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  2021 (4)
DeepACPpred: A Novel Hybrid CNN-RNN Architecture for Predicting Anti-Cancer Peptides. Lane, N.; and Kahanda, I. In Panuccio, G.; Rocha, M.; Fdez-Riverola, F.; Mohamad, M. S.; and Casado-Vara, R., editor(s), Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020), pages 60–69, Cham, 2021. Springer International Publishing
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Vegetation Coverage in Marsh Grass Photography Using Convolutional Neural Networks. Welch, L. W.; Liu, X.; Kahanda, I.; Reddivari, S.; and Umapathy, K. In The International FLAIRS Conference Proceedings, volume 34, 2021.
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Automatically Cataloging Scholarly Articles using Library of Congress Subject Headings. Kazi, N.; Lane, N.; and Kahanda, I. In Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Student Research Workshop, pages 43–49, 2021.
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Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping. Li, H.; Hu, X.; Lovell, J. T; Grabowski, P. P; Mamidi, S.; Chen, C.; Amirebrahimi, M.; Kahanda, I.; Mumey, B.; Barry, K.; and others The Plant Genome,e20110. 2021.
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  2020 (5)
ProPheno 1.0: An Online Dataset for Accelerating the Complete Characterization of the Human Protein-Phenotype Landscape in Biomedical Literature. Pourreza Shahri, M.; and Kahanda, I. In 2020 IEEE 14th International Conference on Semantic Computing (ICSC), pages 416-423, 2020.
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RDoCer: Information Retrieval and Sentence Extraction for Mental Health using Research Domain Criteria. Laden, D.; Jayasundara, S.; and Kahanda, I. In 2020 IEEE 14th International Conference on Semantic Computing (ICSC), pages 226-229, Los Alamitos, CA, USA, feb 2020. IEEE Computer Society
RDoCer: Information Retrieval and Sentence Extraction for Mental Health using Research Domain Criteria [link]Paper   doi   bibtex  
miRNAFinder: A pre-microRNA classifier for plants and analysis of feature impact. Ihalagedara, P.; Lokuge, S.; Jayasundara, S.; Herath, D.; and Kahanda, I. In 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pages 1-7, Oct 2020.
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MRpredT: Using Text Mining for Metamorphic Relation Prediction. Rahman, K.; Kahanda, I.; and Kanewala, U. In Proceedings of the IEEE/ACM 42nd International Conference on Software Engineering Workshops, of ICSEW'20, pages 420–424, New York, NY, USA, 2020. Association for Computing Machinery
MRpredT: Using Text Mining for Metamorphic Relation Prediction [link]Paper   doi   bibtex   abstract  
BRret: Retrieval of Brain Research Related Literature. Anani, M.; Kuntz, M.; and Kahanda, I. AMIA Summits on Translational Science Proceedings, 2020: 53. 2020.
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  2019 (8)
PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature. Pourreza Shahri, M.; Reynolds, G.; Roe, M. M.; and Kahanda, I. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, of BCB '19, pages 414–422, New York, NY, USA, 2019. ACM
PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature [link]Paper   doi   bibtex  
Automatically Generating Psychiatric Case Notes From Digital Transcripts of Doctor-Patient Conversations. Kazi, N.; and Kahanda, I. In Proceedings of the 2nd Clinical Natural Language Processing Workshop, pages 140–148, Minneapolis, Minnesota, USA, June 2019. Association for Computational Linguistics
Automatically Generating Psychiatric Case Notes From Digital Transcripts of Doctor-Patient Conversations [link]Paper   bibtex   abstract  
Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools. Shahri, M. P.; Srinivasan, M.; Reynolds, G.; Bimczok, D.; Kahanda, I.; and Kanewala, U. In 2019 IEEE International Conference On Artificial Intelligence Testing (AITest), pages 140–148, 2019. IEEE
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Board 11: Predicting At-Risk Students in a Circuit Analysis Course Using Supervised Machine Learning. James P. Becker, E. S.; and Kahanda, I. In 2019 ASEE Annual Conference & Exposition, Tampa, Florida, June 2019. ASEE Conferences https://peer.asee.org/32185
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Pangenome-Wide Association Studies with Frequented Regions. Manuweera, B.; Mudge, J.; Kahanda, I.; Ramaraj, T.; Cleary, A.; and Mumey, B. 2019. Manuscript submitted for publication.
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RDoC Task at BioNLP-OST 2019. Anani, M.; Kazi, N.; Kuntz, M.; and Kahanda, I. In Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, pages 216–226, Hong Kong, China, November 2019. Association for Computational Linguistics
RDoC Task at BioNLP-OST 2019 [link]Paper   doi   bibtex   abstract  
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Zhou, N.; Jiang, Y.; Bergquist, T. R; Lee, A. J; Kacsoh, B. Z; Crocker, A. W; Lewis, K. A; Georghiou, G.; Nguyen, H. N; Hamid, M. N.; and others Genome biology, 20(1): 1–23. 2019.
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Computational methods for the ab initio identification of novel microRNA in plants: a systematic review. Manuweera, B.; Reynolds, G.; and Kahanda, I. PeerJ Computer Science, 5: e233. 2019.
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  2018 (6)
Extracting Co-mention Features from Biomedical Literature for Automated Protein Phenotype Prediction using PHENOstruct. Shahri, M. P.; and Kahanda, I. In Proceedings of the 10th International Conference on Bioinformatics and Computational Biology - BICOB-2018, 2018.
Extracting Co-mention Features from Biomedical Literature for Automated Protein Phenotype Prediction using PHENOstruct [pdf]Paper   bibtex  
Exploring frequented regions in pan-genomic graphs. Cleary, A.; Ramaraj, T.; Kahanda, I.; Mudge, J.; and Mumey, B. IEEE/ACM transactions on computational biology and bioinformatics. 2018.
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Automated Biomedical Text Classification with Research Domain Criteria,. Anani, M.; and Kahanda, I. In Proceedings of the 10th International Conference on Bioinformatics and Computational Biology - BICOB-2018, 2018.
Automated Biomedical Text Classification with Research Domain Criteria, [pdf]Paper   bibtex  
Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing. Srinivasan, M.; Shahri, M. P.; Kahanda, I.; and Kanewala, U. In Proceedings of the 3rd International Workshop on Metamorphic Testing, of MET '18, pages 26–33, New York, NY, USA, 2018. ACM
Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing [link]Paper   doi   bibtex  
A look back at the quality of Protein Function Prediction tools in CAFA. Pourreza Shahri, M.; Srinivasan, M.; Bimczok, D.; Kanewala, U.; and Kahanda, I. PeerJ Preprints, 6: e27161v1. August 2018.
A look back at the quality of Protein Function Prediction tools in CAFA [link]Paper   doi   bibtex   abstract  
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Gobeill, J.; Gaudet, P.; Dopp, D.; Morrone, A.; Kahanda, I.; Hsu, Y.; Wei, C.; Lu, Z.; and Ruch, P. Database, 2018(1): bay104. 2018.
Overview of the BioCreative VI text-mining services for Kinome Curation Track [link]Paper   doi   bibtex  
  2017 (3)
KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature. Dopp, D.; Morrone, A.; and Kahanda, I. Proceedings of the BioCreative VI Workshop. Oct 2017.
KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature [link]Paper   bibtex  
GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. Kahanda, I.; and Ben-Hur, A. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, of ACM-BCB '17, pages 60–66, New York, NY, USA, 2017. ACM
GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins [link]Paper   doi   bibtex  
Exploring Frequented Regions in Pan-Genomic Graphs. Cleary, A.; Kahanda, I.; Mumey, B.; Mudge, J.; and Ramaraj, T. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, of ACM-BCB '17, pages 89–97, New York, NY, USA, 2017. ACM
Exploring Frequented Regions in Pan-Genomic Graphs [link]Paper   doi   bibtex  
  2016 (1)
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Jiang, Y.; Oron, T. R.; Clark, W. T; Bankapur, A. R; D’Andrea, D.; Lepore, R.; Funk, C. S; Kahanda, I.; Verspoor, K. M; Ben-Hur, A.; and others Genome biology, 17(1): 1–19. 2016.
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  2015 (3)
A close look at protein function prediction evaluation protocols. Kahanda, I.; Funk, C. S; Ullah, F.; Verspoor, K. M; and Ben-Hur, A. GigaScience, 4(1): s13742–015. 2015.
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Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. Funk, C. S; Kahanda, I.; Ben-Hur, A.; and Verspoor, K. M Journal of biomedical semantics, 6(1): 9. 2015.
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PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. Kahanda, I.; Funk, C.; Verspoor, K.; and Ben-Hur, A. F1000Research, 4. 2015.
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