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 07/13/2016).
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-
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) Shantanu's pre-print on estimating class priors from noisy positive and
unlabeled data is now available on arXiv.
2016) Vikas's paper in
top-10 most cited papers in Protein Science among all papers published
2016) CAFA2 manuscript accepted to Genome Biology, with Yuxiang as the major contributor;
pre-print available on arXiv.
2016) I will be chairing a session at the Gordon Research Conference about
Variant Effects in the
Era of Genome Sequencing. The conference takes place in June 2016.
Abstract and poster submission until May 15, 2016.
2016) I am visiting Technical University Munich
in Germany as an
August-Wilhelm Scheer Visiting Professor.
2016) Chao's paper on identification of cross-linked peptides accepted in
the Journal of Proteome
Research. Manuscript available
2016) Chao defends Ph.D. dissertation on April 11. Congratulations!
Our session of the evolution of molecular function accepted for
Pacific Symposium on Biocomputing 2017.
The session is co-organized with Yana
Matt Hahn. Consider submitting a paper!
Ruiyu's pre-print on new distance metrics on sets, ontologies and functions
is now available on arXiv. The
paper also introduces functional phylogenies.
2016) Vikas receives eScience Moore/Sloan Data Science and Washington
Research Foundation Innovation in Data Science Postdoctoral Fellowship, at
University of Washington.
2016) Shantanu's pre-print on estimating class priors from positive and
unlabeled data is now available on
Evolution of Molecular
Function at PSB 2017
Matt Hahn and I are organizing a session on the evolution of molecular
function at PSB 2017. Details
here. Submit a paper!
(Deadline: August 1, 2016)
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
• Genome interpretation.
• 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.
July 18, 2016