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LETTER

Drosophila genomes" > Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes

David Alvarez-Ponce
Montserrat Aguadé
Julio Rozas

First Published January 13, 2009

LETTER

Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

Webb Miller
Daniela I. Drautz
Jan E. Janecka
Arthur M. Lesk
Aakrosh Ratan
Lynn P. Tomsho Mike Packard Yeting Zhang Lindsay R. McClellan Ji Qi Fangqing Zhao M. Thomas P. Gilbert Love Dalén Juan Luis Arsuaga Per G.P. Ericson Daniel H. Huson
... [+11 authors] ...,
Kristofer M. Helgen
William J. Murphy
Anders Götherström
Stephan C. Schuster

First Published January 12, 2009

LETTER

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

Oliver A. Hampton
Petra Den Hollander
Christopher A. Miller
David A. Delgado
Jian Li
Cristian Coarfa Ronald A. Harris Stephen Richards Steven E. Scherer
... [+4 authors] ...,
Donna M. Muzny
Richard A. Gibbs
Adrian V. Lee
Aleksandar Milosavljevic

First Published December 3, 2008

LETTER

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

Suresh Cuddapah
Raja Jothi
Dustin E. Schones
Tae-Young Roh
Kairong Cui
Keji Zhao

First Published December 3, 2008

LETTER

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

Florian M. Pauler
Mathew A. Sloane
Ru Huang
Kakkad Regha
Martha V. Koerner
Ido Tamir
... [+1 authors] ...,
Andreas Sommer
Andras Aszodi
Thomas Jenuwein
Denise P. Barlow

First Published December 1, 2008

LETTER

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

Hanhui Kuang
Chellappan Padmanabhan
Feng Li
Ayako Kamei
Pudota B. Bhaskar
Shu Ouyang
Jiming Jiang
C. Robin Buell
Barbara Baker

First Published November 26, 2008

LETTER

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Santhosh Girirajan
Lin Chen
Tina Graves
Tomas Marques-Bonet
Mario Ventura
Catrina Fronick Lucinda Fulton Mariano Rocchi
... [+3 authors] ...,
Robert S. Fulton
Richard K. Wilson
Elaine R. Mardis
Evan E. Eichler

First Published November 24, 2008

LETTER

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

Regina S. Baucom
James C. Estill
Jim Leebens-Mack
Jeffrey L. Bennetzen

First Published November 24, 2008

LETTER

Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans

Hidehito Inagaki
Tamae Ohye
Hiroshi Kogo
Takema Kato
Hasbaira Bolor
Mariko Taniguchi
Tamim H. Shaikh
Beverly S. Emanuel
Hiroki Kurahashi

First Published November 7, 2008

LETTER

Arabidopsis differentiation and stress responses" > Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

Besma Ben Amor
Sonia Wirth
Francisco Merchan
Philippe Laporte
Yves d’Aubenton-Carafa
Judith Hirsch Alexis Maizel Allison Mallory Antoine Lucas
... [+4 authors] ...,
Jean Marc Deragon
Herve Vaucheret
Claude Thermes
Martin Crespi

First Published November 7, 2008

LETTER

Widespread balancing selection and pathogen-driven selection at blood group antigen genes

Matteo Fumagalli
Rachele Cagliani
Uberto Pozzoli
Stefania Riva
Giacomo P. Comi
Giorgia Menozzi
Nereo Bresolin
Manuela Sironi

First Published November 7, 2008

LETTER

Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

Anne-Sophie Van Laere
Wouter Coppieters
Michel Georges

First Published November 3, 2008

LETTER

Oryza sativa" > Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

Xuefeng Zhou
Ramanjulu Sunkar
Hailing Jin
Jian-Kang Zhu
Weixiong Zhang

First Published October 29, 2008

LETTER

Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event

M. Katharine Rudd
RaeLynn M. Endicott
Cynthia Friedman
Megan Walker
Janet M. Young
Kazutoyo Osoegawa
Pieter J. de Jong
Eric D. Green
Barbara J. Trask

First Published October 24, 2008

LETTER

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

Diego Ottaviani
Elliott Lever
Richard Mitter
Tania Jones
Tim Forshew
Rossitza Christova Eleni M. Tomazou Vardhman K. Rakyan Stephen A. Krawetz
... [+4 authors] ...,
Adrian E. Platts
Badmavady Segarane
Stephan Beck
Denise Sheer

First Published October 10, 2008

LETTER

In-depth characterization of the microRNA transcriptome in a leukemia progression model

Florian Kuchenbauer
Ryan D. Morin
Bob Argiropoulos
Oleh I. Petriv
Malachi Griffith
Michael Heuser Eric Yung Jessica Piper Allen Delaney Anna-Liisa Prabhu Yongjun Zhao Helen McDonald Thomas Zeng
... [+8 authors] ...,
Martin Hirst
Carl L. Hansen
Marco A. Marra
R. Keith Humphries

First Published October 10, 2008

LETTER

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Philip M. Kim
Hugo Y.K. Lam
Alexander E. Urban
Jan O. Korbel
Jason Affourtit
Fabian Grubert
... [+1 authors] ...,
Xueying Chen
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published October 8, 2008

LETTER

Alu retrotransposons in the human genome" > Active Alu retrotransposons in the human genome

E. Andrew Bennett
Heiko Keller
Ryan E. Mills
Steffen Schmidt
John V. Moran
Oliver Weichenrieder
Scott E. Devine

First Published October 3, 2008

LETTER

Arabidopsis transposed after the origin of the order Brassicales" > Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

Michael Freeling
Eric Lyons
Brent Pedersen
Maqsudul Alam
Ray Ming
Damon Lisch

First Published October 3, 2008

LETTER

E. coli" > Principles of transcriptional regulation and evolution of the metabolic system in E. coli

Aswin S.N. Seshasayee
Gillian M. Fraser
M. Madan Babu
Nicholas M. Luscombe

First Published October 3, 2008

LETTER

E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites

Alina Rabinovich
Victor X. Jin
Roman Rabinovich
Xiaoqin Xu
Peggy J. Farnham

First Published October 3, 2008

LETTER

Dispensability of mammalian DNA

Cory McLean
Gill Bejerano

First Published October 2, 2008

LETTER

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Yong Cheng
David C. King
Louis C. Dore
Xinmin Zhang
Yuepin Zhou
Ying Zhang Christine Dorman Demesew Abebe Swathi A. Kumar Francesca Chiaromonte
... [+5 authors] ...,
Webb Miller
Roland D. Green
Mitchell J. Weiss
Ross C. Hardison

First Published September 25, 2008

LETTER

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

A. Gordon Robertson
Mikhail Bilenky
Angela Tam
Yongjun Zhao
Thomas Zeng
Nina Thiessen Timothee Cezard Anthony P. Fejes Elizabeth D. Wederell Rebecca Cullum Ghia Euskirchen Martin Krzywinski Inanc Birol Michael Snyder
... [+9 authors] ...,
Pamela A. Hoodless
Martin Hirst
Marco A. Marra
Steven J.M. Jones

First Published September 11, 2008

LETTER

Saccharomyces pastorianus" > Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Barbara Dunn
Gavin Sherlock

First Published September 11, 2008

LETTER

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

Marzena Gajecka
Andrew J. Gentles
Albert Tsai
David Chitayat
Katherine L. Mackay
Caron D. Glotzbach
Michael R. Lieber
Lisa G. Shaffer

First Published September 2, 2008

LETTER

HOX gene clusters" > Nucleosome positioning in human HOX gene clusters

Peter V. Kharchenko
Caroline J. Woo
Michael Y. Tolstorukov
Robert E. Kingston
Peter J. Park

First Published August 22, 2008

LETTER

Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster

Ervin D. Nagy
Jeffrey L. Bennetzen

First Published August 21, 2008

LETTER

Copy number variation at the breakpoint region of isochromosome 17q

Claudia M.B. Carvalho
James R. Lupski

First Published August 19, 2008

LETTER

Escherichia coli" > Transcription of foreign DNA in Escherichia coli

René L. Warren
John D. Freeman
Roger C. Levesque
Duane E. Smailus
Stephane Flibotte
Robert A. Holt

First Published August 13, 2008

LETTER

Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity" > A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

Aileen M. Smith
Maria-Jose Sanchez
George A. Follows
Sarah Kinston
Ian J. Donaldson
Anthony R. Green
Berthold Göttgens

First Published August 7, 2008

LETTER

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

Qian-Hao Zhu
Andrew Spriggs
Louisa Matthew
Longjiang Fan
Gavin Kennedy
Frank Gubler
Chris Helliwell

First Published August 7, 2008

LETTER

Impacts of protein–protein interaction domains on organism and network complexity

Kai Xia
Zheng Fu
Lei Hou
Jing-Dong J. Han

First Published August 7, 2008

LETTER

NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund" > A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund

Anne Caroline Wiik
Claire Wade
Tara Biagi
Ernst-Otto Ropstad
Ellen Bjerkås
Kerstin Lindblad-Toh
Frode Lingaas

First Published August 7, 2008

LETTER

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Albino Bacolla
Jacquelynn E. Larson
Jack R. Collins
Jian Li
Aleksandar Milosavljevic
Peter D. Stenson
David N. Cooper
Robert D. Wells

First Published August 7, 2008

LETTER

Reduced purifying selection prevails over positive selection in human copy number variant evolution

Duc-Quang Nguyen
Caleb Webber
Jayne Hehir-Kwa
Rolph Pfundt
Joris Veltman
Chris P. Ponting

First Published August 7, 2008

LETTER

Evolution of the mammalian transcription factor binding repertoire via transposable elements

Guillaume Bourque
Bernard Leong
Vinsensius B. Vega
Xi Chen
Yen Ling Lee
Kandhadayar G. Srinivasan Joon-Lin Chew
... [+2 authors] ...,
Yijun Ruan
Chia-Lin Wei
Huck Hui Ng
Edison T. Liu

First Published August 5, 2008

LETTER

Global organization of replication time zones of the mouse genome

Shlomit Farkash-Amar
Doron Lipson
Andreas Polten
Alon Goren
Charles Helmstetter
Zohar Yakhini
Itamar Simon

First Published July 30, 2008

LETTER

Relaxation of yeast mitochondrial functions after whole-genome duplication

Huifeng Jiang
Wenjun Guan
David Pinney
Wen Wang
Zhenglong Gu

First Published July 30, 2008

LETTER

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

Simon Moxon
Runchun Jing
Gyorgy Szittya
Frank Schwach
Rachel L. Rusholme Pilcher
Vincent Moulton
Tamas Dalmay

First Published July 24, 2008

LETTER

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

Andrew L. Hufton
Detlef Groth
Martin Vingron
Hans Lehrach
Albert J. Poustka
Georgia Panopoulou

First Published July 14, 2008

LETTER

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes

Jeffrey G. Reid
Ankur K. Nagaraja
Francis C. Lynn
Rafal B. Drabek
Donna M. Muzny
Chad A. Shaw Michelle K. Weiss Arash O. Naghavi Mahjabeen Khan Huifeng Zhu Jayantha Tennakoon Gemunu H. Gunaratne David B. Corry Jonathan Miller Michael T. McManus
... [+10 authors] ...,
Michael S. German
Richard A. Gibbs
Martin M. Matzuk
Preethi H. Gunaratne

First Published July 9, 2008

LETTER

Very small mobile repeated elements in cyanobacterial genomes

Jeff Elhai
Michiko Kato
Sarah Cousins
Peter Lindblad
José Luis Costa

First Published July 3, 2008

LETTER

DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya

Wenli Zhang
Xiue Wang
Qingyi Yu
Ray Ming
Jiming Jiang

First Published July 1, 2008

LETTER

Drosophila melanogaster" > Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

Alisha K. Holloway
David J. Begun
Adam Siepel
Katherine S. Pollard

First Published June 26, 2008

LETTER

Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways" > Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Nicholas R. Thomson
Debra J. Clayton
Daniel Windhorst
Georgios Vernikos
Susanne Davidson
Carol Churcher Michael A. Quail Mark Stevens Michael A. Jones Michael Watson Andy Barron Abigail Layton Derek Pickard Robert A. Kingsley Alex Bignell Louise Clark Barbara Harris Doug Ormond Zahra Abdellah Karen Brooks Inna Cherevach Tracey Chillingworth John Woodward Halina Norberczak Angela Lord Claire Arrowsmith Kay Jagels Sharon Moule Karen Mungall Mandy Sanders Sally Whitehead Jose A. Chabalgoity Duncan Maskell Tom Humphrey
... [+29 authors] ...,
Mark Roberts
Paul A. Barrow
Gordon Dougan
Julian Parkhill

First Published June 26, 2008

LETTER

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

Marcel E. Dinger
Paulo P. Amaral
Tim R. Mercer
Ken C. Pang
Stephen J. Bruce
Brooke B. Gardiner Marjan E. Askarian-Amiri Kelin Ru Giulia Soldà Cas Simons Susan M. Sunkin
... [+6 authors] ...,
Mark L. Crowe
Sean M. Grimmond
Andrew C. Perkins
John S. Mattick

First Published June 18, 2008

LETTER

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

Romain A. Studer
Simon Penel
Laurent Duret
Marc Robinson-Rechavi

First Published June 18, 2008

LETTER

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

Linda Z. Holland
Ricard Albalat
Kaoru Azumi
Èlia Benito-Gutiérrez
Matthew J. Blow
Marianne Bronner-Fraser Frederic Brunet Thomas Butts Simona Candiani Larry J. Dishaw David E.K. Ferrier Jordi Garcia-Fernàndez Jeremy J. Gibson-Brown Carmela Gissi Adam Godzik Finn Hallböök Dan Hirose Kazuyoshi Hosomichi Tetsuro Ikuta Hidetoshi Inoko Masanori Kasahara Jun Kasamatsu Takeshi Kawashima Ayuko Kimura Masaaki Kobayashi Zbynek Kozmik Kaoru Kubokawa Vincent Laudet Gary W. Litman Alice C. McHardy Daniel Meulemans Masaru Nonaka Robert P. Olinski Zeev Pancer Len A. Pennacchio Mario Pestarino Jonathan P. Rast Isidore Rigoutsos Marc Robinson-Rechavi Graeme Roch Hidetoshi Saiga Yasunori Sasakura Masanobu Satake Yutaka Satou Michael Schubert Nancy Sherwood Takashi Shiina Naohito Takatori Javier Tello Pavel Vopalensky Shuichi Wada Anlong Xu Yuzhen Ye Keita Yoshida Fumiko Yoshizaki Jr-Kai Yu Qing Zhang Christian M. Zmasek Pieter J. de Jong Kazutoyo Osoegawa
... [+55 authors] ...,
Nicholas H. Putnam
Daniel S. Rokhsar
Noriyuki Satoh
Peter W.H. Holland

First Published June 18, 2008

LETTER

Insights from the amphioxus genome on the origin of vertebrate neural crest

Jr-Kai Yu
Daniel Meulemans
Sonja J. McKeown
Marianne Bronner-Fraser

First Published June 18, 2008

LETTER

Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity

Shengfeng Huang
Shaochun Yuan
Lei Guo
Yanhong Yu
Jun Li
Tao Wu Tong Liu Manyi Yang Kui Wu Huiling Liu Jin Ge Yingcai Yu Huiqing Huang
... [+8 authors] ...,
Meiling Dong
Cuiling Yu
Shangwu Chen
Anlong Xu

First Published June 18, 2008

LETTER

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Travis N. Mavrich
Ilya P. Ioshikhes
Bryan J. Venters
Cizhong Jiang
Lynn P. Tomsho
Ji Qi
Stephan C. Schuster
Istvan Albert
B. Franklin Pugh

First Published June 12, 2008

LETTER

CpG dinucleotides and the mutation rate of non-CpG DNA

Jean-Claude Walser
Loïc Ponger
Anthony V. Furano

First Published June 11, 2008

LETTER

Drosophila" > On the origin of new genes in Drosophila

Qi Zhou
Guojie Zhang
Yue Zhang
Shiyu Xu
Ruoping Zhao
Zubing Zhan
... [+1 authors] ...,
Xin Li
Yun Ding
Shuang Yang
Wen Wang

First Published June 11, 2008

LETTER

Saccharomyces cerevisiae predicted ORFeome" > Revisiting the Saccharomyces cerevisiae predicted ORFeome

Qian-Ru Li
Anne-Ruxandra Carvunis
Haiyuan Yu
Jing-Dong J. Han
Quan Zhong
Nicolas Simonis Stanley Tam Tong Hao Niels J. Klitgord Denis Dupuy Danny Mou Ilan Wapinski
... [+7 authors] ...,
Aviv Regev
David E. Hill
Michael E. Cusick
Marc Vidal

First Published May 23, 2008

LETTER

A diversity profile of the human skin microbiota

Elizabeth A. Grice
Heidi H. Kong
Gabriel Renaud
Alice C. Young
Gerard G. Bouffard
Robert W. Blakesley
Tyra G. Wolfsberg
Maria L. Turner
Julia A. Segre

First Published May 23, 2008

LETTER

ASIP gene is responsible for white and black sheep" > A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep

Belinda J. Norris
Vicki A. Whan

First Published May 20, 2008

LETTER

Cupriavidus taiwanensis and comparative genomics of rhizobia" > Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Claire Amadou
Géraldine Pascal
Sophie Mangenot
Michelle Glew
Cyril Bontemps
Delphine Capela Sébastien Carrère Stéphane Cruveiller Carole Dossat Aurélie Lajus Marta Marchetti Véréna Poinsot Zoé Rouy Bertrand Servin Maged Saad Chantal Schenowitz
... [+11 authors] ...,
Valérie Barbe
Jacques Batut
Claudine Médigue
Catherine Masson-Boivin

First Published May 19, 2008

LETTER

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation

Zheng Lian
Alexander Karpikov
Jin Lian
Milind C. Mahajan
Stephen Hartman
Mark Gerstein
Michael Snyder
Sherman M. Weissman

First Published May 16, 2008

LETTER

TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing" > Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing

David Monk
Alexandre Wagschal
Philippe Arnaud
Pari-Sima Müller
Layla Parker-Katiraee
Déborah Bourc’his
... [+1 authors] ...,
Stephen W. Scherer
Robert Feil
Philip Stanier
Gudrun E. Moore

First Published May 14, 2008

LETTER

C. elegans reveals a lack of universal sequence-dictated positioning" > A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Anton Valouev
Jeffrey Ichikawa
Thaisan Tonthat
Jeremy Stuart
Swati Ranade
Heather Peckham Kathy Zeng Joel A. Malek Gina Costa
... [+4 authors] ...,
Kevin McKernan
Arend Sidow
Andrew Fire
Steven M. Johnson

First Published May 13, 2008

LETTER

The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast

Gabriel Musso
Michael Costanzo
ManQin Huangfu
Andrew M. Smith
Jadine Paw
Bryan-Joseph San Luis Charles Boone
... [+2 authors] ...,
Guri Giaever
Corey Nislow
Andrew Emili
Zhaolei Zhang

First Published May 7, 2008

LETTER

Transcription induces strand-specific mutations at the 5′ end of human genes

Paz Polak
Peter F. Arndt

First Published May 7, 2008

LETTER

A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation

Isabel Aznarez
Yoseph Barash
Ofer Shai
David He
Julian Zielenski
Lap-Chee Tsui
... [+1 authors] ...,
John Parkinson
Brendan J. Frey
Johanna M. Rommens
Benjamin J. Blencowe

First Published May 2, 2008

LETTER

Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: Implication for retrotransposon-mediated genome evolution

Ei-suke Saito
Vincent W. Keng
Junji Takeda
Kyoji Horie

First Published May 2, 2008

LETTER

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts

Brian P. Chadwick

First Published May 2, 2008

LETTER

Two strategies for gene regulation by promoter nucleosomes

Itay Tirosh
Naama Barkai

First Published April 30, 2008

LETTER

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Stefan Kirsch
Claudia Münch
Zhaoshi Jiang
Ze Cheng
Lin Chen
Christiane Batz
Evan E. Eichler
Werner Schempp

First Published April 29, 2008

LETTER

CFTR locus" > Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Hanna M. Petrykowska
Christopher M. Vockley
Laura Elnitski

First Published April 24, 2008

LETTER

A high-resolution map of nucleosome positioning on a fission yeast centromere

Jun S. Song
Xingkun Liu
X. Shirley Liu
Xiangwei He

First Published April 14, 2008

LETTER

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

Ines Hellmann
Yuan Mang
Zhiping Gu
Peter Li
Francisco M. de la Vega
Andrew G. Clark
Rasmus Nielsen

First Published April 14, 2008

LETTER

Francisella tularensis paradigm" > Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm

Bernard La Scola
Khalid Elkarkouri
Wenjun Li
Tara Wahab
Ghislain Fournous
Jean-Marc Rolain Silpak Biswas Michel Drancourt
... [+3 authors] ...,
Catherine Robert
Stéphane Audic
Sven Löfdahl
Didier Raoult

First Published April 11, 2008

LETTER

Mycobacterium marinum on the evolution of Mycobacterium tuberculosis" > Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Timothy P. Stinear
Torsten Seemann
Paul F. Harrison
Grant A. Jenkin
John K. Davies
Paul D.R. Johnson Zahra Abdellah Claire Arrowsmith Tracey Chillingworth Carol Churcher Kay Clarke Ann Cronin Paul Davis Ian Goodhead Nancy Holroyd Kay Jagels Angela Lord Sharon Moule Karen Mungall Halina Norbertczak Michael A. Quail Ester Rabbinowitsch Danielle Walker Brian White Sally Whitehead Pamela L.C. Small Roland Brosch
... [+22 authors] ...,
Lalita Ramakrishnan
Michael A. Fischbach
Julian Parkhill
Stewart T. Cole

First Published April 10, 2008

LETTER

MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair" > Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

Marijke Bauters
Hilde Van Esch
Michael J. Friez
Odile Boespflug-Tanguy
Martin Zenker
Angela M. Vianna-Morgante Carla Rosenberg Jaakko Ignatius Martine Raynaud Karen Hollanders Karen Govaerts Kris Vandenreijt Florence Niel Pierre Blanc Roger E. Stevenson
... [+10 authors] ...,
Jean-Pierre Fryns
Peter Marynen
Charles E. Schwartz
Guy Froyen

First Published April 2, 2008

LETTER

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

Keiko Akagi
Jingfeng Li
Robert M. Stephens
Natalia Volfovsky
David E. Symer

First Published April 1, 2008

LETTER

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias

Mikael Brandström
Hans Ellegren

First Published March 20, 2008

LETTER

Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring" > De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring

Pontus Larsson
Andrea Hinas
David H. Ardell
Leif A. Kirsebom
Anders Virtanen
Fredrik Söderbom

First Published March 17, 2008

LETTER

A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility

Mark P. Keller
YounJeong Choi
Ping Wang
Dawn Belt Davis
Mary E. Rabaglia
Angie T. Oler Donald S. Stapleton Carmen Argmann Kathy L. Schueler Steve Edwards H. Adam Steinberg Elias Chaibub Neto Robert Kleinhanz Scott Turner Marc K. Hellerstein
... [+10 authors] ...,
Eric E. Schadt
Brian S. Yandell
Christina Kendziorski
Alan D. Attie

First Published March 17, 2008

LETTER

Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

Vitalina M. Komashko
Luis G. Acevedo
Sharon L. Squazzo
Sushma S. Iyengar
Alina Rabinovich
Henriette O’Geen
Roland Green
Peggy J. Farnham

First Published March 17, 2008

LETTER

Myotis lucifugus" > Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

David A. Ray
Cedric Feschotte
Heidi J.T. Pagan
Jeremy D. Smith
Ellen J. Pritham
Peter Arensburger
Peter W. Atkinson
Nancy L. Craig

First Published March 13, 2008

LETTER

Genomic evolution of the placenta using co-option and duplication and divergence

Kirstin Knox
Julie C. Baker

First Published March 13, 2008

LETTER

Escherichia coli indicates a causative role for A-/AT-tracts" > Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

Byung-Kwan Cho
Eric M. Knight
Christian L. Barrett
Bernhard Ø. Palsson

First Published March 13, 2008

LETTER

Quantitative evidence for conserved longevity pathways between divergent eukaryotic species

Erica D. Smith
Mitsuhiro Tsuchiya
Lindsay A. Fox
Nick Dang
Di Hu
Emily O. Kerr Elijah D. Johnston Bie N. Tchao Diana N. Pak K. Linnea Welton
... [+5 authors] ...,
Daniel E.L. Promislow
James H. Thomas
Matt Kaeberlein
Brian K. Kennedy

First Published March 13, 2008

LETTER

Pinus contorta and Oryza sativa" > Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

Ryan D. Morin
Gozde Aksay
Elena Dolgosheina
H. Alexander Ebhardt
Vincent Magrini
Elaine R. Mardis
S. Cenk Sahinalp
Peter J. Unrau

First Published March 6, 2008

LETTER

Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion

Ivon Cuscó
Roser Corominas
Mònica Bayés
Raquel Flores
Núria Rivera-Brugués
Victoria Campuzano
Luis A. Pérez-Jurado

First Published February 21, 2008

LETTER

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

LETTER

Chromodomains direct integration of retrotransposons to heterochromatin

Xiang Gao
Yi Hou
Hirotaka Ebina
Henry L. Levin
Daniel F. Voytas

First Published February 6, 2008

LETTER

An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite from an ancient retrovirus

David Ribet
Francis Harper
Anne Dupressoir
Marie Dewannieux
Gérard Pierron
Thierry Heidmann

First Published February 6, 2008

LETTER

Paramecium tetraurelia: A somatic view of the germline" > Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

Laurent Duret
Jean Cohen
Claire Jubin
Philippe Dessen
Jean-François Goût
Sylvain Mousset Jean-Marc Aury Olivier Jaillon Benjamin Noël Olivier Arnaiz
... [+5 authors] ...,
Mireille Bétermier
Patrick Wincker
Eric Meyer
Linda Sperling

First Published February 6, 2008

LETTER

A survey of allelic imbalance in F1 mice

Catarina D. Campbell
Andrew Kirby
James Nemesh
Mark J. Daly
Joel N. Hirschhorn

First Published February 6, 2008

LETTER

Populus" > Genome structure and emerging evidence of an incipient sex chromosome in Populus

Tongming Yin
Stephen P. DiFazio
Lee E. Gunter
Xinye Zhang
Michell M. Sewell
Scott A. Woolbright Gery J. Allan
... [+2 authors] ...,
Collin T. Kelleher
Carl J. Douglas
Mingxiu Wang
Gerald A. Tuskan

First Published February 6, 2008

LETTER

Legionella pneumophila clone that emerged within a highly diverse species" > Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species

Christel Cazalet
Sophie Jarraud
Yad Ghavi-Helm
Frank Kunst
Philippe Glaser
Jerome Etienne
Carmen Buchrieser

First Published February 6, 2008

LETTER

Evolution of protein domain promiscuity in eukaryotes

Malay Kumar Basu
Liran Carmel
Igor B. Rogozin
Eugene V. Koonin

First Published January 29, 2008

LETTER

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

Eva Darai-Ramqvist
Agneta Sandlund
Stefan Müller
George Klein
Stefan Imreh
Maria Kost-Alimova

First Published January 29, 2008

LETTER

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

Alvaro Rada-Iglesias
Adam Ameur
Philipp Kapranov
Stefan Enroth
Jan Komorowski
Thomas R. Gingeras
Claes Wadelius

First Published January 29, 2008

LETTER

Coevolution of gene families in prokaryotes

Otto X. Cordero
Berend Snel
Paulien Hogeweg

First Published January 29, 2008

LETTER

MicroRNA–target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis

Zhongmin Tian
Andrew S. Greene
Jennifer L. Pietrusz
Isaac R. Matus
Mingyu Liang

First Published January 29, 2008

LETTER

Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota" > The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Tomoyuki Kosaka
Souichiro Kato
Takefumi Shimoyama
Shunichi Ishii
Takashi Abe
Kazuya Watanabe

First Published January 24, 2008

LETTER

Evolutionary dynamics of nematode operons: Easy come, slow go

Wenfeng Qian
Jianzhi Zhang

First Published January 24, 2008

LETTER

Positive selection acting on splicing motifs reflects compensatory evolution

Shengdong Ke
Xiang H.-F. Zhang
Lawrence A. Chasin

First Published January 18, 2008

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