M
Michael Fonstein
Researcher at University of Chicago
Publications - 31
Citations - 7358
Michael Fonstein is an academic researcher from University of Chicago. The author has contributed to research in topics: Genome & Cosmid. The author has an hindex of 19, co-authored 31 publications receiving 7058 citations. Previous affiliations of Michael Fonstein include University of Illinois at Chicago & Institut national de la recherche agronomique.
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Journal ArticleDOI
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Ross Overbeek,Tadhg P. Begley,Ralph Butler,Jomuna V. Choudhuri,Han-Yu Chuang,Matthew P. Cohoon,Valérie de Crécy-Lagard,Naryttza N. Diaz,Terry Disz,Robert D. Edwards,Robert D. Edwards,Michael Fonstein,Ed D. Frank,Svetlana Gerdes,Elizabeth M. Glass,Alexander Goesmann,Andrew C. Hanson,Dirk Iwata-Reuyl,Roy A. Jensen,Neema Jamshidi,Lutz Krause,Michael Kubal,Niels Bent Larsen,Burkhard Linke,Alice C. McHardy,Folker Meyer,Heiko Neuweger,Gary J. Olsen,Robert Olson,Andrei L. Osterman,Vasiliy A. Portnoy,Gordon D. Pusch,Dmitry A. Rodionov,Christian Rückert,Jason Steiner,Rick Stevens,Rick Stevens,Ines Thiele,Olga Vassieva,Yuzhen Ye,Olga Zagnitko,Veronika Vonstein +41 more
TL;DR: The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
Journal ArticleDOI
The use of gene clusters to infer functional coupling
TL;DR: The characterization of the parameters that determine the utility of the approach are extended, and it is shown that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.
Journal ArticleDOI
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
Natalia Ivanova,Alexei Sorokin,Iain Anderson,Nathalie Galleron,Benjamin Candelon,Vinayak Kapatral,Anamitra Bhattacharyya,Gary Reznik,Natalia Mikhailova,Alla Lapidus,Lien Chu,Michael Mazur,Eugene Goltsman,Niels Bent Larsen,Mark D'Souza,Theresa L. Walunas,Yuri Grechkin,Gordon D. Pusch,Robert Haselkorn,Michael Fonstein,S. Dusko Ehrlich,Ross Overbeek,Nikos C. Kyrpides +22 more
TL;DR: The sequencing and analysis of the type strain B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables the comparative analysis to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.
Journal ArticleDOI
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
Svetlana Gerdes,Michael D. Scholle,James W. Campbell,Gábor Balázsi,Erzsébet Ravasz,Matthew D. Daugherty,A. L. Somera,Nikos C. Kyrpides,Iain Anderson,Mikhail S. Gelfand,A. Bhattacharya,Vinayak Kapatral,Mark D'Souza,Mark V. Baev,Yuri Grechkin,Faika Mseeh,Michael Fonstein,Ross Overbeek,Albert-László Barabási,Zoltán N. Oltvai,Andrei L. Osterman +20 more
TL;DR: A genetic footprinting technique is used for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media to identify 620 genes as essential and 3,126 genes as dispensable for growth under these conditions.
Journal ArticleDOI
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus
Alexander Bolotin,Benoit Quinquis,Pierre Renault,Alexei Sorokin,S. Dusko Ehrlich,Saulius Kulakauskas,Alla Lapidus,Eugene Goltsman,Michael Mazur,Gordon D. Pusch,Michael Fonstein,Ross Overbeek,Nikos Kyprides,Bénédicte Purnelle,Deborah Prozzi,Katrina Ngui,Katrina Ngui,David Masuy,Frédéric Hancy,Sophie Burteau,Sophie Burteau,Marc Boutry,Jean Delcour,André Goffeau,Pascal Hols +24 more
TL;DR: It is concluded that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.