M
Matt Nolan
Researcher at Lawrence Berkeley National Laboratory
Publications - 221
Citations - 8725
Matt Nolan is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Genome & Whole genome sequencing. The author has an hindex of 39, co-authored 219 publications receiving 7642 citations. Previous affiliations of Matt Nolan include Harvard University & Joint Genome Institute.
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Journal ArticleDOI
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
Dongying Wu,Dongying Wu,Philip Hugenholtz,Konstantinos Mavromatis,Rüdiger Pukall,Eileen Dalin,Natalia Ivanova,Victor Kunin,Lynne Goodwin,Martin Wu,Brian J. Tindall,Sean D. Hooper,Amrita Pati,Athanasios Lykidis,Stefan Spring,Iain Anderson,Patrik D'haeseleer,Patrik D'haeseleer,Adam Zemla,Mitchell Singer,Alla Lapidus,Matt Nolan,Alex Copeland,Cliff Han,Feng Chen,Jan Fang Cheng,Susan Lucas,Cheryl A. Kerfeld,Elke Lang,Sabine Gronow,Patrick S. G. Chain,Patrick S. G. Chain,David Bruce,Edward M. Rubin,Nikos C. Kyrpides,Hans-Peter Klenk,Jonathan A. Eisen,Jonathan A. Eisen +37 more
TL;DR: The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
Journal ArticleDOI
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
Patrick M. Shih,Patrick M. Shih,Dongying Wu,Amel Latifi,Seth D. Axen,David P. Fewer,Emmanuel Talla,Alexandra Calteau,Fei Cai,Nicole Tandeau de Marsac,Rosmarie Rippka,Michael Herdman,Kaarina Sivonen,Thérèse Coursin,Thierry Laurent,Lynne Goodwin,Matt Nolan,Karen W. Davenport,Cliff Han,Edward M. Rubin,Jonathan A. Eisen,Tanja Woyke,Muriel Gugger,Cheryl A. Kerfeld,Cheryl A. Kerfeld +24 more
TL;DR: This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis.
Journal ArticleDOI
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
Helene Feil,William S. Feil,Patrick S. G. Chain,Frank W. Larimer,Genevieve DiBartolo,Alex Copeland,Athanasios Lykidis,Stephen Trong,Matt Nolan,Eugene Goltsman,James Thiel,Stephanie Malfatti,Joyce E. Loper,Alla Lapidus,John C. Detter,Miriam Land,Paul M. Richardson,Nikos C. Kyrpides,Natalia Ivanova,Steven E. Lindow +19 more
TL;DR: The complete genomic sequence of Pseudomonas syringae pv. syringa (Pss B728a) has been determined and is compared with that of P. tomato DC3000 (Pst DC3000).
Journal ArticleDOI
The DNA sequence and biology of human chromosome 19
Jane Grimwood,Laurie Gordon,Laurie Gordon,Anne S. Olsen,Anne S. Olsen,Astrid Terry,Jeremy Schmutz,Jane Lamerdin,Jane Lamerdin,Uffe Hellsten,David Goodstein,Olivier Couronne,Mary Bao Tran-Gyamfi,Mary Bao Tran-Gyamfi,Andrea Aerts,Michael R. Altherr,Michael R. Altherr,Linda K. Ashworth,Linda K. Ashworth,Eva Bajorek,Stacey Black,Elbert Branscomb,Elbert Branscomb,Sean Caenepeel,Anthony V. Carrano,Anthony V. Carrano,Chenier Caoile,Yee Man Chan,Mari Christensen,Mari Christensen,Catherine A. Cleland,Catherine A. Cleland,Alex Copeland,Eileen Dalin,Paramvir S. Dehal,Mirian Denys,John C. Detter,Julio Escobar,Dave Flowers,Dea Fotopulos,Carmen Rosa Albacete García,Anca M. Georgescu,Anca M. Georgescu,Tijana Glavina,Maria Gomez,Eidelyn Gonzales,Matthew Groza,Matthew Groza,Nancy Hammon,Trevor Hawkins,Lauren Haydu,Isaac Ho,Wayne Huang,Sanjay Israni,Jamie Jett,Kristen Kadner,Heather Kimball,Arthur Kobayashi,Arthur Kobayashi,Vladimer Larionov,Sun-Hee Leem,Frederick Lopez,Yunian Lou,Steve Lowry,Stephanie Malfatti,Stephanie Malfatti,Diego Martinez,Paula McCready,Paula McCready,Catherine Medina,Jenna Morgan,Kathryn Nelson,Kathryn Nelson,Matt Nolan,Ivan Ovcharenko,Ivan Ovcharenko,Sam Pitluck,Martin Pollard,Anthony P. Popkie,Paul Predki,Glenda Quan,Glenda Quan,Lucía Ramírez,Sam Rash,James Retterer,Alex Rodriguez,Stephanine Rogers,Asaf Salamov,Angelica Salazar,Xinwei She,Doug Smith,Tom Slezak,Tom Slezak,Victor V. Solovyev,Nina Thayer,Nina Thayer,Hope Tice,Ming Tsai,Anna Ustaszewska,Nu Vo,Mark C. Wagner,Mark C. Wagner,Jeremy Wheeler,Kevin Wu,Gary Xie,Gary Xie,Joan Yang,Inna Dubchak,Terrence S. Furey,Pieter J. deJong,Mark Dickson,David Gordon,Evan E. Eichler,Len A. Pennacchio,Paul G. Richardson,Lisa Stubbs,Lisa Stubbs,Daniel S. Rokhsar,Richard M. Myers,Edward M. Rubin,Susan Lucas +120 more
TL;DR: Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.
Journal ArticleDOI
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Shingo Miyauchi,Enikő Csilla Kiss,Alan Kuo,Elodie Drula,Annegret Kohler,Marisol Sánchez-García,Emmanuelle Morin,Bill Andreopoulos,Kerrie Barry,Gregory Bonito,Marc Buée,Akiko Carver,Cindy Chen,Nicolas Cichocki,Alicia Clum,David E. Culley,Pedro W. Crous,Laure Fauchery,Mariangela Girlanda,Richard D. Hayes,Zsófia Kéri,Kurt LaButti,Anna Lipzen,Vincent Lombard,Jon K. Magnuson,François Maillard,Claude Murat,Matt Nolan,Robin A. Ohm,Jasmyn Pangilinan,Maíra de Freitas Pereira,Silvia Perotto,Martina Peter,Stephanie Pfister,Robert Riley,Yaron Sitrit,J. Benjamin Stielow,Gergely J. Szöllősi,Lucia Žifčáková,Martina Štursová,Joseph W. Spatafora,Leho Tedersoo,Lu-Min Vaario,Akiyoshi Yamada,Mi Yan,Pengfei Wang,Jianping Xu,Thomas D. Bruns,Petr Baldrian,Rytas Vilgalys,Christophe Dunand,Bernard Henrissat,Bernard Henrissat,Igor V. Grigoriev,Igor V. Grigoriev,David S. Hibbett,László Nagy,Francis Martin,Francis Martin +58 more
TL;DR: This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales, and shows that transitions from saprotrophy to symbiosis involve widespread losses of degrading enzymes acting on lignin and cellulose.