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Predrag Radivojac
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Bioinformatics projects Prediction and characterization of protein function and structure • protein function and disease associations • MutPred • protein post-translational modifications • phosphorylation (DisPhos) • methylation (MethylPred) (we are working on the update!) • ubiquitination (UbPred) • intrinsically disordered proteins • VL3 models (best models at CASP5) • VSL2 model (best model at CASP7 and, in a slightly older form, CASP6) • catalytic residues • CRP • database projects, via collaborations • DisProt • MutDB • HIP2
Computational proteomics • prediction of peptide fragmentation spectra (web site) • peptide detectability in MS/MS experiments (web site) • protein inference problem from MS/MS data (web site)
Visualization • visualizing statistically significant differences between two sets of multiple sequence alignments (Two Sample Logo)
Machine Learning/Data Mining Classification from noisy, high-dimensional, class-imbalanced, and heterogeneous data • feature selection algorithms • estimation • exploiting unlabeled data • clustering
Inauthentic paper detection • we are interested in the statistical properties of authentic human-written expository documents, e.g. scientific papers • we are interested in identifying authentic documents using information theory and machine learning • check out this Inauthentic paper detector
Group Meetings and Journal Club Fall 2009: Wednesdays 3:00-4:30pm (I232) - except on September 16 (4-5pm)
For journal coverage click here.
Group meeting web site (maintained by Wyatt Clark).
Active Funding Computational approaches to protein identification and quantification using MS/MS • PI: Predrag Radivojac • National Institutes of Health, R01 RR024236-01A1 • 09/15/08-08/31/11 • $813,146
CAREER: Bioinformatics of protein post-translational modifications • PI: Predrag Radivojac • National Science Foundation, DBI-0644017 • 07/01/07-06/30/12 • $595,948 • $12,500 REU supplement (07/2009)
Informatic profiling of clinically relevant mutation • PI: Sean Mooney, Indiana University School of Medicine • National Institute of Health, R01 LM009722-01 • 10/01/07-09/30/11 • $1,314,515 • Role: co-Investigator
APT: the analytical proteomics team • PI: Fred Regnier, Purdue University • National Cancer Institute, U24 CA126480-01 (CPTAC webpage) (Regnier team webpage) • 10/01/06-08/31/11 • $5,959,801 • Role: co-PI
The center of excellence in systems microbiology • PI: Yves Brun, Indiana University, Dept. of Biology • MetaCyt, Indiana University Award • 01/01/08-12/31/10 • $1,895,385 • Role: co-PI
Completed Funding Acquisition of a high-speed, high capacity storage system to support scientific computing: the data capacitor • PI: Craig Stewart • NSF CNS-0521433 • 10/01/05-09/30/08 • $1,720,000 • Role: senior investigator
A hypothesis testing approach to identification and assessment of statistical significance of peptides and proteins in shotgun proteomics • PI: Olga Vitek, Purdue University • CLSIR, Purdue University - Indiana University pilot grant application program • 01/02/07-12/31/07 • $49,919 • Role: collaborator
Development of a machine learning tool for peptide identification from tandem mass spectrometry data • PI: Randy J. Arnold • Indiana University Faculty Research Support Program • 06/01/05-05/31/06 • $32,408 • Role: co-PI
Last modified: August 29, 2009 |