Predrag Radivojac

Download my curriculum vitae in pdf format (last updated on 12/26/2023). Google Scholar profile.

Interested in working with us? We have broad research interests. Please check our selected three publications in the areas of learning from biased data, semi-supervised learning, evaluation of machine learning algorithms, general machine learning, graphs and hypergraphs, genome interpretation, protein function, mass-spectrometry proteomics, and post-translational modifications. Also see our review papers.

Courtesy appointments. Department of Chemistry and Chemical Biology; Barnett Institute Fellow; Affiliate Faculty of the Roux Institute; Core Faculty Member of the Institute for Experiential AI. 

Recent Updates

• ☀️ (November 2024) Dan defends his Ph.D. thesis! Congratulations Dr. Zeiberg!  
• ☀️ (October 2024) Shawn to go to Google. Congratulations! 
• ☀️ (September 2024) The IGVF Consortium’s marker paper published in Nature. 
• (July 2024) Shawn defends his Ph.D. thesis! Dr. Peng, congratulations!  
• (July 2024) Sarah Stenton’s paper from Anne O’Donnell-Luria’s lab on assessing the performance of variant impact predictors for clinical use accepted in Genetics in Medicine. See an earlier version of the article on medRxiv. 
• (July 2024) Our commentary, led by Rachel Karchin and Dmitriy Sonkin, on variant impact predictors published in Nature Genetics.  
• (July 2024) Shawn’s ISMB 2024 paper on FDR estimation in cross-linking mass spectrometry proteomics published in Bioinformatics.  
• (June 2024) Ruchir Rastogi’s preprint from Nilah Ioannidis’ group, about evaluating missense variant effect predictors posted on bioRxiv.  
• (May 2024) Raiyan Kahn’s from the Pe’er group and Rafael Guerrero’s paper on genetic polymorphisms associated with adverse pregnancy outcomes accepted to Scientific Reports. Collaboration with Matt Hahn, Itsik Pe’er, Ron Wapner, David Haas and others. 
• (April 2024) Sarah Stenton’s paper from Anne O’Donnell-Luria’s lab on the CAGI RGP challenge accepted in Human Genomics. 
• (April 2024) Saurabh Mathur’s paper from Sriraam Natarajan’s group accepted at AIME 2024. 
• (April 2024) Katherine Chao’s and Lily Wang’s paper from Kaitlin Samocha’s lab on regional missense constraint appears on bioRxiv. 
• (April 2024) Karna Mendonca and Ross Stewart to join lab in Fall 2024. Jici Jiang to join Prof. Gyori’s and our lab. Welcome!
• (April 2024) I will present in the CMU-Pitt computational biology seminar series. Look forward to seeing old colleagues and meeting new ones.

Awards and Honors

Honorary Fellow of the Institute for Advanced Study at the Technical University of Munich, 2017

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

President, International Society for Computational Biology (ISCB), 2024-

Board of Directors Member, International Society for Computational Biology (ISCB), 2012-2021

Associate Editor, PLoS Computational Biology, 2014-2021

Editorial Board Member, Bioinformatics, Oxford University Press, 2010-

Editorial Board Member, Human Genetics, Springer, 2020-

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

• 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: November 12, 2024