Mark D'Souza

William L. Trimble, Kevin P. Keegan, Mark D'Souza, Andreas Wilke, Jared Wilkening, Jack A. Gilbert, Folker Meyer: Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics 13: 183 (2012)

Kevin P. Keegan, William L. Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer: A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE. PLoS Computational Biology 8(6) (2012)

Folker Meyer, Daniel Paarmann, Mark D'Souza, Robert Olson, Elizabeth M. Glass, Michael Kubal, Tobias Paczian, Alexis A. Rodriguez, Rick Stevens, Andreas Wilke, Jared Wilkening, Robert A. Edwards: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9 (2008)

Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin: Sentra: a database of signal transduction proteins for comparative genome analysis. Nucleic Acids Research 35(Database-Issue): 271-273 (2007)

Natalia Maltsev, Elizabeth M. Glass, Dinanath Sulakhe, Alexis A. Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, Mark D'Souza: PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Research 34(Database-Issue): 369-372 (2006)

Dinanath Sulakhe, Alex Rodriguez, Mark D'Souza, Michael Wilde, Veronika Nefedova, Ian T. Foster, Natalia Maltsev: GNARE: an environment for grid-based high-throughput genome analysis. CCGRID 2005: 455-462

Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides: The ERGOTM genome analysis and discovery system. Nucleic Acids Research 31(1): 164-171 (2003)

Graziano Pesole, Sabino Liuni, Mark D'Souza: PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 16(5): 439-450 (2000)

Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, Mark D'Souza, Evgeni Selkov Jr., Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, Evgeni Selkov: WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Research 28(1): 123-125 (2000)

Mark D'Souza, Margaret F. Romine, Natalia Maltsev: SENTRA, a database of signal transduction proteins. Nucleic Acids Research 28(1): 335-336 (2000)

Ross A. Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch, Natalia Maltsev: Use of contiguity on the chromosome to predict functional coupling. In Silico Biology 1: 9 (1998)