• Teaching

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Download my curriculum vitae in pdf format (last updated on 06/23/2019). Google Scholar profile.

Recent Updates

• i. ☀️ (August 2019) Pedja to serve one year as Associate Dean of Research in the Khoury College.
• ii. ☀️ (July 2019) Richard’s paper, from Matt Hahn’s group, on mutation accumulation in macaques and offspring sociability available on bioRxiv. 
• iii. ☀️ (July 2019) Kym’s paper on predicting impact of non-frameshifting insertion/deletion variants published in PLoS Computational Biology. Available here.
• iv. ☀️ (July 2019) Another CAGI5 manuscript accepted in Human Mutation. Available here.
• v. ☀️ (June 2019) Rafael accepts a tenure-track position at NC State. Congratulations!
• vi. ☀️ (June 2019) Two CAGI5 manuscripts accepted in Human Mutation. Available here and here.
• vii. (May 2019) CAFA3 manuscript available on bioRxiv. More than a hundred methods evaluated for function prediction and more than a thousand genes, from three species, assigned experimental Gene Ontology annotations.
• viii. (April 2019) Pedja gives a seminar at Worcester Polytechnic Institute.
• ix. (March 2019) Pedja gives an opening keynote at MCBIOS 2019.
• x. (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.  
• xi. (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.
• xii. (March 2019) Vikas receives a K99 award. Congratulations!
• xiii. (February 2019) Pedja gives a talk at a CSAIL’s Computational Biology series at MIT.
• xiv. (February 2019) Shantanu’s paper on identifiability of skew normal mixtures published in Scandinavian Journal of Statistics. The paper available here. An older (and somewhat weaker) version still available on arXiv.
• xv. (January 2019) Vikas, Kym, and Pedja part of the Baboon Genome Analysis Consortium. The paper on the sequencing of six species of the Papio genus now appears in Science Advances. 
• xvi. (January 2019) A CAFA collaboration reveals 11 new long-term memory genes in Drosophila melanogaster. Balint’s and Stephen’s paper from the Bosco group published in G3 and featured on the journal home page. The paper is available here.
• xvii. (January 2019) Rashika’s and Shantanu’s paper on correction of performance estimates in positive-unlabeled learning presented at PSB 2019. The paper is available here.

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: August 6, 2019