Use of contiguity on the chromosome to predict functional coupling. - Ross A. Overbeek; Michael Fonstein; Mark D'Souza; Gordon D. Pusch; Natalia Maltsev (Silico Biol., 1998)

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

SENTRA, a database of signal transduction proteins. - Mark D'Souza; Margaret F. Romine; Natalia Maltsev (Nucleic Acids Res., 2000)

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

The ERGOTM genome analysis and discovery system. - 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; et al. (Nucleic Acids Res., 2003)

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

PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. - Natalia Maltsev; Elizabeth M. Glass; Dinanath Sulakhe; Alexis A. Rodriguez; Mustafa H. Syed; Tanuja Bompada; Yi Zhang 002; Mark D'Souza (Nucleic Acids Res., 2006)

Sentra: a database of signal transduction proteins for comparative genome analysis. - Mark D'Souza; Elizabeth M. Glass; Mustafa H. Syed; Yi Zhang 002; Alexis A. Rodriguez; Natalia Maltsev; Michael Y. Galperin (Nucleic Acids Res., 2007)

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. - 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 (BMC Bioinform., 2008)

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

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

Skyport: container-based execution environment management for multi-cloud scientific workflows. - Wolfgang Gerlach; Wei Tang 001; Kevin P. Keegan; Travis Harrison; Andreas Wilke; Jared Bischof; Mark D'Souza; Scott Devoid; Daniel E. Murphy-Olson; Narayan Desai; Folker Meyer (DataCloud@SC, 2014)

A RESTful API for Accessing Microbial Community Data for MG-RAST. - Andreas Wilke; Jared Bischof; Travis Harrison; Tom Brettin; Mark D'Souza; Wolfgang Gerlach; Hunter Matthews; Tobias Paczian; Jared Wilkening; Elizabeth M. Glass; Narayan Desai; Folker Meyer (PLoS Comput. Biol., 2015)

Lynx: a knowledge base and an analytical workbench for integrative medicine. - Dinanath Sulakhe; Bingqing Xie; Andrew Taylor; Mark D'Souza; Sandhya Balasubramanian; Somaye Hashemifar; Steven White; Utpal J. Dave; Gady Agam; Jinbo Xu; Sheng Wang 001; T. Conrad Gilliam; et al. (Nucleic Acids Res., 2016)

Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. - Dinanath Sulakhe; Mark D'Souza; Sheng Wang 001; Sandhya Balasubramanian; Prashanth Athri; Bingqing Xie; Stefan Canzar; Gady Agam; T. Conrad Gilliam; Natalia Maltsev (Briefings Bioinform., 2019)