J
Jeff Froula
Researcher at Joint Genome Institute
Publications - 18
Citations - 3624
Jeff Froula is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Metagenomics & Genome. The author has an hindex of 12, co-authored 18 publications receiving 2876 citations. Previous affiliations of Jeff Froula include United States Department of Energy & Lawrence Berkeley National Laboratory.
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Journal ArticleDOI
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
TL;DR: MetaBAT as mentioned in this paper integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning, and automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs.
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Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Journal ArticleDOI
Positional cloning of ZNF217 and NABC1: Genes amplified at 20q13.2 and overexpressed in breast carcinoma
Colin Collins,Johanna M. Rommens,David Kowbel,Tony E. Godfrey,Minna Tanner,Soo In Hwang,Daniel Polikoff,Genevieve Nonet,Joanne Cochran,Ken Myambo,Karen E. Jay,Jeff Froula,Thomas Cloutier,Wen Lin Kuo,Paul Yaswen,Shanaz H. Dairkee,Jennifer Giovanola,Gordon B. Hutchinson,Jorma Isola,Olli Kallioniemi,Mike Palazzolo,Christopher Martin,Cheryl L. Ericsson,Daniel Pinkel,Daniel Pinkel,Donna G. Albertson,Donna G. Albertson,Wu Bo Li,Joe W. Gray,Joe W. Gray +29 more
TL;DR: The molecular cloning of an approximately 1-Mb region of recurrent amplification at 20q13.2 in breast cancer and other tumors and the delineation of a 260-kb common region of amplification are reported.
Journal ArticleDOI
The Epigenomic Landscape of Prokaryotes
Matthew J. Blow,Matthew J. Blow,Tyson A. Clark,Chris Daum,Chris Daum,Adam M. Deutschbauer,Alexey Fomenkov,Roxanne Fries,Roxanne Fries,Jeff Froula,Jeff Froula,Dongwan D. Kang,Dongwan D. Kang,Rex R. Malmstrom,Rex R. Malmstrom,Richard D. Morgan,Janos Posfai,Kanwar Singh,Kanwar Singh,Axel Visel,Axel Visel,Kelly M. Wetmore,Zhiying Zhao,Zhiying Zhao,Edward M. Rubin,Edward M. Rubin,Jonas Korlach,Len A. Pennacchio,Len A. Pennacchio,Richard J. Roberts +29 more
TL;DR: The results reveal the pervasive presence ofDNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
Journal ArticleDOI
Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
Weibing Shi,Christina D. Moon,Sinead C. Leahy,Dongwan D. Kang,Dongwan D. Kang,Jeff Froula,Jeff Froula,Sandra Kittelmann,Christina Fan,Christina Fan,Samuel Deutsch,Samuel Deutsch,Dragana Gagic,Henning Seedorf,William J. Kelly,Renee Atua,Carrie Sang,Priya Soni,Dong Li,C. S. Pinares-Patiño,John C. McEwan,Peter H. Janssen,Feng Chen,Feng Chen,Axel Visel,Zhong Wang,Zhong Wang,Zhong Wang,Graeme T. Attwood,Edward M. Rubin,Edward M. Rubin +30 more
TL;DR: A discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields are identified and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.