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William C. Nierman
Researcher at J. Craig Venter Institute
Publications - 155
Citations - 25499
William C. Nierman is an academic researcher from J. Craig Venter Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 65, co-authored 154 publications receiving 23950 citations. Previous affiliations of William C. Nierman include TigerLogic & Korea University.
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Journal ArticleDOI
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Richard A. Gibbs,George M. Weinstock,Michael L. Metzker,Donna M. Muzny,Erica Sodergren,Steven E. Scherer,Graham R. Scott,David Steffen,Kim C. Worley,Paula E. Burch,Geoffrey Okwuonu,Sandra Hines,Lora Lewis,Christine Deramo,Oliver Delgado,Shannon Dugan-Rocha,George Miner,Margaret Morgan,Alicia Hawes,Rachel Gill,Robert A. Holt,Robert A. Holt,Mark Raymond Adams,Mark Raymond Adams,Peter G. Amanatides,Peter G. Amanatides,Holly Baden-Tillson,Holly Baden-Tillson,Mary Barnstead,Soo H. Chin,Cheryl A. Evans,Steve Ferriera,Steve Ferriera,Carl Fosler,A. Glodek,Zhiping Gu,Don Jennings,Cheryl L. Kraft,Cheryl L. Kraft,Trixie Nguyen,Cynthia Pfannkoch,Cynthia Pfannkoch,Cynthia Sitter,Granger G. Sutton,J. Craig Venter,J. Craig Venter,Trevor Woodage,Douglas Smith,Hong Mei Lee,Erik Gustafson,Patrick Cahill,Arnold Kana,Lynn Doucette-Stamm,Keith Weinstock,Kim Fechtel,Robert B. Weiss,Diane M. Dunn,Eric D. Green,Robert W. Blakesley,Gerard G. Bouffard,Pieter J. de Jong,Kazutoyo Osoegawa,Baoli Zhu,Marco A. Marra,Jacqueline E. Schein,Ian Bosdet,Chris Fjell,Steven J.M. Jones,Martin Krzywinski,Carrie Mathewson,Asim Sarosh Siddiqui,Natasja Wye,John Douglas Mcpherson,John Douglas Mcpherson,Shaying Zhao,Claire M. Fraser,Jyoti Shetty,Sofiya Shatsman,Keita Geer,Yixin Chen,Sofyia Abramzon,William C. Nierman,Paul Havlak,Rui Chen,K. James Durbin,Amy Egan,Yanru Ren,Xing Zhi Song,Bingshan Li,Yue Liu,Xiang Qin,Simon Cawley,Austin J. Cooney,Lisa M. D'Souza,Kirt Martin,Jia Qian Wu,Manuel L. Gonzalez-Garay,Andrew R. Jackson,Kenneth J. Kalafus,Michael P. McLeod,Aleksandar Milosavljevic,Davinder Virk,Andrei Volkov,David A. Wheeler,Zhengdong D. Zhang,Jeffrey A. Bailey,Evan E. Eichler,Eray Tüzün,Ewan Birney,Emmanuel Mongin,Abel Ureta-Vidal,Cara Woodwark,Evgeny M. Zdobnov,Peer Bork,Mikita Suyama,David Torrents,Marina Alexandersson,Barbara J. Trask,Janet M. Young,Hui Huang,Huajun Wang,Heming Xing,Sue Daniels,Darryl Gietzen,Jeanette Schmidt,Kristian Stevens,Ursula Vitt,Jim Wingrove,Francisco Camara,M. Mar Albà,Josep F. Abril,Roderic Guigó,Arian F.A. Smit,Inna Dubchak,Inna Dubchak,Edward M. Rubin,Edward M. Rubin,Olivier Couronne,Olivier Couronne,Alexander Poliakov,Norbert Hubner,Detlev Ganten,Claudia Goesele,Claudia Goesele,Oliver Hummel,Oliver Hummel,Thomas Kreitler,Thomas Kreitler,Young-Ae Lee,Jan Monti,Herbert Schulz,Heike Zimdahl,Heinz Himmelbauer,Hans Lehrach,Howard J. Jacob,Susan Bromberg,Jo Gullings-Handley,Michael I. Jensen-Seaman,Anne E. Kwitek,Jozef Lazar,Dean Pasko,Peter J. Tonellato,Simon N. Twigger,Chris P. Ponting,Jose M. Duarte,Stephen Rice,Leo Goodstadt,Scott A. Beatson,Richard D. Emes,Eitan E. Winter,Caleb Webber,Petra Brandt,Gerald Nyakatura,Margaret Adetobi,Francesca Chiaromonte,Laura Elnitski,Pallavi Eswara,Ross C. Hardison,Minmei Hou,Diana L. Kolbe,Kateryna D. Makova,Webb Miller,Anton Nekrutenko,Cathy Riemer,Scott Schwartz,James Taylor,Shan Yang,Yi Zhang,Klaus Lindpaintner,T. Dan Andrews,Mario Caccamo,Michele Clamp,Laura Clarke,Valerie Curwen,Richard Durbin,Eduardo Eyras,Stephen M. J. Searle,Gregory M. Cooper,Serafim Batzoglou,Michael Brudno,Arend Sidow,Eric A. Stone,Bret A. Payseur,Guillaume Bourque,Carlos López-Otín,Xose S. Puente,Kushal Chakrabarti,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Nicolas Bray,Von Bing Yap,Anat Caspi,San Diego Glenn Tesler,Pavel A. Pevzner,Santa Cruz David Haussler,Krishna M. Roskin,Robert Baertsch,Hiram Clawson,Terrence S. Furey,Angie S. Hinrichs,Donna Karolchik,W. J. Kent,Kate R. Rosenbloom,Heather Trumbower,Matt Weirauch,Matt Weirauch,David Neil Cooper,Peter D. Stenson,Bin Ma,Michael R. Brent,Manimozhiyan Arumugam,David Shteynberg,Richard R. Copley,Martin S. Taylor,Harold Riethman,Uma Mudunuri,Jane Peterson,Mark S. Guyer,Adam Felsenfeld,Susan Old,Stephen C. Mockrin,Francis S. Collins +242 more
TL;DR: This first comprehensive analysis of the genome sequence of the Brown Norway (BN) rat strain is reported, which is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution.
Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRat Genome Sequencing Project ConsortiumNature200442849352115057822
Richard A. Gibbs,George M. Weinstock,Michael L. Metzker,Donna M. Muzny,Erica Sodergren,Steven E. Scherer,Graham R. Scott,David Steffen,Kim C. Worley,Paula E. Burch,Geoffrey Okwuonu,Sandra Hines,Lora Lewis,C. DeRamo,Oliver Delgado,S. Dugan Rocha,George Miner,Margaret Morgan,Alicia Hawes,Rachel Gill,Robert A. Holt,Mark Raymond Adams,Peter G. Amanatides,H. Baden Tillson,Mary Barnstead,Soo H. Chin,Cheryl A. Evans,Steve Ferriera,Carl Fosler,A. Glodek,Gu Zp,D. Jennings,Cheryl L. Kraft,T. Nguyen,Cynthia Pfannkoch,Cynthia Sitter,Granger G. Sutton,J. C. Venter,Trevor Woodage,Douglas Smith,H. M. Lee,Erik Gustafson,Patrick Cahill,A. Kana,L. Doucette Stamm,Keith Weinstock,Kim Fechtel,Robert B. Weiss,Diane M. Dunn,Eric D. Green,Robert W. Blakesley,Gerard G. Bouffard,P. J. De Jong,Kazutoyo Osoegawa,Zhu Bl,Marco A. Marra,Jacqueline E. Schein,Ian Bosdet,Chris Fjell,Steven J.M. Jones,Martin Krzywinski,Carrie Mathewson,Asim Sarosh Siddiqui,Natasja Wye,John Douglas Mcpherson,Zhao Sy,Claire M. Fraser,Jyoti Shetty,Sofiya Shatsman,Keita Geer,Chen Yx,S. Abramzon,William C. Nierman,Paul Havlak,Rui Chen,K. J. Durbin,Amy Egan,Ren Yr,Xing Zhi Song,Li Bs,Yue Liu,Xiang Qin,Simon Cawley,Austin J. Cooney,Lisa M. D'Souza,Kirt Martin,Jia Qian Wu,M. L. Gonzalez Garay,Andrew R. Jackson,K. J. Kalafus,Michael P. McLeod,Aleksandar Milosavljevic,D. Virk,A. Volkov,David A. Wheeler,Zhang Zd,Jeffrey A. Bailey,Evan E. Eichler,Eray Tüzün,Ewan Birney,Emmanuel Mongin,A. Ureta Vidal,C. Woodwark,Evgeny M. Zdobnov,Peer Bork,Mikita Suyama,David Torrents,Marina Alexandersson,Barbara J. Trask,Janet M. Young,Hui Huang,Wang Hj,Xing Hm,Sue Daniels,Darryl Gietzen,Jeanette Schmidt,K. Stevens,Ursula Vitt,Jim Wingrove,Francisco Camara,M. Mar Albà,Josep F. Abril,Roderic Guigó,Arian F.A. Smit,Inna Dubchak,Edward M. Rubin,Olivier Couronne,Alexander Poliakov,Norbert Hubner,Detlev Ganten,C. Goesele,Oliver Hummel,Thomas Kreitler,Young-Ae Lee,Jan Monti,Herbert Schulz,Heike Zimdahl,Heinz Himmelbauer,Hans Lehrach,Howard J. Jacob,Susan Bromberg,J. Gullings Handley,M. I. Jensen Seaman,Anne E. Kwitek,Jozef Lazar,Dean Pasko,Peter J. Tonellato,Simon N. Twigger,Chris P. Ponting,Jose M. Duarte,Stephen Rice,Leo Goodstadt,Scott A. Beatson,Richard D. Emes,Eitan E. Winter,Caleb Webber,Petra Brandt,Gerald Nyakatura,M. Adetobi,Francesca Chiaromonte,Laura Elnitski,Pallavi Eswara,Ross C. Hardison,Hou Mm,Diana L. Kolbe,Kateryna D. Makova,Webb Miller,Anton Nekrutenko,Cathy Riemer,Scott Schwartz,James Taylor,Shan Yang,Yi Zhang,Klaus Lindpaintner,T. D. Andrews,Mario Caccamo,Michele Clamp,Laura Clarke,V. Curwen,Richard Durbin,Eduardo Eyras,Stephen M. J. Searle,Gregory M. Cooper,Serafim Batzoglou,Michael Brudno,Arend Sidow,Eric A. Stone,Bret A. Payseur,Guillaume Bourque,C. Lopez Otin,Xose S. Puente,Kushal Chakrabarti,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Nicolas Bray,Von Bing Yap,Anat Caspi,G. Tesler,Pavel A. Pevzner,David Haussler,Krishna M. Roskin,Robert Baertsch,Hiram Clawson,Terrence S. Furey,Angie S. Hinrichs,Donna Karolchik,W. J. Kent,Kate R. Rosenbloom,Heather Trumbower,M. Weirauch,David Neil Cooper,Peter D. Stenson,Bin Ma,Michael R. Brent,Manimozhiyan Arumugam,David Shteynberg,Richard R. Copley,Martin S. Taylor,Harold Riethman,Uma Mudunuri,Jane Peterson,Mark S. Guyer,Adam Felsenfeld,Susan Old,Stephen C. Mockrin,Francis S. Collins +226 more
Abstract: The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality ‘draft’ covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
Journal ArticleDOI
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
John F. Heidelberg,Jonathan A. Eisen,William C. Nelson,Rebecca A. Clayton,Michelle L. Gwinn,Robert J. Dodson,Daniel H. Haft,Erin Hickey,Jeremy Peterson,Lowell Umayam,Steven R. Gill,Karen E. Nelson,Timothy D. Read,Hervé Tettelin,Delwood Richardson,Maria D. Ermolaeva,Jessica Vamathevan,Steven Bass,Haiying Qin,Ioana Dragoi,Patrick Sellers,Lisa McDonald,Teresa Utterback,Robert D. Fleishmann,William C. Nierman,Owen White,Steven L. Salzberg,Hamilton O. Smith,Rita R. Colwell,Rita R. Colwell,John J. Mekalanos,J. Craig Venter,Claire M. Fraser +32 more
TL;DR: The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.
Journal ArticleDOI
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
William C. Nierman,William C. Nierman,Arnab Pain,Michael J. Anderson,Jennifer R. Wortman,Jennifer R. Wortman,H. Stanley Kim,H. Stanley Kim,Javier Arroyo,Matthew Berriman,Keietsu Abe,David B. Archer,Clara Bermejo,Joan W. Bennett,Paul Bowyer,Dan Chen,Dan Chen,Matthew Collins,Richard Coulsen,Robert L. Davies,Paul S. Dyer,Mark L. Farman,Nadia Fedorova,Nadia Fedorova,Natalie D. Fedorova,Natalie D. Fedorova,T. Feldblyum,T. Feldblyum,Reinhard Fischer,Nigel Fosker,Audrey Fraser,José Luis García,María Josefa Marcos García,Ariette Goble,Gustavo H. Goldman,Katsuya Gomi,Sam Griffith-Jones,R. Gwilliam,Brian J. Haas,Brian J. Haas,Hubertus Haas,David Harris,H. Horiuchi,Jiaqi Huang,Jiaqi Huang,Sean Humphray,Javier Jiménez,Nancy P. Keller,H. Khouri,H. Khouri,Katsuhiko Kitamoto,Tetsuo Kobayashi,Sven Konzack,Resham Kulkarni,Resham Kulkarni,Toshitaka Kumagai,Anne Lafton,Jean-Paul Latgé,Weixi Li,Angela Lord,Charles Lu,Charles Lu,William H. Majoros,William H. Majoros,Gregory S. May,Bruce L. Miller,Yasmin Ali Mohamoud,Yasmin Ali Mohamoud,María Molina,Michel Monod,Isabelle Mouyna,Stephanie Mulligan,Stephanie Mulligan,Lee Murphy,Susan O'Neil,Ian T. Paulsen,Ian T. Paulsen,Miguel A. Peñalva,Mihaela Pertea,Mihaela Pertea,Claire Price,Bethan L. Pritchard,Michael A. Quail,Ester Rabbinowitsch,Neil Rawlins,Marie Adele Rajandream,Utz Reichard,Hubert Renauld,Geoffrey D. Robson,Santiago Rodríguez de Córdoba,José Manuel Rodríguez-Peña,Catherine M. Ronning,Catherine M. Ronning,Simon Rutter,Steven L. Salzberg,Steven L. Salzberg,Miguel del Nogal Sánchez,Juan C. Sánchez-Ferrero,David L. Saunders,Kathy Seeger,Rob Squares,S. Squares,Michio Takeuchi,Fredj Tekaia,Geoffrey Turner,Carlos R. Vázquez de Aldana,J. Weidman,J. Weidman,Owen White,Owen White,John Woodward,Jae-Hyuk Yu,Claire M. Fraser,Claire M. Fraser,James E. Galagan,Kiyoshi Asai,Masayuki Machida,Neil Hall,Neil Hall,Bart Barrell,David W. Denning +120 more
TL;DR: The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus and revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype.
Journal ArticleDOI
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
James E. Galagan,Sarah E. Calvo,Christina A. Cuomo,Li-Jun Ma,Jennifer R. Wortman,Serafim Batzoglou,Su-In Lee,Meray Baştürkmen,Christina C. Spevak,John Clutterbuck,Vladimir V. Kapitonov,Jerzy Jurka,Claudio Scazzocchio,Mark L. Farman,Jonathan Butler,Seth Purcell,Steve Harris,Gerhard H. Braus,Oliver W. Draht,Silke Busch,Christophe d'Enfert,Christiane Bouchier,Gustavo H. Goldman,Deborah Bell-Pedersen,Sam Griffiths-Jones,John H. Doonan,Jae-Hyuk Yu,Kay Vienken,Arnab Pain,Michael Freitag,Eric U. Selker,David B. Archer,Miguel A. Peñalva,Berl R. Oakley,Michelle Momany,Toshihiro Tanaka,Toshitaka Kumagai,Kiyoshi Asai,Masayuki Machida,William C. Nierman,David W. Denning,Mark X. Caddick,Michael J. Hynes,Mathieu Paoletti,Reinhard Fischer,Reinhard Fischer,Bruce L. Miller,Paul S. Dyer,Matthew S. Sachs,Stephen A. Osmani,Bruce W. Birren +50 more
TL;DR: The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution, and a comparative study with Aspergillus fumigatus and As pergillus oryzae, used in the production of sake, miso and soy sauce, provides new insight into eukaryotic genome evolution and gene regulation.