S
Scott E. Baker
Researcher at Pacific Northwest National Laboratory
Publications - 161
Citations - 15616
Scott E. Baker is an academic researcher from Pacific Northwest National Laboratory. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 54, co-authored 156 publications receiving 13763 citations. Previous affiliations of Scott E. Baker include Joint BioEnergy Institute & Battelle Memorial Institute.
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Journal ArticleDOI
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
Li-Jun Ma,H. Charlotte van der Does,Katherine A. Borkovich,Jeffrey J. Coleman,Marie Josée Daboussi,Antonio Di Pietro,Marie Dufresne,Michael Freitag,Manfred Grabherr,Bernard Henrissat,Petra M. Houterman,Seogchan Kang,Won-Bo Shim,Charles P. Woloshuk,Xiaohui Xie,Jin-Rong Xu,John F. Antoniw,Scott E. Baker,B. H. Bluhm,Andrew Breakspear,Daren W. Brown,Robert A. E. Butchko,Sinéad B. Chapman,Richard M.R. Coulson,Pedro M. Coutinho,Etienne Danchin,Etienne Danchin,Andrew C. Diener,Liane R. Gale,Donald M. Gardiner,Stephen A. Goff,Kim E. Hammond-Kosack,Karen Hilburn,Aurélie Hua-Van,Wilfried Jonkers,Kemal Kazan,Chinnappa D. Kodira,Michael Koehrsen,Lokesh Kumar,Yong-Hwan Lee,Liande Li,Liande Li,John M. Manners,Diego Miranda-Saavedra,Mala Mukherjee,Gyungsoon Park,Jongsun Park,Sook Young Park,Sook Young Park,Robert H. Proctor,Aviv Regev,M. Carmen Ruiz-Roldán,Divya Sain,Sharadha Sakthikumar,Sean M. Sykes,David C. Schwartz,B. Gillian Turgeon,Ilan Wapinski,Olen C. Yoder,Sarah Young,Qiandong Zeng,Shiguo Zhou,James E. Galagan,Christina A. Cuomo,H. Corby Kistler,Martijn Rep +65 more
TL;DR: Comparison of genomes of three phenotypically diverse Fusarium species revealed lineage-specific genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome, putting the evolution of fungal pathogenicity into a new perspective.
Journal ArticleDOI
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).
Diego Martinez,Diego Martinez,Randy M. Berka,Bernard Henrissat,Markku Saloheimo,Mikko Arvas,Scott E. Baker,Jarod Chapman,Olga Chertkov,Pedro M. Coutinho,Dan Cullen,Etienne Danchin,Igor V. Grigoriev,Paul Harris,Melissa Jackson,Christian P. Kubicek,Cliff Han,Isaac Ho,Luis F. Larrondo,Alfredo Lopez de Leon,Jon K. Magnuson,Sandy Merino,Monica Misra,Beth Nelson,Nicholas H. Putnam,Barbara Robbertse,Asaf Salamov,Monika Schmoll,Astrid Terry,Nina Thayer,Ann Westerholm-Parvinen,Conrad L. Schoch,Jian Yao,Ravi D. Barabote,Mary Anne Nelson,Chris Detter,David Bruce,Cheryl R. Kuske,Gary Xie,Paul G. Richardson,Daniel S. Rokhsar,Susan Lucas,Edward M. Rubin,Nigel Dunn-Coleman,Michael Ward,Thomas Brettin +45 more
TL;DR: This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production.
Journal ArticleDOI
A versatile toolkit for high throughput functional genomics with Trichoderma reesei
André Schuster,André Schuster,Kenneth S. Bruno,James R. Collett,Scott E. Baker,Bernhard Seiboth,Christian P. Kubicek,Monika Schmoll +7 more
TL;DR: A construction kit for gene knock out in T. reesei and a primer database for gene deletion using the pyr4, amdS and hph selection markers are provided to boost research towards efficient exploitation of the resources of T.Reesei for cellulase expression and hence second generation biofuel production.
Journal ArticleDOI
The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization
Christina A. Cuomo,Ulrich Güldener,Jin-Rong Xu,Frances Trail,B. Gillian Turgeon,Antonio Di Pietro,Jonathan D. Walton,Li-Jun Ma,Scott E. Baker,Martijn Rep,Gerhard Adam,John F. Antoniw,Thomas K. Baldwin,Sarah E. Calvo,Yueh-Long Chang,David DeCaprio,Liane R. Gale,Sante Gnerre,Rubella S. Goswami,Kim E. Hammond-Kosack,Linda J. Harris,Karen Hilburn,John C. Kennell,Scott Kroken,Jon K. Magnuson,Gertrud Mannhaupt,Evan Mauceli,Hans-Werner Mewes,Rudolf Mitterbauer,Gary J. Muehlbauer,Martin Münsterkötter,David R. Nelson,Kerry O'Donnell,Thérèse Ouellet,Weihong Qi,Hadi Quesneville,M. Isabel G. Roncero,Kye Yong Seong,Igor V. Tetko,Martin Urban,Cees Waalwijk,Todd J. Ward,Jiqiang Yao,Bruce W. Birren,H. Corby Kistler,H. Corby Kistler +45 more
TL;DR: The genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals, was sequenced and annotated and many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination.
Journal ArticleDOI
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Christian P. Kubicek,Alfredo Herrera-Estrella,Verena Seidl-Seiboth,Diego Martinez,Irina S. Druzhinina,Michael R. Thon,Susanne Zeilinger,Sergio Casas-Flores,Benjamin A. Horwitz,Prasun K. Mukherjee,Mala Mukherjee,László Kredics,Luis David Alcaraz,Andrea Aerts,Zsuzsanna Antal,Lea Atanasova,Mayte G Cervantes-Badillo,Jean F. Challacombe,Olga Chertkov,Kevin McCluskey,Fanny Coulpier,Nandan P. Deshpande,Hans von Döhren,Daniel J. Ebbole,Edgardo Ulises Esquivel-Naranjo,Erzsébet Fekete,Michel Flipphi,Fabian Glaser,Elida Yazmin Gomez-Rodriguez,Sabine Gruber,Cliff Han,Bernard Henrissat,Rosa Hermosa,Miguel Ángel Hernández-Oñate,Levente Karaffa,Idit Kosti,Stéphane Le Crom,Erika Lindquist,Susan Lucas,Mette Lübeck,Peter Stephensen Lübeck,Antoine Margeot,Benjamin Metz,Monica Misra,Helena Nevalainen,Markus Omann,Nicolle H. Packer,Giancarlo Perrone,Edith Elena Uresti-Rivera,Asaf Salamov,Monika Schmoll,Bernhard Seiboth,Harris Shapiro,Serenella A. Sukno,Juan Antonio Tamayo-Ramos,Doris Tisch,Aric Wiest,Heather H. Wilkinson,Michael Zhang,Pedro M. Coutinho,Charles M. Kenerley,Enrique Monte,Scott E. Baker,Scott E. Baker,Igor V. Grigoriev +64 more
TL;DR: A better understanding of mycoparasitism is offered, and the development of improved biocontrol strains for efficient and environmentally friendly protection of plants is enforced.