Scalable heuristics for clustering biological graphs. - Inna Rytsareva; Ananth Kalyanaraman; Kishori M. Konwar; Steven J. Hallam (ICCABS, 2013)

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)

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. - David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Ernest Szeto; Manoj Pillay; Jinghua Huang; Victor M. Markowitz; Torben Nielsen; Marcel Huntemann; T. B. K. Reddy; et al. (Nucleic Acids Res., 2017)

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler. - Connor Morgan-Lang; Ryan J. McLaughlin; Zachary Armstrong; Grace Zhang; Kevin Chan; Steven J. Hallam (Bioinform., 2020)

Metabolic pathway inference using multi-label classification with rich pathway features. - Abdur Rahman Mohd Abul Basher; Ryan J. McLaughlin; Steven J. Hallam (PLoS Comput. Biol., 2020)

Relabeling Metabolic Pathway Data with Groups to Improve Prediction Outcomes. - Abdur Rahman Mohd Abul Basher; Steven J. Hallam (ICCABS, 2021)

Leveraging heterogeneous network embedding for metabolic pathway prediction. - Abdur Rahman Mohd Abul Basher; Steven J. Hallam (Bioinform., 2021)

Hive Panel Explorer: an interactive network visualization tool. - Sarah E. I. Perez; Aria S. Hahn; Martin Krzywinski; Steven J. Hallam (Bioinform., 2021)

Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. - Abdur Rahman Mohd Abul Basher; Ryan J. McLaughlin; Steven J. Hallam (J. Comput. Biol., 2021)

An integrated, modular approach to data science education in microbiology. - Kimberly A. Dill-McFarland; Stephan G. König; Florent Mazel; David C. Oliver; Lisa M. McEwen; Kris Y. Hong; Steven J. Hallam (PLoS Comput. Biol., 2021)

Aggregating Statistically Correlated Metabolic Pathways Into Groups to Improve Prediction Performance. - Abdur Rahman Mohd Abul Basher; Steven J. Hallam (BIOINFORMATICS, 2022)