Steven J. Hallam

Publication Activity (10 Years)

Years Active: 2013-2022
Publications (10 Years): 15

Top Topics

Inter Annotator Agreement

Metabolic Pathways

Visualization Tool

Top Venues

PLoS Comput. Biol.

Publications

Abdur Rahman Mohd Abul Basher, Steven J. Hallam
Aggregating Statistically Correlated Metabolic Pathways Into Groups to Improve Prediction Performance. BIOINFORMATICS (2022)
Sarah E. I. Perez, Aria S. Hahn, Martin Krzywinski, Steven J. Hallam
Hive Panel Explorer: an interactive network visualization tool. Bioinform. 37 (3) (2021)
Kimberly A. Dill-McFarland, Stephan G. König, Florent Mazel, David C. Oliver, Lisa M. McEwen, Kris Y. Hong, Steven J. Hallam
An integrated, modular approach to data science education in microbiology. PLoS Comput. Biol. 17 (2) (2021)
Abdur Rahman Mohd Abul Basher, Ryan McLaughlin, Steven J. Hallam
Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. J. Comput. Biol. 28 (11) (2021)
Abdur Rahman Mohd Abul Basher, Steven J. Hallam
Relabeling Metabolic Pathway Data with Groups to Improve Prediction Outcomes. ICCABS (2021)
Abdur Rahman Mohd Abul Basher, Steven J. Hallam
Leveraging heterogeneous network embedding for metabolic pathway prediction. Bioinform. 37 (6) (2021)
Abdur Rahman Mohd Abul Basher, Ryan McLaughlin, Steven J. Hallam
Metabolic Pathway Prediction using Non-negative Matrix Factorization with Improved Precision. ICCABS (2020)
Abdur Rahman Mohd Abul Basher, Ryan J. McLaughlin, Steven J. Hallam
Metabolic pathway inference using multi-label classification with rich pathway features. PLoS Comput. Biol. 16 (10) (2020)
Connor Morgan-Lang, Ryan McLaughlin, Zachary Armstrong, Grace Zhang, Kevin Chan, Steven J. Hallam
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler. Bioinform. 36 (18) (2020)
A. 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, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine D. McMahon, Steven J. Hallam, Vincent J. Denef, Ricardo Cavicchioli, Sean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, João C. Setubal, Phillip B. Pope, Wen-Tso Liu, Adam R. Rivers, Natalia Ivanova, Nikos Kyrpides
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 45 (Database-Issue) (2017)
Niels W. Hanson, Kishori M. Konwar, Steven J. Hallam
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. Bioinform. 32 (23) (2016)
Dongjae Kim, Aria S. Hahn, Niels W. Hanson, Kishori M. Konwar, Steven J. Hallam
FAST: Fast annotation with synchronized threads. CIBCB (2016)
Aria S. Hahn, Niels W. Hanson, Dongjae Kim, Kishori M. Konwar, Steven J. Hallam
Assembly independent functional annotation of short-read data using SOFA: Short-ORF functional annotation. CIBCB (2015)
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
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. Bioinform. 31 (20) (2015)
Dongjae Kim, Aria S. Hahn, Shang-Ju Wu, Niels W. Hanson, Kishori M. Konwar, Steven J. Hallam
FragGeneScan-plus for scalable high-throughput short-read open reading frame prediction. CIBCB (2015)
Niels W. Hanson, Kishori M. Konwar, Shang-Ju Wu, Steven J. Hallam
MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds. CIBCB (2014)
Kishori M. Konwar, Niels W. Hanson, Antoine P. Pagé, Steven J. Hallam
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinform. 14 (2013)
Inna Rytsareva, Ananth Kalyanaraman, Kishori M. Konwar, Steven J. Hallam
Scalable heuristics for clustering biological graphs. ICCABS (2013)
W. Evan Durno, Niels W. Hanson, Kishori M. Konwar, Steven J. Hallam
Expanding the boundaries of local similarity analysis. BMC Genom. 14 (S-1) (2013)