Search results

• 2022

  Challenges and opportunities in current vaccine technology and administration: A comprehensive survey examining oral vaccine potential in the United States

  Rupassara, S. I., Kindt, J. W., Kazi, N. & Kahanda, I., 2022, In: Human Vaccines and Immunotherapeutics. 18, 6, 2114422.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification

  Lokuge, S., Jayasundara, S., Ihalagedara, P., Kahanda, I. & Herath, D., Jun 2022, In: BioSystems. 215-216, 104662.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2021

  Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes

  Pourreza Shahri, M. & Kahanda, I., Dec 2021, In: BMC Bioinformatics. 22, 1, 500.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• 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., Kudrna, D., Schmutz, J., Lachowiec, J. & Lu, C., Jul 2021, In: Plant Genome. 14, 2, e20110.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Vegetation Coverage in Marsh Grass Photography Using Convolutional Neural Networks

  Welch, L. W., Liu, X., Kahanda, I., Reddivari, S. & Umapathy, K., Apr 18 2021, In: The Florida AI Research Society. 34, 6 p.

  Research output: Contribution to journal › Article › peer-review
• 2019

  Computational methods for the ab initio identification of novel micro RNA in plants: A systematic review

  Manuweera, B., Reynolds, G. & Kahanda, I., 2019, In: PeerJ Computer Science. 2019, 233.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Exploring Frequented Regions in Pan-Genomic Graphs

  Cleary, A., Ramaraj, T., Kahanda, I., Mudge, J. & Mumey, B., Sep 2019, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 5, p. 1424-1435 12 p.

  Research output: Contribution to journal › Article › peer-review

• 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., Davis, L., Dogan, T., Atalay, V., Rifaioglu, A. S., Dalklran, A., Cetin Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L. & Zhang, Y. & 147 others, Bhat, P., Supek, F., Fernández, J. M., Gemovic, B., Perovic, V. R., Davidović, R. S., Sumonja, N., Veljkovic, N., Asgari, E., Mofrad, M. R. K., Profiti, G., Savojardo, C., Martelli, P. L., Casadio, R., Boecker, F., Schoof, H., Kahanda, I., Thurlby, N., McHardy, A. C., Renaux, A., Saidi, R., Gough, J., Freitas, A. A., Antczak, M., Fabris, F., Wass, M. N., Hou, J., Cheng, J., Wang, Z., Romero, A. E., Paccanaro, A., Yang, H., Goldberg, T., Zhao, C., Holm, L., Törönen, P., Medlar, A. J., Zosa, E., Borukhov, I., Novikov, I., Wilkins, A., Lichtarge, O., Chi, P. H., Tseng, W. C., Linial, M., Rose, P. W., Dessimoz, C., Vidulin, V., Dzeroski, S., Sillitoe, I., Das, S., Lees, J. G., Jones, D. T., Wan, C., Cozzetto, D., Fa, R., Torres, M., Warwick Vesztrocy, A., Rodriguez, J. M., Tress, M. L., Frasca, M., Notaro, M., Grossi, G., Petrini, A., Re, M., Valentini, G., Mesiti, M., Roche, D. B., Reeb, J., Ritchie, D. W., Aridhi, S., Alborzi, S. Z., Devignes, M. D., Koo, D. C. E., Bonneau, R., Gligorijević, V., Barot, M., Fang, H., Toppo, S., Lavezzo, E., Falda, M., Berselli, M., Tosatto, S. C. E., Carraro, M., Piovesan, D., Ur Rehman, H., Mao, Q., Zhang, S., Vucetic, S., Black, G. S., Jo, D., Suh, E., Dayton, J. B., Larsen, D. J., Omdahl, A. R., McGuffin, L. J., Brackenridge, D. A., Babbitt, P. C., Yunes, J. M., Fontana, P., Zhang, F., Zhu, S., You, R., Zhang, Z., Dai, S., Yao, S., Tian, W., Cao, R., Chandler, C., Amezola, M., Johnson, D., Chang, J. M., Liao, W. H., Liu, Y. W., Pascarelli, S., Frank, Y., Hoehndorf, R., Kulmanov, M., Boudellioua, I., Politano, G., Di Carlo, S., Benso, A., Hakala, K., Ginter, F., Mehryary, F., Kaewphan, S., Björne, J., Moen, H., Tolvanen, M. E. E., Salakoski, T., Kihara, D., Jain, A., Šmuc, T., Altenhoff, A., Ben-Hur, A., Rost, B., Brenner, S. E., Orengo, C. A., Jeffery, C. J., Bosco, G., Hogan, D. A., Martin, M. J., O'Donovan, C., Mooney, S. D., Greene, C. S., Radivojac, P. & Friedberg, I., Nov 19 2019, In: Genome Biology. 20, 1, 244.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2018

  Overview of the BioCreative VI text-mining services for Kinome Curation Track

  Gobeill, J., Gaudet, P., Dopp, D., Morrone, A., Kahanda, I., Hsu, Y. Y., Wei, C. H., Lu, Z. & Ruch, P., Jan 1 2018, In: Database. 2018, 2018

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2016

  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., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G. & Casadio, R. & 127 others, Cao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Törönen, P., Koskinen, P., Holm, L., Chen, C. T., Hsu, W. L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Bkc, D., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L. C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeño-Cortés, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., Sep 7 2016, In: Genome Biology. 17, 1, 184.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2015

  A close look at protein function prediction evaluation protocols

  Kahanda, I., Funk, C. S., Ullah, F., Verspoor, K. M. & Ben-Hur, A., 2015, In: GigaScience. 4, 1, 41.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct

  Funk, C. S., Kahanda, I., Ben-Hur, A. & Verspoor, K. M., Mar 18 2015, In: Journal of Biomedical Semantics. 6, 1, 9.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources

  Ben-Hur, A., Kahanda, I., Funk, C. & Verspoor, K., 2015, In: F1000Research. 4, p. 1-20 20 p., 259.

  Research output: Contribution to journal › Article › peer-review

  Open Access