Publications

2025

• Ishwor Thapa, Yohan Kim, Fabrice Lucien, Hesham Ali. Reproducible Gating for High-Resolution Flow Cytometric Characterization of Extracellular Vesicles in Next-Generation Biomarker Studies. Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOSIGNALS. 2025. DOI: 10.5220/0013318900003911.
• Ishwor Thapa, Yohan Kim, Fabrice Lucien, Hesham Ali. A Knowledge Graph Model for Analyzing microRNAs in Extracellular Vesicles Data. Proceedings of the 14th International Conference on Complex Networks and their Applications. 2025.

2024

• Suyeon Kim, Ishwor Thapa, Hesham H Ali. A Robust Network Model for Studying Microbiomes in Precision Agriculture Applications. International Conference on Computational Science. 2024.
• Suyeon Kim, Ishwor Thapa, Hesham Ali. A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes. BMC microbiology. 2024.
• Caleb J Pecka, Ishwor Thapa, Amar B Singh, Dhundy Bastola. A computational approach to demonstrate the control of gene expression via chromosomal access in colorectal cancer. BioMedInformatics. 2024.

2023

• Raju Lama Tamang, Balawant Kumar, Sagar M Patel, Ishwor Thapa, Alshomrani Ahmad, Vikas Kumar, Rizwan Ahmad, Donald F Becker, Dundy Bastola, Punita Dhawan, others. Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Carcinogenesis by Modulating Microtubule-Associated Serine/Threonine Kinase-like/Wnt/$\beta$-Catenin Signaling. Cells. 2023.
• Ishwor Thapa, Dario Ghersi. Modeling preferential attraction to infected hosts in vector-borne diseases. Frontiers in Public Health. 2023.
• Rizwan Ahmad, Balawant Kumar, Ishwor Thapa, Geoffrey A Talmon, Jeffrey Salomon, Amanda E Ramer-Tait, Dhundy K Bastola, Punita Dhawan, Amar B Singh. Loss of claudin-3 expression increases colitis risk by promoting Gut Dysbiosis. Gut Microbes. 2023.
• Fransenio Clark, Anna Gil, Ishwor Thapa, Nuray Aslan, Dario Ghersi, Liisa K Selin. Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old. Frontiers in Immunology. 2023.
• Rizwan Ahmad, Balawant Kumar, Ishwor Thapa, Raju Lama Tamang, Santosh K Yadav, Mary K Washington, Geoffrey A Talmon, S Yu Alan, Dhundy K Bastola, Punita Dhawan, others. Claudin-2 protects against colitis-associated cancer by promoting colitis-associated mucosal healing. The Journal of Clinical Investigation. 2023.
• Matthew Beaver, Dragana Noe, Ishwor Thapa, Hesham Ali, Jessica Snowden, Tammy Kielian, Gwenn L Skar. Bacteria commonly associated with central nervous system catheter infections elicit distinct CSF proteome signatures. Frontiers in Neurology. 2023.

2022

• Fabrice Lucien, Yohan Kim, Jing Qian, Jacob J Orme, Henan Zhang, Ali Arafa, Feven Abraha, Ishwor Thapa, Erik J Tryggestad, William S Harmsen, others. Tumor-derived extracellular vesicles predict clinical outcomes in oligometastatic prostate cancer and suppress antitumor immunity. International Journal of Radiation Oncology Biology* Physics*. 2022.
• Yohan Kim, Edwin Van Der Pol, Ali Arafa, Ishwor Thapa, Cameron J Britton, Jorgena Kosti, Siyang Song, Vidhu B Joshi, Ree M Erickson, Hesham Ali, others. Calibration and standardization of extracellular vesicle measurements by flow cytometry for translational prostate cancer research. Nanoscale. 2022.

2021

• Naveenkumar Perumal, Ranjana K Kanchan, David Doss, Noah Bastola, Pranita Atri, Ramakanth Chirravuri-Venkata, Ishwor Thapa, Raghupathy Vengoji, Shailendra K Maurya, David Klinkebiel, others. MiR-212-3p functions as a tumor suppressor gene in group 3 medulloblastoma via targeting nuclear factor I/B (NFIB). Acta neuropathologica communications. 2021.
• Matthew Beaver, Dragana Lagundzin, Ishwor Thapa, Junghyae Lee, Hesham Ali, Tammy Kielian, Gwenn L Skar. Cutibacterium acnes central nervous system catheter infection induces long-term changes in the cerebrospinal fluid proteome. Infection and immunity. 2021.
• Ishwor Thapa, Hesham Ali. A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics. Journal of Computational Biology. 2021.
• Saiprasad Gowrikumar, Mark Primeaux, Kristina Pravoverov, Chao Wu, Bryan C Szeglin, Charles-Etienne Gabriel Sauve, Ishwor Thapa, Dhundy Bastola, Xi Steven Chen, J Joshua Smith, others. A claudin-based molecular signature identifies high-risk, chemoresistant colorectal cancer patients. Cells. 2021.

2020

• Ranjana K Kanchan, Naveenkumar Perumal, Pranita Atri, Ramakanth Chirravuri Venkata, Ishwor Thapa, David Klinkebiel, Andrew M Donson, Deborah Perry, Michael Punsoni, Geoffrey Talmon, others. MiR-1253 exerts tumor suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3). Brain Pathology. 2020.
• Ishwor Thapa, Hesham Ali. A New Graph Database System for Multi-omics Data Integration and Mining Complex Biological Information. Computational Advances in Bio and Medical Sciences. 2020.

2019

• Suyeon Kim, Ishwor Thapa, Ling Zhang, Hesham Ali. On Identifying Candidates for Drug Repurposing for the Treatment of Ulcerative Colitis using Gene Expression Data. International Work-Conference on Bioinformatics and Biomedical Engineering. 2019.
• Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola. Multiplatform biomarker identification using a data-driven approach enables single-sample classification. BMC bioinformatics. 2019.
• Qianran Li, Dario Ghersi, Ishwor Thapa, Ling Zhang, Hesham Ali, Kate Cooper. Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2019.
• Gwenn L Skar, Matthew Beaver, Amy Aldrich, Dragana Lagundzin, Ishwor Thapa, Nicholas Woods, Hesham Ali, Jessica Snowden, Tammy Kielian. Identification of potential cerebrospinal fluid biomarkers to discriminate between infection and sterile inflammation in a rat model of Staphylococcus epidermidis catheter infection. Infection and immunity. 2019.
• Matthew L Hale, Ishwor Thapa, Dario Ghersi. FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis. BMC Bioinformatics. 2019.
• Suyeon Kim, Ishwor Thapa, Ling Zhang, Hesham Ali. A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships. BMC genomics. 2019.

2018

• Seema Chugh, Srikanth Barkeer, Satyanarayana Rachagani, Rama Krishna Nimmakayala, Naveenkumar Perumal, Ramesh Pothuraju, Pranita Atri, Sidharth Mahapatra, Ishwor Thapa, Geoffrey A Talmon, others. Disruption of C1galt1 Gene Promotes Development and Metastasis of Pancreatic Adenocarcinomas in Mice. Gastroenterology. 2018.

2017

• CM Thompson, S Kumar, D Ghersi, R Chirravuri, I Thapa, L Smith, SK Batra. Analysis of Clinical Significance of MUC4 Isoforms in Pancreatic Cancer Patients Using TCGA RNA-Seq Dataset. PANCREAS. 2017.
• Suyeon Kim, Ishwor Thapa, Guoqing Lu, Lifeng Zhu, Hesham H Ali. A systems biology approach for modeling microbiomes using split graphs. Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2017.

2016

• Sunandini Sharma, Kritika Karri, Ishwor Thapa, Dhundy Bastola, Dario Ghersi. Identifying enriched drug fragments as possible candidates for metabolic engineering. BMC Medical Genomics. 2016.
• Oliver Bonham-Carter, Ishwor Thapa, Steven From, Dhundy Bastola. A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. Briefings in bioinformatics. 2016.

2015

• Ishwor Thapa, Howard S Fox, Dhundy R Bastola. Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015.
• Sowmya V Yelamanchili, B Morsey, Emily B Harrison, DA Rennard, K Emanuel, I Thapa, DR Bastola, HS Fox. The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins. Cell death & disease. 2015.
• Peter C Iwen, Ishwor Thapa, Dhundy Bastola. Review of methods for the identification of zygomycetes with an emphasis on advances in molecular diagnostics. Laboratory Medicine. 2015.
• Julia Warnke-Sommer, Ishwor Thapa, Hesham Ali. Next generation sequence assembler mis-assembly of phage genomes with terminal redundancy. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015.
• Sergios Charntikov, Steven T Pittenger, Ishwor Thapa, Dhundy R Bastola, Rick A Bevins, Gurudutt Pendyala. Ibudilast reverses the decrease in the synaptic signaling protein phosphatidylethanolamine-binding protein 1 (PEBP1) produced by chronic methamphetamine intake in rats. Drug & Alcohol Dependence. 2015.
• Jasjit K Banwait, Schuyler P Dougherty, Ishwor Thapa, Dhundy K Bastola. Guilt-by association approach to identify novel human aging-related genes using protein domains. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015.
• Ishwor Thapa, Howard S Fox, Dhundy Bastola. Coexpression network analysis of miRNA-142 overexpression in neuronal cells. BioMed research international. 2015.
• Akshay Balasubramanya, Ishwor Thapa, Dhundy Bastola, Dario Ghersi. A novel approach to identify shared fragments in drugs and natural products. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015.

2014

• Oliver Bonham-Carter, Ishwor Thapa, Dhundy Bastola. Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2014.

2013

• Kathryn Dempsey Cooper, Ishwor Thapa, Claudia Cortes, Zack Eriksen, Dhundy Raj Bastola, Hesham Ali. On Mining Biological Signals Using Correlation Networks. 2013.
• Kathryn Dempsey, Ishwor Thapa, Claudia Cortes, Zach Eriksen, Dhundy K Bastola, Hesham Ali. On Mining Biological Signals Using Correlation Networks. Proceedings of the 2013 IEEE 13th International Conference onData Mining Workshops (ICDMW). 2013.
• Rohan Khazanchi, Kathryn Dempsey, Ishwor Thapa, Hesham Ali. On Identifying and Analyzing Significant Nodes in Protein-Protein Interaction Networks. Proceedings of the 2013 IEEE 13th International Conference on Data Mining Workshops (ICDMW). 2013.
• Kendall A Bryant, Trevor C Van Schooneveld, Ishwor Thapa, Dhundy Bastola, Laurina O Williams, Thomas J Safranek, Steven H Hinrichs, Mark E Rupp, Paul D Fey. KPC-4 Is Encoded within a Truncated Tn4401 in an IncL/M Plasmid, pNE1280, Isolated from Enterobacter cloacae and Serratia marcescens. Antimicrobial agents and chemotherapy. 2013.

2012

• Marcus Lyon, Mark V Wilson, Kerry A Rouhier, David J Symonsbergen, Kiran Bastola, Ishwor Thapa, Andrea E Holmes, Sharmin M Sikich, Abby Jackson. Image Analysis of DETECHIP\textregistered–A Molecular Sensing Array. Advances in Computer Science, Engineering & Applications. 2012.
• Kathryn Dempsey, Ishwor Thapa, Dhundy Bastola, Hesham Ali. Functional identification in correlation networks using gene ontology edge annotation. International journal of computational biology and drug design. 2012.
• Marcus Lyon, Mark V Wilson, Kerry A Rouhier, David J Symonsbergen, Kiran Bastola, Ishwor Thapa, Andrea E Holmes, Sharmin M Sikich, Abby Jackson. Digital Image Analysis for DETCHIP\textregistered Code Determination. Signal and image processing: an international journal. 2012.
• Tom'a\vs Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, others. Bio-logic builder: a non-technical tool for building dynamical, qualitative models. PloS one. 2012.
• Oliver Bonham-Carter, Lotfollah Najjar, Ishwor Thapa, Dhundy Bastola. An analysis of palindromic content in the genic and intergenic regions of bacterial genomes. 2012.
• Dhundy R Bastola, Scott McGrath, Sanjukta Bhowmick, Ishwor Thapa. A Comparison of Computational Approaches in the Molecular Identification of Pathogenic Organisms. Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB). 2012.
• Ishwor Thapa, Sanjukta Bhowmick, Dhundy R Bastola. A comparison between hierarchical clustering and community detection method in the collection of gene targets for molecular identification of pathogenic fungi. Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). 2012.

2011

• Kathryn Dempsey, Ishwor Thapa, Dhundy Bastola, Hesham Ali. Identifying modular function via edge annotation in gene correlation networks using Gene Ontology search. Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). 2011.

2010

• Ishwor Thapa, Harvey Siy. Assessing the impact of refactoring activities on the JHotDraw project. Proceedings of the 2010 ACM Symposium on Applied Computing. 2010.

2009

• Ishwor Thapa. Identifying and assessing the impact of refactoring by mining version repositories. University of Nebraska at Omaha. 2009.

2007

• Sagun Dhakhwa, Patrick AV Hall, Ganesh Bahadur Ghimire, Prakash Manandhar, Ishwor Thapa. Sambad–Computer Interfaces for Non-literates. International Conference on Human-Computer Interaction. 2007.