J
Jason E. Stajich
Researcher at University of California, Riverside
Publications - 303
Citations - 22865
Jason E. Stajich is an academic researcher from University of California, Riverside. The author has contributed to research in topics: Genome & Biology. The author has an hindex of 60, co-authored 250 publications receiving 19483 citations. Previous affiliations of Jason E. Stajich include University of California, Berkeley & Center for Applied Genomics.
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Journal ArticleDOI
The Bioperl Toolkit: Perl Modules for the Life Sciences
Jason E. Stajich,David Block,David Block,Kris Boulez,Steven E. Brenner,Stephen A. Chervitz,Chris Dagdigian,Georg Fuellen,James G. R. Gilbert,Ian F Korf,Hilmar Lapp,Heikki Lehväslaiho,Chad Matsalla,Christopher J. Mungall,Brian I. Osborne,Matthew Pocock,Peter Schattner,Martin Senger,Lincoln Stein,Elia Stupka,Mark Wilkinson,Ewan Birney +21 more
TL;DR: The overall architecture of the Bioperl toolkit is described, the problem domains that it addresses, and specific examples of how the toolkit can be used to solve common life-sciences problems are given.
Journal ArticleDOI
Reconstructing the early evolution of Fungi using a six-gene phylogeny
Timothy Y. James,Frank Kauff,Conrad L. Schoch,P. Brandon Matheny,Valérie Hofstetter,Cymon J. Cox,Cymon J. Cox,Gail Celio,Cécile Gueidan,Emily Fraker,Jolanta Miadlikowska,H. Thorsten Lumbsch,Alexandra Rauhut,Valérie Reeb,A. Elizabeth Arnold,A. Elizabeth Arnold,Anja Amtoft,Jason E. Stajich,Kentaro Hosaka,Kentaro Hosaka,Gi-Ho Sung,Desiree Johnson,Ben O'Rourke,Michael Crockett,Manfred Binder,Judd M. Curtis,Jason C. Slot,Zheng Wang,Zheng Wang,Andrew W. Wilson,Arthur Schüßler,Joyce E. Longcore,Kerry O'Donnell,Sharon E. Mozley-Standridge,David Porter,Peter M. Letcher,Martha J. Powell,John W. Taylor,Merlin M. White,Gareth W. Griffith,David R. Davies,Richard A. Humber,Joseph B. Morton,Junta Sugiyama,Amy Y. Rossman,Jack D. Rogers,Donald H. Pfister,David Hewitt,Karen Hansen,Sarah Hambleton,R. A. Shoemaker,Jan Kohlmeyer,Brigitte Volkmann-Kohlmeyer,Robert A. Spotts,Maryna Serdani,Pedro W. Crous,Karen W. Hughes,Kenji Matsuura,Ewald Langer,Gitta Langer,Wendy A. Untereiner,Robert Lücking,Burkhard Büdel,David M. Geiser,André Aptroot,Paul Diederich,Imke Schmitt,Imke Schmitt,Matthias Schultz,Rebecca Yahr,Rebecca Yahr,David S. Hibbett,François Lutzoni,David J. McLaughlin,Joseph W. Spatafora,Rytas Vilgalys +75 more
TL;DR: It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and the enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
Journal ArticleDOI
The Generic Genome Browser: A Building Block for a Model Organism System Database
Lincoln Stein,Christopher J. Mungall,ShengQiang Shu,Michael Caudy,Marco Mangone,Allen Day,Elizabeth Nickerson,Jason E. Stajich,Todd W. Harris,Adrian Arva,Suzanna E. Lewis +10 more
TL;DR: The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
Journal ArticleDOI
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
Jörg Kämper,Regine Kahmann,Michael Bölker,Li-Jun Ma,Thomas Brefort,Barry J. Saville,Barry J. Saville,Flora Banuett,James W. Kronstad,Scott E. Gold,Olaf Müller,Michael H. Perlin,Han A. B. Wösten,Ronald P. de Vries,Jose Ruiz-Herrera,Cristina G. Reynaga-Peña,Karen M. Snetselaar,Michael P. McCann,José Pérez-Martín,Michael Feldbrügge,Christoph W. Basse,Gero Steinberg,José I. Ibeas,William K. Holloman,Plinio Guzmán,Mark L. Farman,Jason E. Stajich,Rafael Sentandreu,Juan Manuel González-Prieto,John C. Kennell,Lazaro Molina,Jan Schirawski,Artemio Mendoza-Mendoza,Doris Greilinger,Karin Münch,Nicole Rössel,Mario Scherer,Miroslav Vranes,Oliver Ladendorf,Volker Vincon,Uta Fuchs,Björn Sandrock,Shaowu Meng,Eric C.H. Ho,Matt J. Cahill,Kylie J. Boyce,Jana Klose,Steven J. Klosterman,Heine J. Deelstra,Lucila Ortiz-Castellanos,Weixi Li,Patricia Sánchez-Alonso,Peter Schreier,Isolde Häuser-Hahn,Martin Vaupel,Edda Koopmann,Gabi Friedrich,Hartmut Voss,Thomas Schlüter,Jonathan Margolis,Darren Mark Platt,Candace Swimmer,Andreas Gnirke,Feng Chen,Valentina Vysotskaia,Gertrud Mannhaupt,Ulrich Güldener,Martin Münsterkötter,Dirk Haase,Matthias Oesterheld,Hans-Werner Mewes,Evan Mauceli,David DeCaprio,Claire M. Wade,Jonathan Butler,Sarah Young,David B. Jaffe,Sarah E. Calvo,Chad Nusbaum,James E. Galagan,Bruce W. Birren +80 more
TL;DR: The discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi.
Journal ArticleDOI
The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics
Lincoln Stein,Zhirong Bao,Zhirong Bao,Darin Blasiar,Thomas Blumenthal,Michael R. Brent,Nansheng Chen,Asif T. Chinwalla,Laura Clarke,Chris Clee,Avril Coghlan,Alan Coulson,Alan Coulson,Peter D'Eustachio,Peter D'Eustachio,David H. A. Fitch,Lucinda Fulton,Robert E Fulton,Sam Griffiths-Jones,Todd W. Harris,LaDeana W. Hillier,LaDeana W. Hillier,Ravi Kamath,Patricia E. Kuwabara,Elaine R. Mardis,Marco A. Marra,Marco A. Marra,Tracie L. Miner,Patrick Minx,James C. Mullikin,James C. Mullikin,Robert W. Plumb,Jane Rogers,Jacqueline E. Schein,Jacqueline E. Schein,Marc Sohrmann,John Spieth,Jason E. Stajich,Chaochun Wei,David Willey,Richard K. Wilson,Richard Durbin,Robert H. Waterston,Robert H. Waterston +43 more
TL;DR: Comparisons of the two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers, which will help to understand the evolutionary forces that mold nematode genomes.