Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes von Pourreza Shahri, Morteza, Kahanda, Indika

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Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping von Li, Huang, Hu, Xiao, Lovell, John T., Grabowski, Paul P., Mamidi, Sujan, Chen, Cindy, Amirebrahimi, Mojgan, Kahanda, Indika, Mumey, Brendan, Barry, Kerrie, Kudrna, David, Schmutz, Jeremy, Lachowiec, Jennifer, Lu, Chaofu

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Challenges and opportunities in current vaccine technology and administration: A comprehensive survey examining oral vaccine potential in the United States von Rupassara, S Indu, Kindt, Jr, John W, Kazi, Nazmul, Kahanda, Indika

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PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources [version 1; peer review: 2 approved] von Kahanda, Indika, Funk, Christopher, Verspoor, Karin, Ben-Hur, Asa

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Computational methods for the ab initio identification of novel microRNA in plants: a systematic review von Manuweera, Buwani, Reynolds, Gillian, Kahanda, Indika

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A close look at protein function prediction evaluation protocols von Kahanda, Indika, Funk, Christopher S, Ullah, Fahad, Verspoor, Karin M, Ben-Hur, Asa

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miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification von Lokuge, Sandali, Jayasundara, Shyaman, Ihalagedara, Puwasuru, Kahanda, Indika, Herath, Damayanthi

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy von Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M E, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel

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Exploring Frequented Regions in Pan-Genomic Graphs von Cleary, Alan, Ramaraj, Thiruvarangan, Kahanda, Indika, Mudge, Joann, Mumey, Brendan

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DeepACPpred: A Novel Hybrid CNN-RNN Architecture for Predicting Anti-Cancer Peptides von Lane, Nathaniel, Kahanda, Indika

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BRret: Retrieval of Brain Research Related Literature von Anani, Mohammad, Kuntz, Matt, Kahanda, Indika

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Psychiatry Transcript Annotation: Process Study and Improvements von Sridhar, Srinivasan, Kazi, Nazmul, Kahanda, Indika, McCrory, Bernadette

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Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct von Funk, Christopher S, Kahanda, Indika, Ben-Hur, Asa, Verspoor, Karin M

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Overview of the BioCreative VI text-mining services for Kinome Curation Track von Gobeill, Julien, Gaudet, Pascale, Dopp, Daniel, Morrone, Adam, Kahanda, Indika, Hsu, Yi-Yu, Wei, Chih-Hsuan, Lu, Zhiyong, Ruch, Patrick

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Data associated with Automated Biomedical Text Classification with Research Domain Criteria von Anani, Mohammad, Kahanda, Indika

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DeepPPPred Dataset von Pourreza Shahri, Morteza, Kahanda, Indika

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ProPheno 1.0: An Online Dataset for Accelerating the Complete Characterization ofthe Human Protein-phenotype Landscape in Biomedical Literature von Shahri, Morteza Pourreza, Indika Kahanda

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Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing von Srinivasan, Madhusudan, Shahri, Morteza Pourreza, Kanewala, Upulee, Kahanda, Indika

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Graph-Based Machine Learning Approaches for Pangenomics von Kahanda, Indika, Mudge, Joann, Manuweera, Buwani, Ramaraj, Thiruvarangan, Cleary, Alan, Mumey, Brendan

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Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools von Shahri, Morteza Pourreza, Srinivasan, Madhusudan, Reynolds, Gillian, Bimczok, Diane, Kahanda, Indika, Kanewala, Upulee

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