Publications
- Y. Jiang, W.T. Clark, I. Friedberg, and P. Radivojac. The impact of incomplete knowledge on the evaluation of prediction: a structured-output perspective. Bioinformatics, 2014. [Link]
- C. Sisu, B. Pei, J. Leng, A. Frankish, Y. Zhang, S. Balasubramanian, R. Harte, D. Wang, M. Rutenberg-Schoenberg, W.T. Clark, et al. Comparative analysis of pseudogenes across three phyla. Proceedings of the National Academy of Sciences, 2014. [Link]
- W.T. Clark and P. Radivojac. Vector quantization kernels for the classification of protein sequences and structures. Pacific Symposium on Biocomputing, 2014. [Link]
- W.T. Clark and P. Radivojac. Information-theoretic evaluation of predicted ontological annotations. Bioinformatics, 29(13):i53-i61, 2013. [Link, Code](Ian Lawson Van Toch Memorial Award for Outstanding Student Paper)
- P. Radivojac, W.T. Clark, and others. A large-scale evaluation of computational protein function prediction. Nature Methods, 10(3):221–227, 2013. [Link]
- N.L. Nehrt, W.T. Clark*, P. Radivojac, and M.W. Hahn. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS computational biology, 7(6):e1002073, 2011. [Link](*Co-first author)
- W.T. Clark and P. Radivojac. Analysis of protein function and its prediction from amino acid sequence. Proteins: Structure, Function, and Bioinformatics, (79)7:2086–2096, 2011. [Link, Code]
- Y. Zhao, W.T. Clark, M. Mort, D.N. Cooper, P. Radivojac, and S.D. Mooney. Prediction of functional regulatory snps in monogenic and complex disease. Human mutation, 32(10):1183–1190, 2011. [Link]
- P. Radivojac, K. Peng, W.T. Clark, B.J. Peters, A. Mohan, S.M. Boyle, and S.D. Mooney. An integrated approach to inferring gene–disease associations in humans. Proteins: Structure, Function, and Bioinformatics, 72(3):1030–1037, 2008. [Link]
- M.M. Dalkilic, J.C. Costello, W.T. Clark, and P. Radivojac. From protein-disease associations to disease informatics. Front Biosci, 13:3391–3407, 2008. [PDF]
- M.M. Dalkilic, W.T. Clark, J.C. Costello, and P. Radivojac. Using compression to identify classes of inauthentic texts. In Proceedings of the 2006 SIAM Conference on Data Mining, pages 604–608, April 2006. [PDF, Website]