Papers

  • M. Pourreza Shahri, M. Srinivasan, D. Bimczok, U. Kanewala, I. Kahanda, “A look back at the quality of Protein Function Prediction tools in CAFA”, PeerJ Preprints 6:e27161v1 https://doi.org/10.7287/peerj.preprints.27161v1, 2018. (Link)
  • M. Srinivasan, M. Pourreza Shahri, U. Kanewala, and I. Kahanda, “Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing”, Proceedings of the 3rd International Workshop on Metamorphic Testing, ACM, Gothenburg, Sweden, 2018. (Link)
  • M. Pourreza Shahri and I. Kahanda, “Extracting Co-mention Features from Biomedical Literature for Automated Protein Phenotype Prediction using PHENOstruct”, 10th International Conference on Bioinformatics and Computational Biology (BiCOB), Las Vegas, NV, USA, 2018. (Link)

Abstracts

  • M. Pourreza Shahri, M. Srinivasan, U. Kanewala, and I. Kahanda, “A Look Back at the Quality of Protein Function Prediction Tools in CAFA”, 26th Conference on Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, USA, 2018. (Link)
  • M. Pourreza Shahri and I. Kahanda, “Evaluating the effectiveness of using literature features for automated protein phenotype prediction using PHENOstruct”, 15th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA, 2017. (Proceedings)
  • M. Pourreza Shahri, M. Srinivasan, U. Kanewala, and I. Kahanda, “Quality assurance of bioinformatics software”, 15th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA, 2017. (Proceedings)

Posters

  • M. Pourreza Shahri, M. Srinivasan, D. Bimczok, U. Kanewala, and I. Kahanda, “A Look Back at the Quality of Protein Function Prediction Tools in CAFA”, (poster) (PDF)
  • M. Pourreza Shahri and I. Kahanda, “Evaluating the effectiveness of using literature features for automated protein phenotype prediction using PHENOstruct” [version 1; not peer reviewed], F1000Research 2018, 7:432 (poster) (doi: 10.7490/f1000research.1115370.1) (PDF)
  • M. Pourreza Shahri, M. Srinivasan, U. Kanewala, and I. Kahanda, “Quality assurance of bioinformatics software” [version 1; not peer reviewed], F1000Research 2018, 7(ISCB Comm J):480 (poster) (doi: 10.7490/f1000research.1115396.1) (PDF)

Talks

  • A Look Back at the Quality of Protein Function Prediction Tools in CAFA, 26th Conference on Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, USA, 2018.
  • Characterizing the Protein-Phenotype Landscape in Biomedical Literature, Graduate Seminar Series, Montana State University, Bozeman, MT, USA, 2018.
  • Extracting Co-mention Features from Biomedical Literature for Automated Protein Phenotype Prediction using PHENOstruct, 10th International Conference on Bioinformatics and Computational Biology (BiCOB), Las Vegas, NV, USA, 2017.

Poster Presentations

  • A Look Back at the Quality of Protein Function Prediction Tools in CAFA, 26th Conference on Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, USA, 2018.
  • Evaluating the Effectiveness of Using Literature Features for Automated Protein Phenotype Prediction using PHENOstruct, Bobcat 125th Birthday Bash Graduate Scholars Poster Galleria, Montana State University, Bozeman, MT, USA, 2018.
  • Evaluating the Effectiveness of Using Literature Features for Automated Protein Phenotype Prediction using PHENOstruct, 15th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA, 2017.
  • Quality Assurance of Bioinformatics Software, 15th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA, 2017.
  • Evaluating the Effectiveness of Using Literature Features for Automated Protein Phenotype Prediction using PHENOstruct, The 2017 Graduate Student Research Rendezvous, Montana State University, Bozeman, MT, USA, 2017.