Professor of Computer Science
Adjunct Professor of Statistics
Department of Computer Science and Informatics
150 South Woodlawn Avenue
Bloomington, IN 47405
Office: Lindley Hall 301F
Phone: (812) 856-1851
Download my curriculum vitae
in pdf format (last updated on 12/24/2016).
Google Scholar profile.
Post-doctoral fellow, Bioinformatics, Indiana
University School of Medicine, Indianapolis, Indiana, 2004
Ph.D., Computer and Information Sciences, Temple University,
Philadelphia, Pennsylvania, 2003
M.S., Electrical Engineering, University of
Belgrade, Serbia, 1997
B.S., Electrical Engineering, University of
Novi Sad, Serbia, 1994
Board of Directors Member, International Society for Computational Biology (ISCB), 2012-
Associate Editor, PLoS Computational Biology, 2014-
Editorial Board Member,
Bioinformatics, Oxford University Press, 2010-
Assessment of Functional Annotations (CAFA) at ISMB 2017
CAFA3 experiment is currently on. The submission deadline is
22 February 2, 2017. Check out the following papers about CAFA:
CAFA2, and a gentle
introduction to CAFA.
An even gentler introduction to protein function prediction is available
2017) Shantanu to give a talk at
Jose defends Ph.D. dissertation on December 12. Congratulations! Staying at
Indiana on the Precision Health Initiative Project!
Pedja awarded August-Wilhelm Scheer Visiting Professor position at
Technical University of Munich
in Germany, 2017. Also visited in
Vikas defends Ph.D. dissertation on November 17. Congratulations! Moving
soon to University of Washington (eScience Moore/Sloan Data Science
(November 2016) Shantanu's
paper about performance estimation in positive-unlabeled learning accepted for
Shantanu receives travel award for NIPS 2016.
2016) Pedja to give a talk at the NIPS workshop on
Challenges in Machine Learning.
2016) Sujun's paper accepted to the Journal of Proteome Research; available
2016) CAFA2 paper officially published, with Yuxiang being the first author; available
2016) We have pre-computed MutPred scores for about 80 million possible human
variants; available here.
2016) Shantanu's paper accepted to NIPS 2016; pre-print available on arXiv.
2016) Jose's paper on the functional significance of disease mutations
PLoS Computational Biology.
2016) Krishna Reddy's paper (U South Florida) with Vikas and me as coauthors
accepted to Journal of Biomolecular Structure and Dynamics.
2016) Our review paper, with Burkhard Rost (TUM) and Yana Bromberg (Rutgers) on protein function, machine learning and precision
medicine accepted to FEBS Letters.
2016) Kym gave a talk at ISMB's
VarI-SIG in Orlando, Florida.
Jose, Vikas, Ruiyu and Yuxiang all attended
2016) Vikas's paper in
top-10 most cited papers in Protein Science among all papers published
Center for Algorithms and Machine Learning (CAML)
Center for Bioinformatics Research (CBR)
Bioinformatics and Computational Biology
• Protein structure and function; method
development and evaluation for function prediction
• Post-translational modifications (PTMs)
spectrometry (MS) and MS/MS proteomics
Biomedical Informatics and Applications to
• Development of computational models for
understanding and predicting molecular mechanisms of disease
• Candidate gene prioritization and biomarker
• Genome interpretation and precision
• Supervised and semi-supervised
learning: learning from positive and unlabeled data; learning from biased data
• Structured-output learning and evaluation;
• Kernel-based inference on
sequences, time-series, and graphs
January 14, 2017