R
Rex R. Malmstrom
Researcher at Joint Genome Institute
Publications - 90
Citations - 8368
Rex R. Malmstrom is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Metagenomics & Genome. The author has an hindex of 39, co-authored 76 publications receiving 6390 citations. Previous affiliations of Rex R. Malmstrom include Massachusetts Institute of Technology & University of Delaware.
Papers
More filters
Journal ArticleDOI
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers,Nikos C. Kyrpides,Ramunas Stepanauskas,Miranda Harmon-Smith,Devin F. R. Doud,T. B. K. Reddy,Frederik Schulz,Jessica K. Jarett,Adam R. Rivers,Adam R. Rivers,Emiley A. Eloe-Fadrosh,Susannah G. Tringe,Susannah G. Tringe,Natalia Ivanova,Alex Copeland,Alicia Clum,Eric D. Becraft,Rex R. Malmstrom,Bruce W. Birren,Mircea Podar,Peer Bork,George M. Weinstock,George M. Garrity,Jeremy A. Dodsworth,Shibu Yooseph,Granger G. Sutton,Frank Oliver Gloeckner,Jack A. Gilbert,William C. Nelson,Steven J. Hallam,Sean P. Jungbluth,Sean P. Jungbluth,Thijs J. G. Ettema,Scott Tighe,Konstantinos T. Konstantinidis,Wen Tso Liu,Brett J. Baker,Thomas Rattei,Jonathan A. Eisen,Brian P. Hedlund,Katherine D. McMahon,Noah Fierer,Rob Knight,Robert D. Finn,Guy Cochrane,Ilene Karsch-Mizrachi,Gene W. Tyson,Christian Rinke,Alla Lapidus,Folker Meyer,Pelin Yilmaz,Donovan H. Parks,A. M. Eren,Lynn M. Schriml,Jillian F. Banfield,Philip Hugenholtz,Tanja Woyke +56 more
TL;DR: Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Journal ArticleDOI
Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.
Nadav Kashtan,Sara E. Roggensack,Sébastien Rodrigue,Sébastien Rodrigue,Jessie W. Thompson,Steven J. Biller,Allison Coe,Huiming Ding,Pekka Marttinen,Rex R. Malmstrom,Roman Stocker,Michael J. Follows,Ramunas Stepanauskas,Sallie W. Chisholm +13 more
TL;DR: In this paper, the authors applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus and found that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes.
Journal ArticleDOI
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
Jay McCarren,Jamie W. Becker,Daniel J. Repeta,Yanmei Shi,Curtis R. Young,Rex R. Malmstrom,Sallie W. Chisholm,Edward F. DeLong +7 more
TL;DR: The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover, suggesting that coordinated, cooperative activities of a variety of bacterial “specialists” may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
Journal ArticleDOI
Minimum information about an uncultivated virus genome (MIUVIG)
Simon Roux,Evelien M. Adriaenssens,Bas E. Dutilh,Eugene V. Koonin,Andrew M. Kropinski,Mart Krupovic,Jens H. Kuhn,Rob Lavigne,J. Rodney Brister,Arvind Varsani,Arvind Varsani,Clara Amid,Ramy K. Aziz,Seth R. Bordenstein,Peer Bork,Mya Breitbart,Guy Cochrane,Rebecca A. Daly,Christelle Desnues,Melissa B. Duhaime,Joanne B. Emerson,François Enault,Jed A. Fuhrman,Pascal Hingamp,Philip Hugenholtz,Bonnie L. Hurwitz,Natalia Ivanova,Jessica M. Labonté,Kyung Bum Lee,Rex R. Malmstrom,Manuel Martinez-Garcia,Ilene Karsch Mizrachi,Hiroyuki Ogata,David Paez-Espino,Marie-Agnès Petit,Catherine Putonti,Thomas Rattei,Alejandro Reyes,Francisco Rodriguez-Valera,Karyna Rosario,Lynn M. Schriml,Frederik Schulz,Grieg F. Steward,Matthew B. Sullivan,Shinichi Sunagawa,Curtis A. Suttle,Ben Temperton,Susannah G. Tringe,Rebecca Vega Thurber,Nicole S. Webster,Nicole S. Webster,Katrine Whiteson,Steven W. Wilhelm,K. Eric Wommack,Tanja Woyke,Kelly C. Wrighton,Pelin Yilmaz,Takashi Yoshida,Mark J. Young,Natalya Yutin,Lisa Zeigler Allen,Lisa Zeigler Allen,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +63 more
TL;DR: The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.
Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
Nadav Kashtan,Sara E. Roggen,Sébastien Rodrigue,Jessica Weidemier Thompson,Steven J. Biller,Allison Coe,Huiming Ding,Pekka Marttinen,Rex R. Malmstrom,Roman Stocker,Michael J. Follows,Ramunas Stepanauskas,Sallie W. Chisholm,Sara E. Roggensack +13 more
TL;DR: Large-scale single-cell genomics is applied to study populations of the globally abundant marine cyanobacterium Prochlorococcus to show that they are composed of hundreds of subpopulations with distinct “genomic backbones,” each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes.