MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. - Kishori M. Konwar; Niels W. Hanson; Antoine P. Pagé; Steven J. Hallam (BMC Bioinform., 2013)

Expanding the boundaries of local similarity analysis. - W. Evan Durno; Niels W. Hanson; Kishori M. Konwar; Steven J. Hallam (BMC Genom., 2013)

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds. - Niels W. Hanson; Kishori M. Konwar; Shang-Ju Wu; Steven J. Hallam (CIBCB, 2014)

Assembly independent functional annotation of short-read data using SOFA: Short-ORF functional annotation. - Aria S. Hahn; Niels W. Hanson; Dongjae Kim; Kishori M. Konwar; Steven J. Hallam (CIBCB, 2015)

FragGeneScan-plus for scalable high-throughput short-read open reading frame prediction. - Dongjae Kim; Aria S. Hahn; Shang-Ju Wu; Niels W. Hanson; Kishori M. Konwar; Steven J. Hallam (CIBCB, 2015)

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. - Kishori M. Konwar; Niels W. Hanson; Maya P. Bhatia; Dongjae Kim; Shang-Ju Wu; Aria S. Hahn; Connor Morgan-Lang; Hiu Kan Cheung; Steven J. Hallam (Bioinform., 2015)

FAST: Fast annotation with synchronized threads. - Dongjae Kim; Aria S. Hahn; Niels W. Hanson; Kishori M. Konwar; Steven J. Hallam (CIBCB, 2016)

LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. - Niels W. Hanson; Kishori M. Konwar; Steven J. Hallam (Bioinform., 2016)