Sambad - Computer Interfaces for Non-literates. - Sagun Dhakhwa; Patrick A. V. Hall; Ganesh Bahadur Ghimire; Prakash Manandhar; Ishwor Thapa (HCI (1), 2007)

Assessing the impact of refactoring activities on the JHotDraw project. - Ishwor Thapa; Harvey P. Siy (SAC, 2010)

Identifying modular function via edge annotation in gene correlation networks using Gene Ontology search. - Kathryn Dempsey; Ishwor Thapa; Dhundy Bastola; Hesham H. Ali (BIBM Workshops, 2011)

A comparison between hierarchical clustering and community detection method in the collection of gene targets for molecular identification of pathogenic fungi. - Ishwor Thapa; Sanjukta Bhowmick; Dhundy Bastola (BIBM Workshops, 2012)

A Comparison of Computational Approaches in the Molecular Identification of Pathogenic Organisms. - Dhundy Bastola; Scott McGrath; Sanjukta Bhowmick; Ishwor Thapa (HISB, 2012)

Functional identification in correlation networks using gene ontology edge annotation. - Kathryn Dempsey; Ishwor Thapa; Dhundy Bastola; Hesham H. Ali (Int. J. Comput. Biol. Drug Des., 2012)

On Mining Biological Signals Using Correlation Networks. - Kathryn Dempsey; Ishwor Thapa; Claudia Cortes; Zach Eriksen; Dhundy Bastola; Hesham H. Ali (ICDM Workshops, 2013)

On Identifying and Analyzing Significant Nodes in Protein-Protein Interaction Networks. - Rohan Khazanchi; Kathryn Dempsey; Ishwor Thapa; Hesham H. Ali (ICDM Workshops, 2013)

Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms. - Oliver Bonham-Carter; Ishwor Thapa; Dhundy Bastola (BCB, 2014)

A novel approach to identify shared fragments in drugs and natural products. - Akshay Balasubramanya; Ishwor Thapa; Dhundy Bastola; Dario Ghersi (BIBM, 2015)

Guilt-by association approach to identify novel human aging-related genes using protein domains. - Jasjit K. Banwait; Schuyler P. Dougherty; Ishwor Thapa; Dhundy Kiran Bastola (BIBM, 2015)

Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. - Ishwor Thapa; Howard S. Fox; Dhundy R. Bastola (BIBM, 2015)

Next generation sequence assembler mis-assembly of phage genomes with terminal redundancy. - Julia Warnke-Sommer; Ishwor Thapa; Hesham H. Ali (BIBM, 2015)

A systems biology approach for modeling microbiomes using split graphs. - Suyeon Kim; Ishwor Thapa; Guoqing Lu; Lifeng Zhu; Hesham H. Ali (BIBM, 2017)

A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. - Oliver Bonham-Carter; Ishwor Thapa; Steven G. From; Dhundy Bastola (Briefings Bioinform., 2017)

A Graph-Theoretic Approach for Identifying Bacterial Inter-correlations and Functional Pathways in Microbiome Data. - Suyeon Kim; Ishwor Thapa; Hesham H. Ali (BIBM, 2018)

Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage. - Qianran Li; Dario Ghersi; Ishwor Thapa; Ling Zhang; Hesham Ali 001; Kate Cooper 001 (BIBM, 2019)

A New Graph Database System for Multi-omics Data Integration and Mining Complex Biological Information. - Ishwor Thapa; Hesham Ali 001 (ICCABS, 2019)

On Identifying Candidates for Drug Repurposing for the Treatment of Ulcerative Colitis using Gene Expression Data. - Suyeon Kim; Ishwor Thapa; Ling Zhang; Hesham Ali 001 (IWBBIO (1), 2019)

FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis. - Matthew L. Hale; Ishwor Thapa; Dario Ghersi (BMC Bioinform., 2019)

Multiplatform biomarker identification using a data-driven approach enables single-sample classification. - Ling Zhang; Ishwor Thapa; Christian Haas 003; Dhundy Bastola (BMC Bioinform., 2019)

Computational Approaches for Drug Design: A Focus on Drug Repurposing. - Suyeon Kim; Ishwor Thapa; Farial Samadi; Hesham Ali 001 (IWBBIO, 2020)

Measurement of structural change in co-expression networks from cancer gene expression data. - Qianran Li; Dario Ghersi; Ishwor Thapa; Ling Zhang; Hesham Ali 001; Kate Cooper 001 (Int. J. Data Min. Bioinform., 2020)

A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics. - Ishwor Thapa; Hesham Ali 001 (J. Comput. Biol., 2021)

A multi-omics graph database for data integration and knowledge extraction. - Suyeon Kim; Ishwor Thapa; Hesham Ali 001 (BCB, 2022)

A Robust Network Model for Studying Microbiomes in Precision Agriculture Applications. - Suyeon Kim; Ishwor Thapa; Hesham H. Ali (ICCS (6), 2024)

Reproducible Gating for High-Resolution Flow Cytometric Characterization of Extracellular Vesicles in Next-Generation Biomarker Studies. - Ishwor Thapa; Yohan Kim; Fabrice Lucien; Hesham Ali 001 (BIOSTEC (1), 2025)

Explainable AI-enhanced machine learning for CBR prediction in stabilized and unstabilized subgrade soils. - Ishwor Thapa; Sufyan Ghani (Appl. Soft Comput., 2025)

Revealing the nature of soil liquefaction using machine learning. - Sufyan Ghani; Ishwor Thapa; Sunita Kumari; António Gomes Correia; Panagiotis G. Asteris (Earth Sci. Informatics, 2025)