Our laboratory develops computational methods and tools to facilitate new biological discoveries. We apply a variety of computational techniques, including data mining, visualization, information and knowledge management, machine learning and statistics to contribute to significant biomedical problems. The current focus of the lab is:

  • Language Workbench and Composable Languages in Bioinformatics. Our lab studies how Language Workbench technology can help transform how we perform analysis of biological data. See our latest prototypes: MetaR and NextflowWorkbench, part of the NYoSh Analysis Workbench. The NYoSh article and BDval for MPS at PeerJ. More information about the MPS language workbench, used in this line of research, is available here.
  • Goby: a next-gen data management framework that facilitates the implementation of efficient and scalable analysis pipelines.
  • GobyWeb: an intuitive web-based application to streamline consistent analyses of hundreds of next-gen samples
  • Analysis of samples from kidney transplant recipient and donors to develop non invasive diagnostic tests of acute rejection and other significant clinical endpoints (in collaboration with Drs. Manikkam Suthanthiran and Muthukumar Thangamani, Dept of Medicine, Nephrology).

Past projects include:

  • Study of the function of the CALHM1 gene in relation to Late onset Alzheimer’s Disease (in collaboration with Philippe Marambaud at the Feinstein Institute).
  • Reliable protocols for biomarker discovery and biomarker candidate model selection (in collaboration with the MAQC-II consortium).
  • Knowledge base about GPCR oligomerization: GPCR-OKB (collaboration with Marta Filizola at the Mount Sinai School of Medicine).
  • Integration of gene expression and epigenetic data to study non genetic inheritance of behavioral traits (in collaboration with Dr. Miklos Toth, Dept of Pharmacology).
  • Study of DNA methylation in DLBCL patients, to develop predictive models of survival and identify new drug targets (in collaboration with Drs. Rita Shaknovich and Ari Melnick, Dept of Medicine, Hematology and Oncology). See our article in Blood.

We are physically located in the Institute for Computational Biomedicine, at the Weill Medical College of Cornell University (New York, NY, USA).