M
Mark D'Souza
Researcher at University of Chicago
Publications - 46
Citations - 9577
Mark D'Souza is an academic researcher from University of Chicago. The author has contributed to research in topics: Genome & Medicine. The author has an hindex of 25, co-authored 37 publications receiving 9013 citations. Previous affiliations of Mark D'Souza include Argonne National Laboratory.
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Journal ArticleDOI
The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
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.
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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.
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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.
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The genome sequence of the facultative intracellular pathogen Brucella melitensis
Vito G. DelVecchio,Vinayak Kapatral,Rajendra J. Redkar,Guy Patra,Cesar V. Mujer,Tamara Los,Natalia Ivanova,Iain Anderson,Anamitra Bhattacharyya,Athanasios Lykidis,Gary Reznik,Lynn Jablonski,Niels Bent Larsen,Mark D'Souza,Axel Bernal,Mikhail Mazur,Eugene Goltsman,Eugene Selkov,Philip H. Elzer,Sue D. Hagius,David O'Callaghan,Jean-Jacques Letesson,Robert Haselkorn,Nikos C. Kyrpides,Ross Overbeek +24 more
TL;DR: The genome of B. melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes encoding 3,197 ORFs, similar to other α-proteobacteria.