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Download my curriculum vitae in pdf format (last updated on 12/26/2019). Google Scholar profile.

Recent Updates

• i. ☀️ (February 2020) Richard’s paper, from Matt Hahn’s group, on estimating sequencing error rates available on bioRxiv. Distinct error rates observed on reference vs. non-reference genotypes.
• ii. ☀️ (February 2020) Jay’s paper giving a citation analysis of computational biology conferences published in Bioinformatics. Available here.
• iii. ☀️ (December 2019) Moses’ paper on revisiting the ortholog conjecture (OC) available on bioRxiv. The results confirm the original doubts in the OC and quantify the value of paralogs when predicting protein function. 
• iv. ☀️ (December 2019) Shantanu’s paper on identifiability of skew normal mixtures published in Scandinavian Journal of Statistics. The paper available here. 
• v. (November 2019) CAFA3 paper published in Genome Biology. More than a hundred methods evaluated for protein function prediction and more than a thousand genes, from three species, assigned experimental Gene Ontology annotations. Coverage in Genome Web.
• vi. (November 2019) Two papers accepted for AAAI 2020. Congratulations Shantanu, Dan, Justin, and Himanshu!
• vii. (October 2019) CAFA4 starts. Prediction deadline is February 10, 2020. Details here. 
• viii. (September 2019) CAGI special issues published in Human Mutation.
• ix. (August 2019) Pedja to serve one year as Associate Dean of Research in the Khoury College.
• x. (July 2019) Richard’s paper, from Matt Hahn’s group, on mutation accumulation in macaques and offspring sociability available on bioRxiv. 
• xi. (July 2019) Kym’s paper on predicting impact of non-frameshifting insertion/deletion variants published in PLoS Computational Biology. Available here.
• xii. (July 2019) Another CAGI5 manuscript accepted in Human Mutation. Available here.
• xiii. (June 2019) Rafael accepts a tenure-track position at NC State. Congratulations!
• xiv. (April 2019) Pedja gives a seminar at Worcester Polytechnic Institute.
• xv. (March 2019) Pedja gives an opening keynote at MCBIOS 2019.
• xvi. (March 2019) Ruiyu’s and Yuxiang’s article introducing and evaluating new distance metrics accepted in Knowledge Discovery and Data Mining. The paper is available here. A bit older version is on arXiv.  
• xvii. (March 2019) Santosh’s article, from Jim Reilly’s group, on identifying N-terminal processing sites in proteins accepted in Rapid Communications in Mass Spectrometry. The article is available here.
• xviii. (March 2019) Vikas receives a K99 award. Congratulations!

Awards and Honors

August-Wilhelm Scheer Visiting Professor at Technical University of Munich, 2016

Senior Member, International Society for Computational Biology, 2015

National Science Foundation CAREER Award, 2007

Outstanding Young Researcher, University of Novi Sad, 1998

Major Student Awards

Kymberleigh Pagel, Ian Lawson Van Toch Memorial Award, ISMB/ECCB 2017

Wyatt Clark, Ian Lawson Van Toch Memorial Award, ISMB/ECCB 2013

Professional Activities

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-

Research Interests

Bioinformatics and Computational Biology

• • Protein structure and function; method development and evaluation of function prediction
• • Post-translational modifications (PTMs)
• • Mass spectrometry (MS) and MS/MS proteomics

Biomedical Informatics

• • Understanding and predicting molecular mechanisms of disease
• • Genome interpretation
• • Precision medicine and precision health

Machine Learning

• • Supervised and semi-supervised learning: learning from positive and unlabeled data; learning from biased data
• • Structured-output learning and evaluation; extreme classification
• • Kernel-based inference on sequences, time-series, and graphs

 Last updated: February 7, 2020