Using large-scale genomic datasets we develop new machine learning models that facilitate discovery and interpretation. We work on a variety of biological problems ranging from multi-omics analysis to molecular evolution.
We work with genomics data consortia
We are part of the Epigenetic CHaracterization and Observation (ECHO) . The program is building a man-portable device that analyzes an individual’s epigenetic “fingerprint” to potentially reveal a detailed history of that individual’s exposure to WMD or their precursors.
Our group is part of the Molecular Transducers of Physical Activity Consortium (MoTraPAC) . This is a large study looking at the effects of exercies through multiple genomic assays.
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University of Pittsburgh School of Medicine
Department of Computational and Systems Biology
3501 Fifth Ave,
Pittsburgh, PA 15260
Carnegie Mellon - University of Pittsburgh
Ph.D. Program in Computational Biology

News
- New-preprint: "Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements" bioRxiv
- “Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data is now online at Bioinformatics
- New preprint: Widespread redundancy in -omics profiles of cancer mutation states. In corllaboration with Casey Geene's group bioRxiv
- “DataRemix: a universal data transformation for optimal inference from gene expression datasets” is now online at Bioinformatics
- “Causal network perturbations for instance-specific analysis of single cell and disease samples” with Kristina Buschur and Takis Benos is now online at Bioinformatics
- PLIER is used to infer gene-enironment eQTL interactions. Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain
- Our method PLIER is online at Nature Methods. Nature Methods
- Wynn's paper is online at Science With write-ups in NYtimes and National Geographic
Contact Maria
phone: 412 648 3338
email: mchikina@pitt.edu