Mark D'Souza
Mark D'Souza
University of Chicago, Argonne National Laboratory
Verified email at
Cited by
Cited by
The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes
F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, ...
BMC bioinformatics 9, 1-8, 2008
The use of gene clusters to infer functional coupling
R Overbeek, M Fonstein, M D’souza, GD Pusch, N Maltsev
Proceedings of the National Academy of Sciences 96 (6), 2896-2901, 1999
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
N Ivanova, A Sorokin, I Anderson, N Galleron, B Candelon, V Kapatral, ...
Nature 423 (6935), 87-91, 2003
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
SY Gerdes, MD Scholle, JW Campbell, G Balazsi, E Ravasz, ...
Journal of bacteriology 185 (19), 5673-5684, 2003
The genome sequence of the facultative intracellular pathogen Brucella melitensis
VG DelVecchio, V Kapatral, RJ Redkar, G Patra, C Mujer, T Los, ...
Proceedings of the National Academy of Sciences 99 (1), 443-448, 2002
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
R Overbeek, N Larsen, GD Pusch, M D’Souza, ES Jr, N Kyrpides, ...
Nucleic acids research 28 (1), 123-125, 2000
Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586
V Kapatral, I Anderson, N Ivanova, G Reznik, T Los, A Lykidis, ...
Journal of bacteriology 184 (7), 2005-2018, 2002
Searching for patterns in genomic data
M Dsouza, N Larsen, R Overbeek
Trends in Genetics 13 (12), 497–498, 1997
From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways
SY Gerdes, MD Scholle, M D'Souza, A Bernal, MV Baev, M Farrell, ...
Journal of Bacteriology 184 (16), 4555-4572, 2002
The ERGO TM genome analysis and discovery system
R Overbeek, N Larsen, T Walunas, M D'Souza, G Pusch, E Selkov Jr, ...
Nucleic acids research 31 (1), 164-171, 2003
Use of contiguity on the chromosome to predict functional coupling
R Overbeek, M Fonstein, M D'Souza, GD Pusch, N Maltsev
In Silico Biology 1 (2), 93-108, 1999
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains
A Bhattacharyya, S Stilwagen, N Ivanova, M D'Souza, A Bernal, A Lykidis, ...
Proceedings of the National Academy of Sciences 99 (19), 12403-12408, 2002
Skyport-container-based execution environment management for multi-cloud scientific workflows
W Gerlach, W Tang, K Keegan, T Harrison, A Wilke, J Bischof, M D'Souza, ...
2014 5th International Workshop on Data-Intensive Computing in the Clouds, 25-32, 2014
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
G Pesole, S Liuni, M D’Souza
Bioinformatics 16 (5), 439-450, 2000
Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights
A Bhattacharyya, S Stilwagen, G Reznik, H Feil, WS Feil, I Anderson, ...
Genome research 12 (10), 1556-1563, 2002
Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis
I Anderson, A Sorokin, V Kapatral, G Reznik, A Bhattacharya, ...
FEMS Microbiology Letters 250 (2), 175-184, 2005
A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE
KP Keegan, WL Trimble, J Wilkening, A Wilke, T Harrison, M D'Souza, ...
PLoS computational biology 8 (6), e1002541, 2012
Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586
V Kapatral, N Ivanova, I Anderson, G Reznik, A Bhattacharyya, ...
Genome research 13 (6a), 1180-1189, 2003
A RESTful API for accessing microbial community data for MG-RAST
A Wilke, J Bischof, T Harrison, T Brettin, M D'Souza, W Gerlach, ...
PLoS computational biology 11 (1), e1004008, 2015
PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways
N Maltsev, E Glass, D Sulakhe, A Rodriguez, MH Syed, T Bompada, ...
Nucleic acids research 34 (suppl_1), D369-D372, 2006
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