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LETTER

sting-2 Quantitative Trait Locus for Defensive Behavior in the Honey Bee, Apis mellifera" > Genomic Analysis in the sting-2 Quantitative Trait Locus for Defensive Behavior in the Honey Bee, Apis mellifera

Neil F. Lobo
Lucas Q. Ton
Catherine A. Hill
Christine Emore
Jeanne Romero-Severson
Greg J. Hunt
Frank H. Collins

First Published December 1, 2003

ARTICLE

Arabidopsis thaliana Genome?" > Does Recombination Shape the Distribution and Evolution of Tandemly Arrayed Genes (TAGs) in the Arabidopsis thaliana Genome?

Liqing Zhang
Brandon S. Gaut

First Published December 1, 2003

LETTER

A Genome-Wide Survey of Human Pseudogenes

David Torrents
Mikita Suyama
Evgeny Zdobnov
Peer Bork

First Published December 1, 2003

LETTER

Vibrio vulnificus, a Marine Pathogen" > Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen

Chung-Yung Chen
Keh-Ming Wu
Yo-Cheng Chang
Chuan-Hsiung Chang
Hui-Chi Tsai
Tsai-Lien Liao Yen-Ming Liu Hsiang-Ju Chen Arthur Bo-Ting Shen Jian-Chiuan Li Teh-Li Su
... [+6 authors] ...,
Chung-Ping Shao
Chung-Te Lee
Lien-I Hor
Shih-Feng Tsai

First Published December 1, 2003

ARTICLE

Alu-Mediated Recombination Events During Evolution" > Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution

Melanie Babcock
Adam Pavlicek
Elizabeth Spiteri
Catherine D. Kashork
Ilya Ioshikhes
Lisa G. Shaffer
Jerzy Jurka
Bernice E. Morrow

First Published December 1, 2003

ARTICLE

Identification and Characterization of Multi-Species Conserved Sequences

Elliott H. Margulies
Mathieu Blanchette
David Haussler
Eric D. Green

First Published December 1, 2003

LETTER

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome

Zhaolei Zhang
Paul M. Harrison
Yin Liu
Mark Gerstein

First Published December 1, 2003

LETTER

From Gene Networks to Gene Function

Thomas Schlitt
Kimmo Palin
Johan Rung
Sabine Dietmann
Michael Lappe
Esko Ukkonen
Alvis Brazma

First Published December 1, 2003

RESOURCE

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Paul Shannon
Andrew Markiel
Owen Ozier
Nitin S. Baliga
Jonathan T. Wang
Daniel Ramage
Nada Amin
Benno Schwikowski
Trey Ideker

First Published November 3, 2003

Methods

Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation

Johan Elf
Måns Ehrenberg

First Published November 3, 2003

RESOURCE

Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation

Sol Efroni
David Harel
Irun R. Cohen

First Published November 3, 2003

LETTER

Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles" > Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles

Rosa María Gutiérrez-Ríos
David A. Rosenblueth
José Antonio Loza
Araceli M. Huerta
Jeremy D. Glasner
Fred R. Blattner
Julio Collado-Vides

First Published November 3, 2003

COMMENTARY

Systems Biology Is Taking Off

Måns Ehrenberg
Johan Elf
Erik Aurell
Rickard Sandberg
Jesper Tegnér

First Published November 3, 2003

Preface

The Logic of Life

Måns Ehrenberg
Erik Aurell
Johan Elf
Rickard Sandberg
Jesper Tegnér

First Published November 3, 2003

ARTICLE

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

Daniel E. Zak
Gregory E. Gonye
James S. Schwaber
Francis J. Doyle

First Published November 3, 2003

ARTICLE

A Biophysical Approach to Transcription Factor Binding Site Discovery

Marko Djordjevic
Anirvan M. Sengupta
Boris I. Shraiman

First Published November 3, 2003

ARTICLE

Limitations of Quantitative Gene Regulation Models: A Case Study

Philip M. Kim
Bruce Tidor

First Published November 3, 2003

RESOURCE

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

Suraj Peri
J. Daniel Navarro
Ramars Amanchy
Troels Z. Kristiansen
Chandra Kiran Jonnalagadda
Vineeth Surendranath Vidya Niranjan Babylakshmi Muthusamy T.K.B. Gandhi Mads Gronborg Nieves Ibarrola Nandan Deshpande K. Shanker H.N. Shivashankar B.P. Rashmi M.A. Ramya Zhixing Zhao K.N. Chandrika N. Padma H.C. Harsha A.J. Yatish M.P. Kavitha Minal Menezes Dipanwita Roy Choudhury Shubha Suresh Neelanjana Ghosh R. Saravana Sreenath Chandran Subhalakshmi Krishna Mary Joy Sanjeev K. Anand V. Madavan Ansamma Joseph Guang W. Wong William P. Schiemann Stefan N. Constantinescu Lily Huang Roya Khosravi-Far Hanno Steen Muneesh Tewari Saghi Ghaffari Gerard C. Blobe Chi V. Dang Joe G.N. Garcia Jonathan Pevsner Ole N. Jensen Peter Roepstorff Krishna S. Deshpande
... [+43 authors] ...,
Arul M. Chinnaiyan
Ada Hamosh
Aravinda Chakravarti
Akhilesh Pandey

First Published October 2, 2003

Methods

Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database

Christian E.V. Storm
Erik L.L. Sonnhammer

First Published October 2, 2003

Methods

RNAi Microarray Analysis in Cultured Mammalian Cells

Spyro Mousses
Natasha J. Caplen
Robert Cornelison
Don Weaver
Mark Basik
Sampsa Hautaniemi Abdel G. Elkahloun Roberto A. Lotufo
... [+3 authors] ...,
Ashish Choudary
Edward R. Dougherty
Ed Suh
Olli Kallioniemi

First Published October 2, 2003

Methods

High-Throughput Selection of Effective RNAi Probes for Gene Silencing

Rajeev Kumar
Douglas S. Conklin
Vivek Mittal

First Published October 2, 2003

Methods

DNA Enrichment by Allele-Specific Hybridization (DEASH): A Novel Method for Haplotyping and for Detecting Low-Frequency Base Substitutional Variants and Recombinant DNA Molecules

Alec J. Jeffreys
Celia A. May

First Published October 2, 2003

LETTER

Ethnic India: A Genomic View, With Special Reference to Peopling and Structure

Analabha Basu
Namita Mukherjee
Sangita Roy
Sanghamitra Sengupta
Sanat Banerjee
Madan Chakraborty Badal Dey Monami Roy
... [+3 authors] ...,
Bidyut Roy
Nitai P. Bhattacharyya
Susanta Roychoudhury
Partha P. Majumder

First Published October 2, 2003

LETTER

Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population

Yun Freudenberg-Hua
Jan Freudenberg
Nadine Kluck
Sven Cichon
Peter Propping
Markus M. Nöthen

First Published October 2, 2003

LETTER

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

Dmitri M. Krylov
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published October 2, 2003

LETTER

Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

Daniel Dieringer
Christian Schlötterer

First Published October 2, 2003

ARTICLE

Drosophila" > An Evolutionary Analysis of Orphan Genes in Drosophila

Tomislav Domazet-Loso
Diethard Tautz

First Published October 2, 2003

LETTER

MRG, a Neuron-Specific Gene Family Implicated in Nociception" > Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception

Sun Shim Choi
Bruce T. Lahn

First Published October 2, 2003

ARTICLE

Trans-Splicing in Drosophila" > Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila

Mariano Labrador
Victor G. Corces

First Published October 2, 2003

RESOURCE

GANESH: Software for Customized Annotation of Genome Regions

Derek Huntley
Holger Hummerich
Damian Smedley
Sasivimol Kittivoravitkul
Mark McCarthy
Peter Little
Marek Sergot

First Published September 2, 2003

Methods

A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes

Gerli Pielberg
Andy E. Day
Graham S. Plastow
Leif Andersson

First Published September 2, 2003

Methods

PCAP: A Whole-Genome Assembly Program

Xiaoqiu Huang
Jianmin Wang
Srinivas Aluru
Shiaw-Pyng Yang
LaDeana Hillier

First Published September 2, 2003

Methods

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Li Li
Christian J. Stoeckert
David S. Roos

First Published September 2, 2003

LETTER

Global Haplotype Diversity in the Human Insulin Gene Region

John D.H. Stead
Matthew E. Hurles
Alec J. Jeffreys

First Published September 2, 2003

Methods

Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly" > Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly

Shiguo Zhou
Erika Kvikstad
Andrew Kile
Jessica Severin
Dan Forrest
Rod Runnheim Chris Churas Jason W. Hickman Chris Mackenzie
... [+4 authors] ...,
Madhusudan Choudhary
Timothy Donohue
Samuel Kaplan
David C. Schwartz

First Published September 2, 2003

Methods

PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

Paul D. Thomas
Michael J. Campbell
Anish Kejariwal
Huaiyu Mi
Brian Karlak
Robin Daverman
Karen Diemer
Anushya Muruganujan
Apurva Narechania

First Published September 2, 2003

LETTER

Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations

Joseph H. Nadeau
Lindsay C. Burrage
Joe Restivo
Yoh-Han Pao
Gary Churchill
Brian D. Hoit

First Published September 2, 2003

LETTER

Drosophila melanogaster" > Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster

Huaiyu Mi
Jody Vandergriff
Michael Campbell
Apurva Narechania
William Majoros
Suzanna Lewis
Paul D. Thomas
Michael Ashburner

First Published September 2, 2003

LETTER

Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms

Xin Lu
Tianhua Niu
Jun S. Liu

First Published September 2, 2003

LETTER

Asymmetric Sequence Divergence of Duplicate Genes

Gavin C. Conant
Andreas Wagner

First Published September 2, 2003

LETTER

Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes

Luba Katz
Christopher B. Burge

First Published September 2, 2003

LETTER

4" > Conserved Noncoding Sequences in the Grasses4

Dan Choffnes Inada
Ali Bashir
Chunghau Lee
Brian C. Thomas
Cynthia Ko
Stephen A. Goff
Michael Freeling

First Published September 2, 2003

ARTICLE

ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus" > Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus

Ningxin Zhang
Annette L. Harrex
Barbara R. Holland
Lauren E. Fenton
Richard D. Cannon
Jan Schmid

First Published September 2, 2003

LETTER

Yersinia pestis and Yersinia pseudotuberculosis" > Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Stewart J. Hinchliffe
Karen E. Isherwood
Richard A. Stabler
Michael B. Prentice
Alexander Rakin
Richard A. Nichols
... [+1 authors] ...,
Petra C.F. Oyston
Jason Hinds
Richard W. Titball
Brendan W. Wren

First Published September 2, 2003

REVIEW

The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

Jef D. Boeke

First Published September 2, 2003

ARTICLE

Schizosaccharomyces pombe" > Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe

Nathan J. Bowen
I. King Jordan
Jonathan A. Epstein
Valerie Wood
Henry L. Levin

First Published September 2, 2003

ERRATUM

Correction for Volume 13, p. 1111

First Published August 5, 2003

Methods

Automated Detection of Informative Combined Effects in Genetic Association Studies of Complex Traits

Nadia Tahri-Daizadeh
David-Alexandre Tregouet
Viviane Nicaud
Nicolas Manuel
François Cambien
Laurence Tiret

First Published August 5, 2003

Methods

Expanding the Use of Zymography by the Chemical Linkage of Small, Defined Substrates to the Gel Matrix

Vladimir R. Kaberdin
Kenneth J. McDowall

First Published August 5, 2003

RESOURCE

A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence

Denis M. Larkin
Annelie Everts-van der Wind
Mark Rebeiz
Peter A. Schweitzer
Sharon Bachman
Cheryl Green Chris L. Wright Edhilvia J. Campos Leslie D. Benson Jennifer Edwards Lei Liu
... [+6 authors] ...,
Kazutoyo Osoegawa
James E. Womack
Pieter J. de Jong
Harris A. Lewin

First Published August 5, 2003

Methods

Estimating the Repeat Structure and Length of DNA Sequences Using ℓ-Tuples

Xiaoman Li
Michael S. Waterman

First Published August 5, 2003

Methods

RDS/Peripherin Gene" > Detection and Assignment of Mutations and Minihaplotypes in Human DNA Using Peptide Mass Signature Genotyping (PMSG): Application to the Human RDS/Peripherin Gene

Cheryl A. Telmer
Adam R. Retchless
Ashley D. Kinsey
Yvette Conley
Brian Rigatti
Michael B. Gorin
Jonathan W. Jarvik

First Published August 5, 2003

LETTER

Arabidopsis thaliana" > Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thaliana

Stephen I. Wright
Newton Agrawal
Thomas E. Bureau

First Published August 5, 2003

LETTER

Allelic Variation in Gene Expression Is Common in the Human Genome

H. Shuen Lo
Zhining Wang
Ying Hu
Howard H. Yang
Sheryl Gere
Kenneth H. Buetow
Maxwell P. Lee

First Published August 5, 2003

LETTER

Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes

Edward Yang
Erik van Nimwegen
Mihaela Zavolan
Nikolaus Rajewsky
Mark Schroeder
Marcelo Magnasco
James E. Darnell

First Published August 5, 2003

LETTER

A Population Threshold for Functional Polymorphisms

Gane Ka-Shu Wong
Zhiyong Yang
Douglas A. Passey
Miho Kibukawa
Marcia Paddock
Chun-Rong Liu
Lars Bolund
Jun Yu

First Published August 5, 2003

LETTER

Sinorhizobium meliloti: Novel Genomic Architectures" > Natural Genomic Design in Sinorhizobium meliloti: Novel Genomic Architectures

Xianwu Guo
Margarita Flores
Patrick Mavingui
Sara Isabel Fuentes
Georgina Hernández
Guillermo Dávila
Rafael Palacios

First Published August 5, 2003

LETTER

C. elegans" > A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans

Art B. Owen
Josh Stuart
Kathy Mach
Anne M. Villeneuve
Stuart Kim

First Published August 5, 2003

ARTICLE

Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome" > Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome

Didier Raoult
Hiroyuki Ogata
Stéphane Audic
Catherine Robert
Karsten Suhre
Michel Drancourt
Jean-Michel Claverie

First Published August 5, 2003

LETTER

Comparative DNA Sequence Analysis of Wheat and Rice Genomes

Mark E. Sorrells
Mauricio La Rota
Catherine E. Bermudez-Kandianis
Robert A. Greene
Ramesh Kantety
Jesse D. Munkvold Miftahudin Ahmed Mahmoud Xuefeng Ma Perry J. Gustafson Lili L. Qi Benjamin Echalier Bikram S. Gill David E. Matthews Gerard R. Lazo Shiaoman Chao Olin D. Anderson Hugh Edwards Anna M. Linkiewicz Jorge Dubcovsky Eduard D. Akhunov Jan Dvorak Deshui Zhang Henry T. Nguyen Junhua Peng Nora L.V. Lapitan Jose L. Gonzalez-Hernandez James A. Anderson Khwaja Hossain Venu Kalavacharla Shahryar F. Kianian Dong-Woog Choi Timothy J. Close Muharrem Dilbirligi Kulvinder S. Gill
... [+30 authors] ...,
Camille Steber
Mary K. Walker-Simmons
Patrick E. McGuire
Calvin O. Qualset

First Published August 5, 2003

Methods

E. coli Selection of Human Genes Encoding Secreted and Membrane Proteins Based on cDNA Fusions to a Leaderless β-Lactamase Reporter" > E. coli Selection of Human Genes Encoding Secreted and Membrane Proteins Based on cDNA Fusions to a Leaderless β-Lactamase Reporter

Ruoying Tan
Xin Jiang
Alan Jackson
Pei Jin
Junming Yang
Ernestine Lee
Brendan Duggan
Laura L. Stuve
Glenn K. Fu

First Published July 17, 2003

LETTER

The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals

William J. Murphy
Lutz Frönicke
Stephen J. O'Brien
Roscoe Stanyon

First Published July 17, 2003

LETTER

Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes

Sven Nelander
Petter Mostad
Per Lindahl

First Published July 17, 2003

Methods

Gene Prediction by Spectral Rotation Measure: A New Method for Identifying Protein-Coding Regions

Daniel Kotlar
Yizhar Lavner

First Published July 17, 2003

Methods

Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis

Shawn Hoon
Kiran Kumar Ratnapu
Jer-ming Chia
Balamurugan Kumarasamy
Xiao Juguang
Michele Clamp
... [+1 authors] ...,
Arne Stabenau
Simon Potter
Laura Clarke
Elia Stupka

First Published July 17, 2003

ARTICLE

Cryptosporidium parvum" > Integrated Mapping, Chromosomal Sequencing and Sequence Analysis of Cryptosporidium parvum

Alan T. Bankier
Helen F. Spriggs
Berthold Fartmann
Bernard A. Konfortov
Martin Madera
Christine Vogel
Sarah A. Teichmann
Al Ivens
Paul H. Dear

First Published July 17, 2003

LETTER

Drosophila melanogaster Genome" > Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome

Emmanuelle Lerat
Carène Rizzon
Christian Biémont

First Published July 17, 2003

Methods

Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units

Vladimir B. Bajic
Seng Hong Seah

First Published July 17, 2003

LETTER

Phytophthora" > EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora

Trudy A. Torto
Shuang Li
Allison Styer
Edgar Huitema
Antonino Testa
Neil A.R. Gow
Pieter van West
Sophien Kamoun

First Published July 1, 2003

LETTER

Identification of a Large Novel Imprinted Gene Cluster on Mouse Proximal Chromosome 6

Ryuichi Ono
Hirosuke Shiura
Hiroyuki Aburatani
Takashi Kohda
Tomoko Kaneko-Ishino
Fumitoshi Ishino

First Published July 1, 2003

Methods

Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring

Qinghong Yang
Alla Lishanski
Wendy Yang
Sandra Hatcher
Henrietta Seet
Jeffrey P. Gregg

First Published July 1, 2003

Methods

Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data

Philip M. Kim
Bruce Tidor

First Published July 1, 2003

ARTICLE

An Evolutionarily Structured Universe of Protein Architecture

Gustavo Caetano-Anollés
Derek Caetano-Anollés

First Published July 1, 2003

LETTER

Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse

Rotem Sorek
Gil Ast

First Published July 1, 2003

LETTER

Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons" > Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons

Olivier Jaillon
Carole Dossat
Ralph Eckenberg
Karin Eiglmeier
Béatrice Segurens
Jean-Marc Aury Charles W. Roth
... [+2 authors] ...,
Claude Scarpelli
Paul T. Brey
Jean Weissenbach
Patrick Wincker

First Published July 1, 2003

LETTER

Quantitative Assessment of Transcriptome Differences Between Brain Territories

Michel de Chaldée
Marie-Claude Gaillard
Nicolas Bizat
Jean-Marie Buhler
Olivier Manzoni
Joël Bockaert
Philippe Hantraye
Emmanuel Brouillet
Jean-Marc Elalouf

First Published July 1, 2003

LETTER

Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes

Kateryna D. Makova
Wen-Hsiung Li

First Published July 1, 2003

LETTER

Mitochondrial Genome Variation and Evolutionary History of Australian and New Guinean Aborigines

Max Ingman
Ulf Gyllensten

First Published July 1, 2003

LETTER

Comparative Analysis of Gene-Expression Patterns in Human and African Great Ape Cultured Fibroblasts

Mazen W. Karaman
Marlys L. Houck
Leona G. Chemnick
Shailender Nagpal
Daniel Chawannakul
Dominick Sudano
... [+1 authors] ...,
Brian L. Pike
Vincent V. Ho
Oliver A. Ryder
Joseph G. Hacia

First Published July 1, 2003

LETTER

The Balance of Driving Forces During Genome Evolution in Prokaryotes

Victor Kunin
Christos A. Ouzounis

First Published July 1, 2003

ARTICLE

Corynebacterium efficiens" > Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability of Corynebacterium efficiens

Yousuke Nishio
Yoji Nakamura
Yutaka Kawarabayasi
Yoshihiro Usuda
Eiichiro Kimura
Shinichi Sugimoto Kazuhiko Matsui
... [+2 authors] ...,
Akihiko Yamagishi
Hisashi Kikuchi
Kazuho Ikeo
Takashi Gojobori

First Published July 1, 2003

Methods

Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis

Shreeram Akilesh
Daniel J. Shaffer
Derry Roopenian

First Published July 1, 2003

Methods

Identification of Novel ErbB3-Interacting Factors Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System

Safia Thaminy
Daniel Auerbach
Anthony Arnoldo
Igor Stagljar

First Published July 1, 2003

Methods

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

Huseyin Sumer
Jeffrey M. Craig
Mandy Sibson
K.H. Andy Choo

First Published July 1, 2003

LETTER

Alu Insertion Polymorphisms" > Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms

W. Scott Watkins
Alan R. Rogers
Christopher T. Ostler
Steve Wooding
Michael J. Bamshad
Anna-Marie E. Brassington Marion L. Carroll Son V. Nguyen Jerilyn A. Walker B.V. Ravi Prasad
... [+5 authors] ...,
P. Govinda Reddy
Pradipta K. Das
Mark A. Batzer
Lynn B. Jorde

First Published June 12, 2003

Methods

Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay

Shirin Khambata-Ford
Yueyi Liu
Christopher Gleason
Mark Dickson
Russ B. Altman
Serafim Batzoglou
Richard M. Myers

First Published June 12, 2003

Methods

Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis

Andrea Barczak
Madeleine Willkom Rodriguez
Kristina Hanspers
Laura L. Koth
Yu Chuan Tai
Benjamin M. Bolstad
Terence P. Speed
David J. Erle

First Published June 12, 2003

ARTICLE

Archaea Methanogenium frigidum and Methanococcoides burtonii" > Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

Neil F.W. Saunders
Torsten Thomas
Paul M.G. Curmi
John S. Mattick
Elizabeth Kuczek
Rob Slade John Davis Peter D. Franzmann David Boone Karl Rusterholtz Robert Feldman Chris Gates Shellie Bench Kevin Sowers Kristen Kadner Andrea Aerts Paramvir Dehal Chris Detter Tijana Glavina Susan Lucas Paul Richardson
... [+16 authors] ...,
Frank Larimer
Loren Hauser
Miriam Land
Ricardo Cavicchioli

First Published June 12, 2003

Methods

Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins

Nobuaki Toyoda
Shigenori Nagai
Yuya Terashima
Kazushi Motomura
Makoto Haino
Shin-ichi Hashimoto
Hajime Takizawa
Kouji Matsushima

First Published June 12, 2003

LETTER

Treponema pallidum Open Reading Frames for Protein Expression and Antigen Discovery" > Systematic Cloning of Treponema pallidum Open Reading Frames for Protein Expression and Antigen Discovery

Matthew McKevitt
Krupa Patel
David Smajs
Michael Marsh
Melanie McLoughlin
Steven J. Norris
George M. Weinstock
Timothy Palzkill

First Published June 12, 2003

LETTER

Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci

Xiaosong Wang
Isabelle Le Roy
Edwige Nicodeme
Renhua Li
Richard Wagner
Christina Petros Gary A. Churchill Stephen Harris
... [+3 authors] ...,
Ariel Darvasi
Jorge Kirilovsky
Pierre L. Roubertoux
Beverly Paigen

First Published June 12, 2003

LETTER

Tetraodon nigroviridis" > An Active Non-LTR Retrotransposon With Tandem Structure in the Compact Genome of the Pufferfish Tetraodon nigroviridis

Laurence Bouneau
Cécile Fischer
Catherine Ozouf-Costaz
Alexander Froschauer
Olivier Jaillon
Jean-Pierre Coutanceau
... [+1 authors] ...,
Cornelia Körting
Jean Weissenbach
Alain Bernot
Jean-Nicolas Volff

First Published June 12, 2003

Abstracts

Analysis of Gene Expression Profiles Based on Clustering

Yoichi Takenaka
Hideo Matsuda

First Published June 2, 2003

RESOURCE

Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS

Takeshi Nagashima
Diego G. Silva
Nikolai Petrovsky
Luis A. Socha
Harukazu Suzuki
Rintaro Saito
... [+1 authors] ...,
Takeya Kasukawa
Igor V. Kurochkin
Akihiko Konagaya
Christian Schönbach

First Published June 2, 2003

LETTER

Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome

Harukata Miki
Mitsutoshi Setou
Nobutaka Hirokawa

First Published June 2, 2003

RESOURCE

Connecting Sequence and Biology in the Laboratory Mouse

Richard M. Baldarelli
David P. Hill
Judith A. Blake
Jun Adachi
Masaaki Furuno
Dirck Bradt Lori E. Corbani Sharon Cousins Kenneth S. Frazer Dong Qi Longlong Yang Sridhar Ramachandran Deborah Reed Yunxia Zhu Takeya Kasukawa Martin Ringwald Benjamin L. King Lois J. Maltais Louise M. McKenzie Lynn M. Schriml Donna Maglott Deanna M. Church Kim Pruitt
... [+18 authors] ...,
Janan T. Eppig
Joel E. Richardson
Jim A. Kadin
Carol J. Bult

First Published June 2, 2003

LETTER

Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans

John C. Reed
Kutbuddin Doctor
Ana Rojas
Juan M. Zapata
Christian Stehlik
Loredana Fiorentino Jason Damiano Wilfried Roth Shu-ichi Matsuzawa Ruchi Newman Shinichi Takayama
... [+6 authors] ...,
Hiroyuki Marusawa
Famming Xu
Guy Salvesen
Adam Godzik

First Published June 2, 2003

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Piero Carninci
Kazunori Waki
Toshiyuki Shiraki
Hideaki Konno
Kazuhiro Shibata
Masayoshi Itoh Katsunori Aizawa Takahiro Arakawa Yoshiyuki Ishii Daisuke Sasaki Hidemasa Bono Shinji Kondo Yuichi Sugahara Rintaro Saito Naoki Osato Shiro Fukuda Kenjiro Sato Akira Watahiki Tomoko Hirozane-Kishikawa Mari Nakamura Yuko Shibata Ayako Yasunishi Noriko Kikuchi Atsushi Yoshiki Moriaki Kusakabe Stefano Gustincich Kirk Beisel William Pavan Vassilis Aidinis Akira Nakagawara William A. Held Hiroo Iwata Tomohiro Kono Hiromitsu Nakauchi Paul Lyons Christine Wells David A. Hume Michela Fagiolini Takao K. Hensch Michelle Brinkmeier Sally Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 2003

LETTER

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

Hidenori Kiyosawa
Itaru Yamanaka
Naoki Osato
Shinji Kondo
Yoshihide Hayashizaki

First Published June 2, 2003

Abstracts

Exon Structure Analysis, Ortholog Identification, and SNP Candidate Screening by Mapping Mouse RIKEN Sequences to Multiple Genome Assemblies

Serge Batalov
Colin F. Fletcher

First Published June 2, 2003

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