Current Protocols in Bioinformatics

Editors & Contributors

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EDITORIAL BOARD

Andreas D. Baxevanis (Editor-in-Chief)
Bethesda, Maryland

Gregory A. Petsko
Brandeis University
Waltham, Massachusetts

Lincoln D. Stein
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York

Gary D. Stormo
Washington University School of Medicine
St. Louis, Missouri

GUEST EDITOR

John R. Yates III
The Scripps Research Institute
La Jolla, California

ADVISORY EDITOR

Daniel B. Davison
Morrisville, Pennsylvania

PAST EDITOR

Roderic D. M. Page
University of Glasgow
Glasgow, Scotland

CONTRIBUTORS

Paul D. Adams
Lawrence Berkeley Laboratory
Berkeley, California

Kiyoko F. Aoki
Bioinformatics Center
Kyoto University
Kyoto, Japan

Rolf Apweiler
The EMBL Outstation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge

Isaiah T. Arkin
The Hebrew University
Jerusalem, Israel

Patricia Babbitt
University of California, San Francisco
San Francisco, California

Timothy L. Bailey
University of Queensland
Brisbane, Australia

Alex Bateman
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambs, United Kingdom

Andreas D. Baxevanis
Bethesda, Maryland

Ronald Beavis
Beavis Informatics Ltd.
Winnipeg, Manitoba
Canada

Tanya Z. Berardini
Carnegie Institution
Stanford, California

Helen M. Berman
Rutgers University
Piscataway, New Jersey

John Besemer
School of Biology
Georgia Institute of Technology
Atlanta, Georgia

Judith A. Blake
The Jackson Laboratory
Bar Harbor, Maine

Enrique Blanco
Universitat Pompeu Fabra
Barcelona, Spain

Wolfgang F. Bluhm
University of California, San Diego
La Jolla, California

Mark Borodovsky
School of Biology and School of Biomedical Engineering
Georgia Institute of Technology
Atlanta, Georgia

Christopher M.L.S. Bouton
LION Bioscience Research
Cambridge, Massachusetts

Michael R. Brent
Washington University
St. Louis, Missouri

Susan K. Bromberg
Human and Molecular Genetics Center
Medical College of Wisconsin
Milwaukee, Wisconsin

Shoshana Brown
University of California, San Francisco
San Francisco, California

Richard Burhans
The Pennsylvania State University
University Park, Pennsylvania

Kyle Burkhardt
Rutgers University
Piscataway, New Jersey

Duccio Cavalieri
Bauer Center for Genomics Research
Harvard University
Cambridge, Massachusetts

Gianni Cesareni
University of Rome Tor Vergata
Rome, Italy

Nansheng Chen
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York

Yidong Chen
National Human Genome Research Institute
National Institutes of Health
Bethesda, Maryland

Nadia A. Chuzhanova
Cardiff University
Cardiff, United Kingdom

Christopher M. Colangelo
Yale University
New Haven, Connecticut

Andrew Conway
Silicon Genetics
Redwood City, California

David N. Cooper
Cardiff University
Cardiff, United Kingdom

Richard G.H. Cotton
Genomic Disorders Research Centre
St. Vincent’s Hospital Melbourne
Fitzroy, Australia and
The University of Melbourne
Melbourne, Australia

Kam D. Dahlquist
Vassar College
Poughkeepsie, New York

Daniel B. Davison
Bristol-Myers Squibb Pharmaceutical Research Institute
Hopewell, New Jersey

Ramana V. Davuluri
Ohio State University
Columbus, Ohio

David W. Deerfield II
Pittsburgh Supercomputing Center
Pittsburgh, Pennsylvania

Arthur L. Delcher
The Institute for Genomic Research
Rockville, Maryland and
Computer Science Department
Loyola College in Maryland
Baltimore, Maryland

Charles DeLisi
Boston University
Boston, Massachusetts

Richard Desper
Department of Biology
University College
London, United Kingdom

Dimitris Dimitropoulos
European Bioinformatics Institute
Hinxton, Cambridgeshire
United Kingdom

Shuchismita Dutta
Rutgers University
Piscataway, New Jersey

Bjarte Dysvik
University of Bergen MolMine AS
Bergen, Norway

Laura Elnitski
The Pennsylvania State University
University Park, Pennsylvania

David Emmert
Harvard University
Cambridge, Massachusetts

Jimmy K. Eng
Fred Hutchinson Cancer Research Center
Seattle, Washington

David Eramian
University of California at San Francisco
San Francisco, California

Narayanan Eswar
University of California at San Francisco
San Francisco, California

David Fenyo
GE Healthcare
Piscataway, New Jersey

Jacquelyn S. Fetrow
Wake Forest University
Winston-Salem, North Carolina

Robert Finn
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambs, United Kingdom

Andras Fiser
Department of Biochemistry and Seaver Foundation Center for Bioinformatics
Albert Einstein College of Medicine
Bronx, New York

Olivier Gascuel
Equipe “Méthodes et Algorithmes pour la Bioinformatique”
LRMM-CNRS
Montpellier, France

Toby. J. Gibson
European Molecular Biology Laboratory
Heidelberg, Germany

Don Gilbert
Indiana University
Bloomington, Indiana

Shawn M. Gomez
Unité de Biochimie et Biologie Moléculaire des Insectes (BBMI)
Institut Pasteur
Paris, France

Matthew Goode
Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution
University of Auckland
Auckland, New Zealand

David S. Goodsell
The Scripps Research Institute
La Jolla, California

David Gordon
Howard Hughes Medical Institute
University of Washington
Seattle, Washington

David F. Green
Massachusetts Institute of Technology
Cambridge, Massachusetts

Elizabeth A. Greene
Fred Hutchinson Cancer Research Center
Seattle, Washington

Anoop Grewal
Silicon Genetics
Redwood City, California

Sam Griffiths-Jones
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
United Kingdom

Paul Grosu
Bauer Center for Genomics Research
Harvard University
Cambridge, Massachusetts

Roderic Guigó
Universitat Pompeu Fabra
Barcelona, Spain

Erol E. Gulcicek
Yale University
New Haven, Connecticut

Kannan Gunasekaran
Laboratory of Experimental and Computational Biology
National Cancer Institute
Frederick, Maryland

David K. Han
University of Connecticut Health Center
Farmington, Connecticut

Ross Hardison
The Pennsylvania State University
University Park, Pennsylvania

Midori A. Harris
Wellcome Trust Genome Campus
Cambridge, United Kingdom

Nomi Harris
University of California
Berkeley, California

Matthew Healy
Bristol-Myers Squibb Pharmaceutical Research Institute
Wallingford, Connecticut

Manuela Helmer-Citterich
University of Rome Tor Vergata
Rome, Italy

Jorja G. Henikoff
Fred Hutchinson Cancer Research Center
Seattle, Washington

Steven Henikoff
Fred Hutchinson Cancer Research Center
Seattle, Washington

Kim Henrick
European Bioinformatics Institute
Hinxton, Cambridgeshire
United Kingdom

Jaap Heringa
Integrative Bioinformatics Institute (IBIVU)
Free University
Amsterdam, The Netherlands

Des G. Higgins
University College
Cork, Ireland

Ivo L. Hofacker
University of Vienna
Vienna, Austria

Christopher W.V. Hogue
The Blueprint Initiative
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
Toronto, Ontario, Canada

Liisa Holm
Institute of Biotechnology
University of Helsinki
Helsinki, Finland

Ourania Horaitis
Genomic Disorders Research Centre
St. Vincent’s Hospital Melbourne
Fitzroy, Australia

Ping Hu
Washington University
St. Louis, Missouri

Zhenjun Hu
Boston University
Boston, Massachusetts

Xiaoqiu Huang
Iowa State University
Ames, Iowa

Daniel H. Huson
Center for Bioinformatics Tübingen
Tübingen University
Tübingen, Germany

Doug Hyatt
Oak Ridge National Laboratory
Oak Ridge, Tennessee

John Ionides
European Bioinformatics Institute
Hinxton, Cambridgeshire
United Kingdom

Nikolai Ivanov
School of Biology
Georgia Institute of Technology
Atlanta, Georgia

Mitsuo Iwadate
Kitasato University
Tokyo, Japan

Vishwanath R. Iyer
University of Texas at Austin
Austin, Texas

D. Curtis Jamison
George Mason University
Manassas, Virginia

Bino John
Laboratory of Molecular Biophysics
The Rockefeller University
New York, New York

Inge Jonassen
University of Bergen MolMine AS
Bergen, Norway

Sakari Kääriäinen
Institute of Biotechnology
University of Helsinki
Helsinki, Finland

Minoru Kanehisa
Bioinformatics Center
Kyoto University
Kyoto, Japan

Donna Karolchik
University of California
Santa Cruz, California

Deepak Kaushal
St. Jude Children’s Research Hospital
Memphis, Tennessee

W. James Kent
University of California
Santa Cruz, California

Patrick J. Killion
University of Texas at Austin
Austin, Texas

Jens Kleinjung
Integrative Bioinformatics Institute (IBIVU)
Free University
Amsterdam, The Netherlands

Uzi Kochva
The Hebrew University
Jerusalem, Israel

Nandini Krishnamurthy
University of California
Berkeley, California

Alexander Kurosky
University of Texas Medical Branch
Galveston, Texas

Istvan Ladunga
Celera Genomics
Foster City, California and
Research Group for Evolutionary Genetics
Hungarian Academy of Sciences
Eötvös University
Budapest, Hungary

Peter Lambert
Silicon Genetics
Redwood City, California

Charles E. Lawrence
Brown University
Providence, Rhode Island

Yuandan Lee
The Institute for Genomic Research
Rockville, Maryland

Shonda A. Leonard
Rockville, Maryland

Hadas Leonov
The Hebrew University
Jerusalem, Israel

Timothy G. Littlejohn
IBM Life Sciences
St. Leonards, NSW, Australia

Alex Lomsadze
School of Biology
Georgia Institute of Technology
Atlanta, Georgia

Deborah H. Lundgren
University of Connecticut Health Center
Farmington, Connecticut

Aaron J. Mackey
University of Virginia
Charlottesville, Virginia

M.S. Madhusudhan
University of California at San Francisco
San Francisco, California

Marc A. Marti-Renom
University of California at San Francisco
San Francisco, California

David H. Mathews
University of Rochester Medical Center
Rochester, New York

Lee Ann McCue
Center for Bioinformatics
The Wadsworth Center
New York State Department of Health
Albany, New York

Walter McMurray
Yale University
New Haven, Connecticut

Joseph Mellor
Boston University
Boston, Massachusetts

Paul S. Meltzer
National Human Genome Research Institute
National Institutes of Health
Bethesda, Maryland

Webb Miller
The Pennsylvania State University
University Park, Pennsylvania

Ryan Mills
School of Biology
Georgia Institute of Technology
Atlanta, Georgia

Nebojsa Mirkovic
Laboratory of Molecular Biophysics
The Rockefeller University
New York, New York

Sima Misra
University of California
Berkeley, California

Nicola J. Mulder
The EMBL Outstation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge

Juliane Murphy
National Human Genome Research Institute
National Institutes of Health
Bethesda, Maryland

Clayton W. Naeve
St. Jude Children’s Research Hospital
Memphis, Tennessee

Vijay Narayanasamy
Medical College of Wisconsin
Milwaukee, Wisconsin

Hugh B. Nicholas Jr.
Pittsburgh Supercomputing Center
Pittsburgh, Pennsylvania

Cedric Notredame
Swiss Institute of Bioinformatics
Epalinges, Switzerland and
Information Genetique et Structurale, CNRS
Marseilles, France

Ruth Nussinov
Laboratory of Experimental and Computational Biology
SAIC-Frederick
Frederick, Maryland and
Tel Aviv University
Tel Aviv, Israel

Mary Jo Ondrechen
Northeastern University
Boston, Massachusetts

Assaf Oron
Tel Aviv University
Tel Aviv, Israel

Roderic D.M. Page
University of Glasgow
Glasgow, Scotland

Genís Parra
Universitat Pompeu Fabra
Barcelona, Spain

Giulio Pavesi
University of Milan
Milan, Italy

William Pearson
University of Virginia School of Medicine
Charlottesville, Virginia

Robert M. Peitzsch
Pfizer Global Research and Development
Groton, Connecticut

Mihaela Pertea
The Institute for Genomic Research
Rockville, Maryland

Graziano Pesole
University of Milan
Milan, Italy

Gregory A. Petsko
Brandeis University
Waltham, Massachusetts

Jonathan Pevsner
Kennedy Krieger Institute and
Johns Hopkins University School of Medicine
Baltimore, Maryland

Adam M. Phillippy
The Institute for Genomic Research
Rockville, Maryland

Ursula Pieper
University of California at San Francisco
San Francisco, California

Shmuel Pietrokovski
Weizmann Institute of Science
Rehovot, Israel

Dariusz Plewczynski
Interdisciplinary Centre for Mathematical and Computation Modeling
University of Warsaw
Warsaw, Poland

David Posada
Universidad de Vigo
Vigo, Spain

John Quackenbush
The Institute for Genomic Research
Rockville, Maryland

Leonore Reiser
The Arabidopsis Information Resource
Carnegie Institution
Stanford, California

David Remsen
BioCurrents Research Center
Marine Biological Laboratory
Woods Hole, Massachusetts

Seung Yon Rhee
Carnegie Institution
Stanford, California

Cathy Riemer
The Pennsylvania State University
University Park, Pennsylvania

Richard J. Roberts
New England Biolabs
Beverly, Massachusetts

Allen G. Rodrigo
Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution
University of Auckland
Auckland, New Zealand

Alexander J. Ropelewski
Pittsburgh Supercomputing Center
Pittsburgh, Pennsylvania

Ravi Sachidanandam
Sachidanandam Lab
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York

Andrej Sali
University of California at San Francisco
San Francisco, California

Steven L. Salzberg
The Institute for Genomic Research
Rockville, Maryland

Heiko A. Schmidt
Max-Planck-Institut fur Molekulare Genetik
Berlin, Germany

Jonathan Schug
Center for Bioinformatics
University of Pennsylvania
Philadelphia, Pennsylvania

Scott Schwartz
The Pennsylvania State University
University Park, Pennsylvania

Erich M. Schwarz
California Institute of Technology
Pasadena, California

Manesh Shah
Oak Ridge National Laboratory
Oak Ridge, Tennessee

David Shaw
MGI User Support
The Jackson Laboratory
Bar Harbor, Maine

Min-yi Shen
University of California at San Francisco
San Francisco, California

Victor Simossis
Integrative Bioinformatics Institute (IBIVU)
Free University
Amsterdam, The Netherlands

Kimmen Sjölander
University of California
Berkeley, California

Jennifer S. Smith
Human and Molecular Genetics Center
Medical College of Wisconsin
Milwaukee, Wisconsin

Peter J. S. Smith
BioCurrents Research Center
Marine Biological Laboratory
Woods Hole, Massachusetts

Heidi Spratt
University of Texas Medical Branch
Galveston, Texas

Lincoln D. Stein
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York

Peter D. Stenson
Cardiff University
Cardiff, United Kingdom

Paul W. Sternberg
Howard Hughes Medical Institute
California Institute of Technology
Pasadena, California

Jordan Stockton
Silicon Genetics
Redwood City, California

Kathryn Stone
Yale University
New Haven, Connecticut

Gary D. Stormo
Washington University School of Medicine
St. Louis, Missouri

Ashley Stuart
Laboratory of Molecular Biophysics
The Rockefeller University
New York, New York

Karsten Suhre
Information Genetique et Structurale, CNRS
Marseilles, France

David Swofford
Florida State University
Tallahassee, Florida

Nick Taylor
Fred Hutchinson Cancer Research Center
Seattle, Washington

Julie D. Thompson
Institut de Génétique et de Biologie Moléculaire et Cellulaire
Illkirch Cedex, France

Steven M. Thompson
Florida State University
Tallahassee, Florida

William Thompson
Brown University
Providence, Rhode Island

Bruce Tidor
Massachusetts Institute of Technology
Cambridge, Massachusetts

Simon N. Twigger
Human and Molecular Genetics Center
Medical College of Wisconsin
Milwaukee, Wisconsin

Edward C. Uberbacher
Oak Ridge National Laboratory
Oak Ridge, Tennessee

Hideaki Umeyama
Kitasato University
Tokyo, Japan

Arndt von Haeseler
HHU Düsseldorf
Düsseldorf, Germany and FZ Julich
Jülich, Germany

Ben Webb
University of California at San Francisco
San Francisco, California

David Wheeler
Human Genome Center
Baylor College of Medicine
Houston, Texas

James C. Wilgenbusch
Florida State University
Tallahassee, Florida

Kenneth Williams
Yale University
New Haven, Connecticut

Randall C Willis
The Blueprint Initiative
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
Toronto, Ontario, Canada

Chris Wilton
Institute of Biotechnology
University of Helsinki
Helsinki, Finland

Tyra G. Wolfsberg
National Human Genome Research Institute
National Institutes of Health
Bethesda, Maryland

Haim Wolfson
Tel Aviv University
Tel Aviv, Israel

Baolin Wu
University of Minnesota
Minneapolis, Minnesota

Terence Wu
Yale University
New Haven, Connecticut

Iris Xu
Carnegie Institution
Stanford, California

Shiaw-Pyng Yang
Washington University Medical School
St. Louis, Missouri

Bozidar Yerkovichi
The Rockefeller University
New York, New York

Danny Yoo
Carnegie Institution
Stanford, California

Michael Q. Zhang
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York

Peili Zhang
Harvard University
Cambridge, Massachusetts

Hongyu Zhao
Yale University
New Haven, Connecticut

Pinglei Zhou
Harvard University
Cambridge, Massachusetts

Angela Zuniga-Meyer
Human and Molecular Genetics Center
Medical College of Wisconsin
Milwaukee, Wisconsin