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Methods

Genome-wide prediction of imprinted murine genes

Philippe P. Luedi
Alexander J. Hartemink
Randy L. Jirtle

First Published June 1, 2005

RESOURCE

Drosophila buzzatii genome" > A BAC-based physical map of the Drosophila buzzatii genome

Josefa González
Michael Nefedov
Ian Bosdet
Ferran Casals
Oriol Calvete
Alejandra Delprat Heesun Shin Readman Chiu Carrie Mathewson Natasja Wye
... [+5 authors] ...,
Roger A. Hoskins
Jacqueline E. Schein
Pieter de Jong
Alfredo Ruiz

First Published June 1, 2005

Methods

cis-regulatory elements" > Footer: A quantitative comparative genomics method for efficient recognition of cis-regulatory elements

David L. Corcoran
Eleanor Feingold
Jessica Dominick
Marietta Wright
Jo Harnaha
Massimo Trucco
Nick Giannoukakis
Panayiotis V. Benos

First Published June 1, 2005

LETTER

Streptomyces coelicolor A3(2) metabolism" > Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Irina Borodina
Preben Krabben
Jens Nielsen

First Published June 1, 2005

Methods

Discovering functional transcription-factor combinations in the human cell cycle

Zhou Zhu
Jay Shendure
George M. Church

First Published June 1, 2005

Methods

Discovering regulatory binding-site modules using rule-based learning

Torgeir R. Hvidsten
Bartosz Wilczyński
Andriy Kryshtafovych
Jerzy Tiuryn
Jan Komorowski
Krzysztof Fidelis

First Published June 1, 2005

LETTER

Operon formation is driven by co-regulation and not by horizontal gene transfer

Morgan N. Price
Katherine H. Huang
Adam P. Arkin
Eric J. Alm

First Published June 1, 2005

LETTER

Drosophila melanogaster populations" > Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations

Penelope R. Haddrill
Kevin R. Thornton
Brian Charlesworth
Peter Andolfatto

First Published June 1, 2005

ARTICLE

Dichotomous splicing signals in exon flanks

Xiang H-F. Zhang
Christina S. Leslie
Lawrence A. Chasin

First Published June 1, 2005

LETTER

Alu retrotransposons suggests an alternative model for 5′-end attachment requiring microhomology-mediated end-joining" > Analysis of 5′ junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5′-end attachment requiring microhomology-mediated end-joining

Nora Zingler
Ute Willhoeft
Hans-Peter Brose
Volker Schoder
Thomas Jahns
Kay-Martin O. Hanschmann
Tammy A. Morrish
Johannes Löwer
Gerald G. Schumann

First Published June 1, 2005

ARTICLE

Xanthomonas campestris pv. campestris" > Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris

Wei Qian
Yantao Jia
Shuang-Xi Ren
Yong-Qiang He
Jia-Xun Feng
Ling-Feng Lu Qihong Sun Ge Ying Dong-Jie Tang Hua Tang Wei Wu Pei Hao Lifeng Wang Bo-Le Jiang Shenyan Zeng Wen-Yi Gu Gang Lu Li Rong Yingchuan Tian Zhijian Yao Gang Fu Baoshan Chen Rongxiang Fang Boqin Qiang
... [+19 authors] ...,
Zhu Chen
Guo-Ping Zhao
Ji-Liang Tang
Chaozu He

First Published May 17, 2005

Methods

Direct isolation and identification of promoters in the human genome

Tae Hoon Kim
Leah O. Barrera
Chunxu Qu
Sara Van Calcar
Nathan D. Trinklein
Sara J. Cooper Rosa M. Luna
... [+2 authors] ...,
Christopher K. Glass
Michael G. Rosenfeld
Richard M. Myers
Bing Ren

First Published May 17, 2005

LETTER

homothorax mRNA splicing" > Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

Evgeny A. Glazov
Michael Pheasant
Elizabeth A. McGraw
Gill Bejerano
John S. Mattick

First Published May 17, 2005

Methods

Identification of genomic features using microsyntenies of domains: Domain teams

Sophie Pasek
Anne Bergeron
Jean-Loup Risler
Alexandra Louis
Emmanuelle Ollivier
Mathieu Raffinot

First Published May 17, 2005

RESOURCE

A. gambiae functional genomics" > AnoEST: Toward A. gambiae functional genomics

Evgenia V. Kriventseva
Anastasios C. Koutsos
Claudia Blass
Fotis C. Kafatos
George K. Christophides
Evgeny M. Zdobnov

First Published May 17, 2005

RESOURCE

Begin at the beginning: Predicting genes with 5′ UTRs

Randall H. Brown
Samuel S. Gross
Michael R. Brent

First Published May 2, 2005

RESOURCE

Genome-wide assembly and analysis of alternative transcripts in mouse

Alexei A. Sharov
Dawood B. Dudekula
Minoru S.H. Ko

First Published May 2, 2005

Methods

Classification of a large microarray data set: Algorithm comparison and analysis of drug signatures

Georges Natsoulis
Laurent El Ghaoui
Gert R.G. Lanckriet
Alexander M. Tolley
Fabrice Leroy
Shane Dunlea
... [+1 authors] ...,
Barrett P. Eynon
Cecelia I. Pearson
Stuart Tugendreich
Kurt Jarnagin

First Published May 2, 2005

Methods

Drosophila" > Target-selected mutant screen by TILLING in Drosophila

Sylke Winkler
Anja Schwabedissen
Dana Backasch
Christian Bökel
Claudia Seidel
Stefanie Bönisch Maximilian Fürthauer
... [+2 authors] ...,
Antje Kuhrs
Laura Cobreros
Michael Brand
Marcos González-Gaitán

First Published May 2, 2005

RESOURCE

Exploring relationships and mining data with the UCSC Gene Sorter

W.J. Kent
Fan Hsu
Donna Karolchik
Robert M. Kuhn
Hiram Clawson
Heather Trumbower
David Haussler

First Published May 2, 2005

Methods

Cell-free cotranslation and selection using in vitro virus for high-throughput analysis of protein–protein interactions and complexes

Etsuko Miyamoto-Sato
Masamichi Ishizaka
Kenichi Horisawa
Seiji Tateyama
Hideaki Takashima
Shinichiro Fuse
... [+1 authors] ...,
Kaori Sue
Naoya Hirai
Kazuyo Masuoka
Hiroshi Yanagawa

First Published May 2, 2005

LETTER

Drosophila Hox gene complex" > Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex

Bárbara Negre
Sònia Casillas
Magali Suzanne
Ernesto Sánchez-Herrero
Michael Akam
Michael Nefedov
Antonio Barbadilla
Pieter de Jong
Alfredo Ruiz

First Published May 2, 2005

LETTER

Evolution of base-substitution gradients in primate mitochondrial genomes

Sameer Z. Raina
Jeremiah J. Faith
Todd R. Disotell
Hervé Seligmann
Caro-Beth Stewart
David D. Pollock

First Published May 2, 2005

LETTER

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Yoav Gilad
Scott A. Rifkin
Paul Bertone
Mark Gerstein
Kevin P. White

First Published May 2, 2005

LETTER

Alu amplification" > Under the genomic radar: The Stealth model of Alu amplification

Kyudong Han
Jinchuan Xing
Hui Wang
Dale J. Hedges
Randall K. Garber
Richard Cordaux
Mark A. Batzer

First Published May 2, 2005

ARTICLE

Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants

Christos Noutsos
Erik Richly
Dario Leister

First Published May 2, 2005

LETTER

Cis-acting expression quantitative trait loci in mice" > Cis-acting expression quantitative trait loci in mice

Sudheer Doss
Eric E. Schadt
Thomas A. Drake
Aldons J. Lusis

First Published April 18, 2005

ARTICLE

C. elegans daf-2 mutants using serial analysis of gene expression" > Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression

Julius Halaschek-Wiener
Jaswinder S. Khattra
Sheldon McKay
Anatoli Pouzyrev
Jeff M. Stott
George S. Yang Robert A. Holt
... [+2 authors] ...,
Steven J.M. Jones
Marco A. Marra
Angela R. Brooks-Wilson
Donald L. Riddle

First Published April 18, 2005

LETTER

Saccharomyces species" > Identification of functional transcription factor binding sites using closely related Saccharomyces species

Scott W. Doniger
Juyoung Huh
Justin C. Fay

First Published April 18, 2005

ARTICLE

Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation" > The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

Nicholas R. Thomson
Corin Yeats
Kenneth Bell
Matthew T.G. Holden
Stephen D. Bentley
Morag Livingstone Ana M. Cerdeño-Tárraga Barbara Harris Jon Doggett Doug Ormond Karen Mungall Kay Clarke Theresa Feltwell Zahra Hance Mandy Sanders Michael A. Quail
... [+11 authors] ...,
Claire Price
Bart G. Barrell
Julian Parkhill
David Longbottom

First Published April 18, 2005

ARTICLE

Retroviruses and yeast retrotransposons use overlapping sets of host genes

Becky Irwin
Michael Aye
Pierre Baldi
Nadejda Beliakova-Bethell
Henry Cheng
Yimeng Dou
Willy Liou
Suzanne Sandmeyer

First Published April 18, 2005

RESOURCE

C. elegans ORFeome by cloning TWINSCAN predictions" > Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions

Chaochun Wei
Philippe Lamesch
Manimozhiyan Arumugam
Jennifer Rosenberg
Ping Hu
Marc Vidal
Michael R. Brent

First Published April 1, 2005

Methods

Forcing interactions as a genetic screen to identify proteins that exert a defined activity

Michael DeVit
Paul J. Cullen
Margaret Branson
George F. Sprague
Stanley Fields

First Published April 1, 2005

ERRATUM

Correction for Volume 15, p. 231

Janet M. Young
Marijo Kambere
Barbara J. Trask
Robert P. Lane

First Published April 1, 2005

Methods

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

Namshin Kim
Seokmin Shin
Sanghyuk Lee

First Published April 1, 2005

LETTER

Functional insights from the distribution and role of homopeptide repeat-containing proteins

Noel G. Faux
Stephen P. Bottomley
Arthur M. Lesk
James A. Irving
John R. Morrison
Maria Garcia de la Banda
James C. Whisstock

First Published April 1, 2005

RESOURCE

CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models

Hiroyuki Kurata
Kouichi Masaki
Yoshiyuki Sumida
Rei Iwasaki

First Published April 1, 2005

LETTER

Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels

Edwige Isidore
Beatrice Scherrer
Boulos Chalhoub
Catherine Feuillet
Beat Keller

First Published April 1, 2005

LETTER

Novel specificities emerge by stepwise duplication of functional modules

José B. Pereira-Leal
Sarah A. Teichmann

First Published April 1, 2005

ERRATUM

Correction for Volume 15, p. 376

First Published April 1, 2005

RESOURCE

5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: A tool for identifying differentially regulated genes" > Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: A tool for identifying differentially regulated genes

Shawn Lewenza
Reza K. Falsafi
Geoff Winsor
W. James Gooderham
Joseph B. McPhee
Fiona S.L. Brinkman
Robert E.W. Hancock

First Published April 1, 2005

LETTER

Brassica oleracea and its application to gene discovery and annotation in Arabidopsis" > Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis

Mulu Ayele
Brian J. Haas
Nikhil Kumar
Hank Wu
Yongli Xiao
Susan Van Aken
... [+1 authors] ...,
Teresa R. Utterback
Jennifer R. Wortman
Owen R. White
Christopher D. Town

First Published April 1, 2005

LETTER

Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana" > Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana

Krithika Yogeeswaran
Amy Frary
Thomas L. York
Alison Amenta
Andrew H. Lesser
June B. Nasrallah
Steven D. Tanksley
Mikhail E. Nasrallah

First Published April 1, 2005

LETTER

Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana" > Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana

Manpreet S. Katari
Vivekanand Balija
Richard K. Wilson
Robert A. Martienssen
W. Richard McCombie

First Published April 1, 2005

In This Issue

Flower Power

Hillary E. Sussman

First Published April 1, 2005

ARTICLE

Gerbera hybrida (Asteraceae)" > Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae)

Roosa A.E. Laitinen
Juha Immanen
Petri Auvinen
Stephen Rudd
Edward Alatalo
Lars Paulin Miia Ainasoja
... [+2 authors] ...,
Mika Kotilainen
Satu Koskela
Teemu H. Teeri
Paula Elomaa

First Published March 21, 2005

ARTICLE

Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized

Hidenori Kiyosawa
Nathan Mise
Shigeru Iwase
Yoshihide Hayashizaki
Kuniya Abe

First Published March 21, 2005

ARTICLE

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

Francisco M. De La Vega
Hadar Isaac
Andrew Collins
Charles R. Scafe
Bjarni V. Halldórsson
Xiaoping Su Ross A. Lippert Yu Wang Marion Laig-Webster Ryan T. Koehler Janet S. Ziegle Lewis T. Wogan Junko F. Stevens Kyle M. Leinen Sheri J. Olson Karl J. Guegler Xiaoqing You Lily H. Xu Heinz G. Hemken Francis Kalush Mitsuo Itakura Yi Zheng Guy de Thé Stephen J. O'Brien Andrew G. Clark
... [+20 authors] ...,
Sorin Istrail
Michael W. Hunkapiller
Eugene G. Spier
Dennis A. Gilbert

First Published March 21, 2005

LETTER

Brassiceae" > Chromosome triplication found across the tribe Brassiceae

Martin A. Lysak
Marcus A. Koch
Ales Pecinka
Ingo Schubert

First Published March 21, 2005

RESOURCE

Database of mRNA gene expression profiles of multiple human organs

Chang Gue Son
Sven Bilke
Sean Davis
Braden T. Greer
Jun S. Wei
Craig C. Whiteford
Qing-Rong Chen
Nicola Cenacchi
Javed Khan

First Published March 1, 2005

Methods

Post-entrapment genome engineering: First exon size does not affect the expression of fusion transcripts generated by gene entrapment

Anna B. Osipovich
Aparna Singh
H. Earl Ruley

First Published March 1, 2005

LETTER

Protein structure and evolutionary history determine sequence space topology

Boris E. Shakhnovich
Eric Deeds
Charles Delisi
Eugene Shakhnovich

First Published March 1, 2005

ERRATUM

Correction for Volume 14, p. 2412

First Published March 1, 2005

LETTER

From genome to “venome”: Molecular origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences and related body proteins

Bryan G. Fry

First Published March 1, 2005

LETTER

Prokaryotic phylogenies inferred from protein structural domains

Eric J. Deeds
Hooman Hennessey
Eugene I. Shakhnovich

First Published March 1, 2005

RESOURCE

novoSNP, a novel computational tool for sequence variation discovery

Stefan Weckx
Jurgen Del-Favero
Rosa Rademakers
Lieve Claes
Marc Cruts
Peter De Jonghe
Christine Van Broeckhoven
Peter De Rijk

First Published March 1, 2005

LETTER

Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat

Jun Yan
Thomas G. Marr

First Published March 1, 2005

LETTER

Drosophila case study" > Protein interaction mapping: A Drosophila case study

Etienne Formstecher
Sandra Aresta
Vincent Collura
Alexandre Hamburger
Alain Meil
Alexandra Trehin Céline Reverdy Virginie Betin Sophie Maire Christine Brun Bernard Jacq Monique Arpin Yohanns Bellaiche Saverio Bellusci Philippe Benaroch Michel Bornens Roland Chanet Philippe Chavrier Olivier Delattre Valérie Doye Richard Fehon Gérard Faye Thierry Galli Jean-Antoine Girault Bruno Goud Jean de Gunzburg Ludger Johannes Marie-Pierre Junier Vincent Mirouse Ashim Mukherjee Dora Papadopoulo Franck Perez Anne Plessis Carine Rossé Simon Saule Dominique Stoppa-Lyonnet Alain Vincent Michael White
... [+33 authors] ...,
Pierre Legrain
Jérôme Wojcik
Jacques Camonis
Laurent Daviet

First Published February 14, 2005

ARTICLE

Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes" > Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes

Toshiaki Fukui
Haruyuki Atomi
Tamotsu Kanai
Rie Matsumi
Shinsuke Fujiwara
Tadayuki Imanaka

First Published February 14, 2005

Methods

DIP-chip: Rapid and accurate determination of DNA-binding specificity

Xiao Liu
David M. Noll
Jason D. Lieb
Neil D. Clarke

First Published February 14, 2005

ARTICLE

Complex genomic rearrangements lead to novel primate gene function

Francesca D. Ciccarelli
Christian von Mering
Mikita Suyama
Eoghan D. Harrington
Elisa Izaurralde
Peer Bork

First Published February 14, 2005

LETTER

Naturally occurring antisense: Transcriptional leakage or real overlap?

Dvir Dahary
Orna Elroy-Stein
Rotem Sorek

First Published February 14, 2005

LETTER

C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones" > New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones

Anita G. Fernandez
Kristin C. Gunsalus
Jerry Huang
Ling-Shiang Chuang
Nancy Ying
Hsiao-lan Liang Caroline Tang Aaron J. Schetter Charles Zegar Jean-François Rual
... [+5 authors] ...,
David E. Hill
Valerie Reinke
Marc Vidal
Fabio Piano

First Published February 1, 2005

LETTER

Escherichia coli/Shigella species" > Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species

Tony Le Gall
Pierre Darlu
Patricia Escobar-Páramo
Bertrand Picard
Erick Denamur

First Published February 1, 2005

Methods

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay

Paul Hardenbol
Fuli Yu
John Belmont
Jennifer MacKenzie
Carsten Bruckner
Tiffany Brundage Andrew Boudreau Steve Chow Jim Eberle Ayca Erbilgin Mat Falkowski Ron Fitzgerald Sy Ghose Oleg Iartchouk Maneesh Jain George Karlin-Neumann Xiuhua Lu Xin Miao Bridget Moore Martin Moorhead Eugeni Namsaraev Shiran Pasternak Eunice Prakash Karen Tran Zhiyong Wang
... [+20 authors] ...,
Hywel B. Jones
Ronald W. Davis
Thomas D. Willis
Richard A. Gibbs

First Published February 1, 2005

Methods

Mapping segmental and sequence variations among laboratory mice using BAC array CGH

Antoine M. Snijders
Norma J. Nowak
Bing Huey
Jane Fridlyand
Sindy Law
Jeffrey Conroy Taku Tokuyasu Kubilay Demir Readman Chiu Jian-Hua Mao Ajay N. Jain
... [+6 authors] ...,
Steven J.M. Jones
Allan Balmain
Daniel Pinkel
Donna G. Albertson

First Published February 1, 2005

Methods

Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen" > Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen

Shawn Lewenza
Jennifer L. Gardy
Fiona S.L. Brinkman
Robert E.W. Hancock

First Published February 1, 2005

Methods

Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays

James Ronald
Joshua M. Akey
Jacqueline Whittle
Erin N. Smith
Gael Yvert
Leonid Kruglyak

First Published February 1, 2005

Methods

Pooled genomic indexing of rhesus macaque

Aleksandar Milosavljevic
Ronald A. Harris
Erica J. Sodergren
Andrew R. Jackson
Ken J. Kalafus
Anne Hodgson Andrew Cree Weilie Dai Miklos Csuros
... [+4 authors] ...,
Baoli Zhu
Pieter J. de Jong
George M. Weinstock
Richard A. Gibbs

First Published February 1, 2005

Methods

A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome

Hui-Yun Wang
Minjie Luo
Irina V. Tereshchenko
Danielle M. Frikker
Xiangfeng Cui
James Y. Li Guohong Hu Yi Chu Marco A. Azaro Yong Lin Li Shen Qifeng Yang
... [+7 authors] ...,
Manousos E. Kambouris
Richeng Gao
Weichung Shih
Honghua Li

First Published February 1, 2005

RESOURCE

ProbCons: Probabilistic consistency-based multiple sequence alignment

Chuong B. Do
Mahathi S.P. Mahabhashyam
Michael Brudno
Serafim Batzoglou

First Published February 1, 2005

LETTER

A high-resolution multistrain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns

Jinghui Zhang
Kent W. Hunter
Michael Gandolph
William L. Rowe
Richard P. Finney
Jenny M. Kelley
Michael Edmonson
Kenneth H. Buetow

First Published February 1, 2005

LETTER

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Yoav Gilad
Orna Man
Gustavo Glusman

First Published February 1, 2005

LETTER

Gene conversion and evolution of Xq28 duplicons involved in recurring inversions causing severe hemophilia A

Richard D. Bagnall
Karen L. Ayres
Peter M. Green
Francesco Giannelli

First Published February 1, 2005

Methods

Making connections between novel transcription factors and their DNA motifs

Kai Tan
Lee Ann McCue
Gary D. Stormo

First Published January 14, 2005

ARTICLE

Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence

Chen-Shan Chin
Jeffrey H. Chuang
Hao Li

First Published January 14, 2005

ARTICLE

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

Stefan Kirsch
Birgit Weiß
Tracie L. Miner
Robert H. Waterston
Royden A. Clark
Evan E. Eichler
Claudia Münch
Werner Schempp
Gudrun Rappold

First Published January 14, 2005

LETTER

Divergent V1R repertoires in five species: Amplification in rodents, decimation in primates, and a surprisingly small repertoire in dogs

Janet M. Young
Marijo Kambere
Barbara J. Trask
Robert P. Lane

First Published January 14, 2005

ARTICLE

Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution" > Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Stephen Richards
Yue Liu
Brian R. Bettencourt
Pavel Hradecky
Stan Letovsky
Rasmus Nielsen Kevin Thornton Melissa J. Hubisz Rui Chen Richard P. Meisel Olivier Couronne Sujun Hua Mark A. Smith Peili Zhang Jing Liu Harmen J. Bussemaker Marinus F. van Batenburg Sally L. Howells Steven E. Scherer Erica Sodergren Beverly B. Matthews Madeline A. Crosby Andrew J. Schroeder Daniel Ortiz-Barrientos Catharine M. Rives Michael L. Metzker Donna M. Muzny Graham Scott David Steffen David A. Wheeler Kim C. Worley Paul Havlak K. James Durbin Amy Egan Rachel Gill Jennifer Hume Margaret B. Morgan George Miner Cerissa Hamilton Yanmei Huang Lenée Waldron Daniel Verduzco Kerstin P. Clerc-Blankenburg Inna Dubchak Mohamed A.F. Noor Wyatt Anderson Kevin P. White Andrew G. Clark
... [+43 authors] ...,
Stephen W. Schaeffer
William Gelbart
George M. Weinstock
Richard A. Gibbs

First Published January 3, 2005

Methods

Identification of polymorphic motifs using probabilistic search algorithms

Analabha Basu
Probal Chaudhuri
Partha P. Majumder

First Published January 3, 2005

LETTER

Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional “strand-switch” domain as a major feature

Samson O. Obado
Martin C. Taylor
Shane R. Wilkinson
Elizabeth V. Bromley
John M. Kelly

First Published January 3, 2005

Methods

Gene and alternative splicing annotation with AIR

Liliana Florea
Valentina Di Francesco
Jason Miller
Russell Turner
Alison Yao
Michael Harris Brian Walenz Clark Mobarry Gennady V. Merkulov Rosane Charlab Ian Dew
... [+6 authors] ...,
Zuoming Deng
Sorin Istrail
Peter Li
Granger Sutton

First Published January 3, 2005

Methods

High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification

Eric Chiao
Jeff Leonard
Kari Dickinson
Julie C. Baker

First Published January 3, 2005

LETTER

High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium

Luísa Pereira
Martin Richards
Ana Goios
Antonio Alonso
Cristina Albarrán
Oscar Garcia Doron M. Behar Mukaddes Gölge Jiři Hatina
... [+4 authors] ...,
Lihadh Al-Gazali
Daniel G. Bradley
Vincent Macaulay
António Amorim

First Published January 3, 2005

Methods

Linkage group selection: Rapid gene discovery in malaria parasites

Richard Culleton
Axel Martinelli
Paul Hunt
Richard Carter

First Published January 3, 2005

Methods

Arabidopsis thaliana" > Computational prediction of miRNAs in Arabidopsis thaliana

Alex Adai
Cameron Johnson
Sizolwenkosi Mlotshwa
Sarah Archer-Evans
Varun Manocha
Vicki Vance
Venkatesan Sundaresan

First Published January 3, 2005

LETTER

KIR) loci in primates" > Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

Jennifer G. Sambrook
Arman Bashirova
Sophie Palmer
Sarah Sims
John Trowsdale
Laurent Abi-Rached
Peter Parham
Mary Carrington
Stephan Beck

First Published January 3, 2005

Chicken Special/Letters

Ascl2/Mash2–Igf2–H19 region" > Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region

Takaaki Yokomine
Hisao Shirohzu
Wahyu Purbowasito
Atsushi Toyoda
Hisakazu Iwama
Kazuho Ikeo Tetsuya Hori Shigeki Mizuno Masaoki Tsudzuki
... [+4 authors] ...,
Yoh-ichi Matsuda
Masahira Hattori
Yoshiyuki Sakaki
Hiroyuki Sasaki

First Published December 8, 2004

Chicken Special/Letters

Evolution of the Beckwith-Wiedemann syndrome region in vertebrates

Martina Paulsen
Tarang Khare
Christopher Burgard
Sascha Tierling
Jörn Walter

First Published December 8, 2004

Chicken Special/Letters

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Guillaume Bourque
Evgeny M. Zdobnov
Peer Bork
Pavel A. Pevzner
Glenn Tesler

First Published December 8, 2004

Chicken Special/Resources

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Ivan Ovcharenko
Gabriela G. Loots
Belinda M. Giardine
Minmei Hou
Jian Ma
Ross C. Hardison
Lisa Stubbs
Webb Miller

First Published December 8, 2004

Chicken Special/Resources

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Simon J. Hubbard
Darren V. Grafham
Kevin J. Beattie
Ian M. Overton
Stuart R. McLaren
Michael D.R. Croning Paul E. Boardman James K. Bonfield Joan Burnside Robert M. Davies Elizabeth R. Farrell Matthew D. Francis Sam Griffiths-Jones Sean J. Humphray Christopher Hyland Carol E. Scott Haizhou Tang Ruth G. Taylor Cheryll Tickle
... [+14 authors] ...,
William R.A. Brown
Ewan Birney
Jane Rogers
Stuart A. Wilson

First Published December 8, 2004

Chicken Special/Letters

Evolution and functional classification of vertebrate gene deserts

Ivan Ovcharenko
Gabriela G. Loots
Marcelo A. Nobrega
Ross C. Hardison
Webb Miller
Lisa Stubbs

First Published December 8, 2004

Chicken Special/Letters

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes

Erik Axelsson
Matthew T. Webster
Nick G.C. Smith
David W. Burt
Hans Ellegren

First Published December 8, 2004

Chicken Special/Resources

Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates

Wendy A. Kellner
Robert T. Sullivan
Brian H. Carlson
James W. Thomas

First Published December 8, 2004

Chicken Special/Letters

Comparison of splice sites in mammals and chicken

Josep F. Abril
Robert Castelo
Roderic Guigó

First Published December 8, 2004

ERRATUM

Correction for Volume 13, p. 875

First Published December 1, 2004

RESOURCE

EAnnot: A genome annotation tool using experimental evidence

Li Ding
Aniko Sabo
Nicolas Berkowicz
Rekha R. Meyer
Yoram Shotland
Mark R. Johnson
Kymberlie H. Pepin
Richard K. Wilson
John Spieth

First Published December 1, 2004

ERRATUM

Correction for Volume 14, p. 2221

First Published December 1, 2004

ERRATUM

Correction for Volume 14, p. 1786

First Published December 1, 2004

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