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.

Our collaborations leverage our strong biomedical community

Current collaborators include:

• Nathan Clark Group, Department of Computational and Systems Biology
  Current project: RERconverge method for connecting evolutionary forces with phenotypes.
• Mark Shlomchik Group, Department of Immunology
  Current project: Understanding memory B-cell subtypes through multiomics analysis.
• Hassane Zarour's Group, UPMC Hillman Cancer Institute
  Current project: Translational tumor immunology
• Paul Monga's Group, Department of Pathology
  Current project: Liver disease models.

Our Home

News

• You can now read our new preprint about controlling type-I error in phylogenetic analyses. "Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context" 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