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Research
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Bioinformatics Prediction and characterization of protein function and structure ▪ protein function and disease associations ▪ prediction and analysis of protein post-translational modification sites ▫ methylation (we are working on the update!) ▪ predictor of intrinsically disordered proteins ▫ VL3 models (best models at CASP5) ▫ VSL2 model (best model at CASP7 and, in a slightly older form, CASP6) ▪ database of intrinsically disordered proteins ▫ DisProt ▪ prediction and analysis of catalytic residues
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)
Prediction and characterization of functionally deleterious mutations ▪ prediction of functionally deleterious mutations
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
Authentic 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 2008: Wednesdays 3pm-4:30pm, Informatics 232
Group meeting web site.
Advisees and Co-advisees Post-doctoral fellows ▪ Biao Li
Ph.D. students ▪ Yong Li (primary advisor: Haixu Tang)
Master's students ▪ Jun Ma (primary advisor: Haixu Tang)
Undergraduate students ▪ Gitte Schimmelmann
Student Awards
Alumni
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
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) ▪ 10/01/06-08/31/11 ▪ $5,959,801 ▪ 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: September 12, 2008 |