Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: Comparison with high-throughput experimental data

Sailu Yellaboina
Kshama Goyal
Shekhar C. Mande

First Published March 5, 2007

Methods

Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling

Jacob G. Bundy
Balázs Papp
Rebecca Harmston
Roy A. Browne
Edward M. Clayson
Nicola Burton
Richard J. Reece
Stephen G. Oliver
Kevin M. Brindle

First Published March 5, 2007

RESOURCE

Saccharomyces cerevisiae" > Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae

Yanhui Hu
Andreas Rolfs
Bhupinder Bhullar
Tellamraju V. S. Murthy
Cong Zhu
Michael F. Berger Anamaria A. Camargo Fontina Kelley Seamus McCarron Daniel Jepson Aaron Richardson Jacob Raphael Donna Moreira Elena Taycher Dongmei Zuo Stephanie Mohr Michael F. Kane Janice Williamson Andrew Simpson Martha L. Bulyk
... [+15 authors] ...,
Edward Harlow
Gerald Marsischky
Richard D. Kolodner
Joshua LaBaer

First Published February 23, 2007

LETTER

Using genomic data to unravel the root of the placental mammal phylogeny

William J. Murphy
Thomas H. Pringle
Tess A. Crider
Mark S. Springer
Webb Miller

First Published February 23, 2007

LETTER

The genetic code is nearly optimal for allowing additional information within protein-coding sequences

Shalev Itzkovitz
Uri Alon

First Published February 9, 2007

Methods

Caenorhabditis elegans" > Identification of muscle-specific regulatory modules in Caenorhabditis elegans

Guoyan Zhao
Lawrence A. Schriefer
Gary D. Stormo

First Published February 6, 2007

COMMENTARY

Canid genomics: Mapping genes for behavior in the silver fox

Tyrone C. Spady
Elaine A. Ostrander

First Published February 6, 2007

LETTER

Improvement of whole-genome annotation of cereals through comparative analyses

Wei Zhu
C. Robin Buell

First Published February 6, 2007

RESOURCE

A meiotic linkage map of the silver fox, aligned and compared to the canine genome

Anna V. Kukekova
Lyudmila N. Trut
Irina N. Oskina
Jennifer L. Johnson
Svetlana V. Temnykh
Anastasiya V. Kharlamova Darya V. Shepeleva Rimma G. Gulievich
... [+3 authors] ...,
Svetlana G. Shikhevich
Alexander S. Graphodatsky
Gustavo D. Aguirre
Gregory M. Acland

First Published February 6, 2007

LETTER

mtDNA phylogeny and evolution of laboratory mouse strains

Ana Goios
Luísa Pereira
Molly Bogue
Vincent Macaulay
António Amorim

First Published February 6, 2007

LETTER

Eimeria tenella reveals a unique segmental organization" > Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

King-Hwa Ling
Marie-Adele Rajandream
Pierre Rivailler
Alasdair Ivens
Soon-Joo Yap
Alda M.B.N. Madeira Karen Mungall Karen Billington Wai-Yan Yee Alan T. Bankier Fionnadh Carroll Alan M. Durham Nicholas Peters Shu-San Loo Mohd Noor Mat Isa Jeniffer Novaes Michael Quail Rozita Rosli Mariana Nor Shamsudin Tiago J.P. Sobreira Adrian R. Tivey Siew-Fun Wai Sarah White Xikun Wu Arnaud Kerhornou Damer Blake Rahmah Mohamed Martin Shirley Arthur Gruber
... [+24 authors] ...,
Matthew Berriman
Fiona Tomley
Paul H. Dear
Kiew-Lian Wan

First Published February 6, 2007

Methods

Identification of novel peptide hormones in the human proteome by hidden Markov model screening

Olivier Mirabeau
Emerald Perlas
Cinzia Severini
Enrica Audero
Olivier Gascuel
Roberta Possenti
Ewan Birney
Nadia Rosenthal
Cornelius Gross

First Published February 6, 2007

LETTER

AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12

Melanie Babcock
Svetlana Yatsenko
Pawel Stankiewicz
James R. Lupski
Bernice E. Morrow

First Published February 6, 2007

REVIEW

Multiple sequence alignment: In pursuit of homologous DNA positions

Sudhir Kumar
Alan Filipski

First Published February 1, 2007

LETTER

WFDC locus in the primate lineage" > Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage

Belen Hurle
Willie Swanson
Eric D. Green

First Published January 31, 2007

Methods

Refinement and expansion of signaling pathways: The osmotic response network in yeast

Irit Gat-Viks
Ron Shamir

First Published January 31, 2007

Methods

Caenorhabditis elegans by array comparative genomic hybridization" > Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization

Jason S. Maydan
Stephane Flibotte
Mark L. Edgley
Joanne Lau
Rebecca R. Selzer
Todd A. Richmond
Nathan J. Pofahl
James H. Thomas
Donald G. Moerman

First Published January 31, 2007

Methods

High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays

Jan Oosting
Esther H. Lips
Ronald van Eijk
Paul H.C. Eilers
Károly Szuhai
Cisca Wijmenga
Hans Morreau
Tom van Wezel

First Published January 31, 2007

LETTER

Large-scale identification of novel transcripts in the human genome

Brock A. Peters
Brad St. Croix
Tobias Sjöblom
Jordan M. Cummins
Natalie Silliman
Janine Ptak
... [+1 authors] ...,
Saurabh Saha
Kenneth W. Kinzler
Christos Hatzis
Victor E. Velculescu

First Published January 31, 2007

LETTER

Molecular cloning of a translocation breakpoint hotspot in 22q11

Hiroki Kurahashi
Hidehito Inagaki
Eriko Hosoba
Takema Kato
Tamae Ohye
Hiroshi Kogo
Beverly S. Emanuel

First Published January 31, 2007

RESOURCE

MEGAN analysis of metagenomic data

Daniel H. Huson
Alexander F. Auch
Ji Qi
Stephan C. Schuster

First Published January 25, 2007

Methods

Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography–mass spectrometry

Vladislav A. Petyuk
Wei-Jun Qian
Mark H. Chin
Haixing Wang
Eric A. Livesay
Matthew E. Monroe Joshua N. Adkins Navdeep Jaitly
... [+3 authors] ...,
David J. Anderson
David G. Camp
Desmond J. Smith
Richard D. Smith

First Published January 25, 2007

REVIEW

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Nathan M. Springer
Robert M. Stupar

First Published January 25, 2007

LETTER

Mycobacterium ulcerans, the causative agent of Buruli ulcer" > Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Timothy P. Stinear
Torsten Seemann
Sacha Pidot
Wafa Frigui
Gilles Reysset
Thierry Garnier Guillaume Meurice David Simon Christiane Bouchier Laurence Ma Magali Tichit Jessica L. Porter Janine Ryan Paul D.R. Johnson John K. Davies Grant A. Jenkin Pamela L.C. Small Louis M. Jones Fredj Tekaia
... [+14 authors] ...,
Françoise Laval
Mamadou Daffé
Julian Parkhill
Stewart T. Cole

First Published January 8, 2007

LETTER

Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land

Peng Shi
Jianzhi Zhang

First Published January 8, 2007

Methods

Predicting tissue-specific enhancers in the human genome

Len A. Pennacchio
Gabriela G. Loots
Marcelo A. Nobrega
Ivan Ovcharenko

First Published January 8, 2007

LETTER

Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters

Daehyun Baek
Colleen Davis
Brent Ewing
David Gordon
Phil Green

First Published January 8, 2007

LETTER

Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing

Bin Tian
Zhenhua Pan
Ju Youn Lee

First Published January 8, 2007

Methods

A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices

Aaron E. Tenney
Jia Qian Wu
Laura Langton
Paul Klueh
Ralph Quatrano
Michael R. Brent

First Published January 8, 2007

LETTER

Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana" > Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Takeshi Itoh
Tsuyoshi Tanaka
Roberto A. Barrero
Chisato Yamasaki
Yasuyuki Fujii
Phillip B. Hilton Baltazar A. Antonio Hideo Aono Rolf Apweiler Richard Bruskiewich Thomas Bureau Frances Burr Antonio Costa de Oliveira Galina Fuks Takuya Habara Georg Haberer Bin Han Erimi Harada Aiko T. Hiraki Hirohiko Hirochika Douglas Hoen Hiroki Hokari Satomi Hosokawa Yue Hsing Hiroshi Ikawa Kazuho Ikeo Tadashi Imanishi Yukiyo Ito Pankaj Jaiswal Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Hiroaki Kawashima Jitendra P. Khurana Shoshi Kikuchi Setsuko Komatsu Kanako O. Koyanagi Hiromi Kubooka Damien Lieberherr Yao-Cheng Lin David Lonsdale Takashi Matsumoto Akihiro Matsuya W. Richard McCombie Joachim Messing Akio Miyao Nicola Mulder Yoshiaki Nagamura Jongmin Nam Nobukazu Namiki Hisataka Numa Shin Nurimoto Claire O’Donovan Hajime Ohyanagi Toshihisa Okido Satoshi OOta Naoki Osato Lance E. Palmer Francis Quetier Saurabh Raghuvanshi Naomi Saichi Hiroaki Sakai Yasumichi Sakai Katsumi Sakata Tetsuya Sakurai Fumihiko Sato Yoshiharu Sato Heiko Schoof Motoaki Seki Michie Shibata Yuji Shimizu Kazuo Shinozaki Yuji Shinso Nagendra K. Singh Brian Smith-White Jun-ichi Takeda Motohiko Tanino Tatiana Tatusova Supat Thongjuea Fusano Todokoro Mika Tsugane Akhilesh K. Tyagi Apichart Vanavichit Aihui Wang Rod A. Wing Kaori Yamaguchi Mayu Yamamoto Naoyuki Yamamoto Yeisoo Yu Hao Zhang Qiang Zhao
... [+86 authors] ...,
Kenichi Higo
Benjamin Burr
Takashi Gojobori
Takuji Sasaki

First Published January 8, 2007

LETTER

Serum response factor binding sites differ in three human cell types

Sara J. Cooper
Nathan D. Trinklein
Loan Nguyen
Richard M. Myers

First Published January 2, 2007

LETTER

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

Austen R.D. Ganley
Takehiko Kobayashi

First Published January 2, 2007

Methods

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

Michael R. Miller
Joseph P. Dunham
Angel Amores
William A. Cresko
Eric A. Johnson

First Published December 22, 2006

Methods

Improving gene annotation using peptide mass spectrometry

Stephen Tanner
Zhouxin Shen
Julio Ng
Liliana Florea
Roderic Guigó
Steven P. Briggs
Vineet Bafna

First Published December 22, 2006

RESOURCE

Molecular refinement of gibbon genome rearrangements

Roberta Roberto
Oronzo Capozzi
Richard K. Wilson
Elaine R. Mardis
Mariana Lomiento
Eray Tuzun Ze Cheng
... [+2 authors] ...,
Alan R. Mootnick
Nicoletta Archidiacono
Mariano Rocchi
Evan E. Eichler

First Published December 21, 2006

Methods

Evidence for large inversion polymorphisms in the human genome from HapMap data

Vikas Bansal
Ali Bashir
Vineet Bafna

First Published December 21, 2006

LETTER

The origin and evolution of human ampliconic gene families and ampliconic structure

Bejon Kumar Bhowmick
Yoko Satta
Naoyuki Takahata

First Published December 21, 2006

Methods

Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin" > FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

Paul G. Giresi
Jonghwan Kim
Ryan M. McDaniell
Vishwanath R. Iyer
Jason D. Lieb

First Published December 19, 2006

ARTICLE

Frankia sp. strains reflect host range and host plant biogeography" > Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Philippe Normand
Pascal Lapierre
Louis S. Tisa
Johann Peter Gogarten
Nicole Alloisio
Emilie Bagnarol Carla A. Bassi Alison M. Berry Derek M. Bickhart Nathalie Choisne Arnaud Couloux Benoit Cournoyer Stephane Cruveiller Vincent Daubin Nadia Demange Maria Pilar Francino Eugene Goltsman Ying Huang Olga R. Kopp Laurent Labarre Alla Lapidus Celine Lavire Joelle Marechal Michele Martinez Juliana E. Mastronunzio Beth C. Mullin James Niemann Pierre Pujic Tania Rawnsley Zoe Rouy Chantal Schenowitz Anita Sellstedt Fernando Tavares Jeffrey P. Tomkins David Vallenet Claudio Valverde
... [+31 authors] ...,
Luis G. Wall
Ying Wang
Claudine Medigue
David R. Benson

First Published December 6, 2006

RESOURCE

Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA

Eva K. Freyhult
Jonathan P. Bollback
Paul P. Gardner

First Published December 6, 2006

LETTER

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Kenji Ichiyanagi
Ryo Nakajima
Masaki Kajikawa
Norihiro Okada

First Published December 6, 2006

Methods

Intra- and interpopulation genotype reconstruction from tagging SNPs

Peristera Paschou
Michael W. Mahoney
Asif Javed
Judith R. Kidd
Andrew J. Pakstis
Sheng Gu
Kenneth K. Kidd
Petros Drineas

First Published December 6, 2006

REVIEW

Synthetic biology projects in vitro

Anthony C. Forster
George M. Church

First Published December 6, 2006

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