A. Cancer genomics, epigenomics, and public datasets

Without a doubt, our current understanding of cancer biology and all its clinical implications  is heavily influenced  by the advent of modern genomics. Various genome-wide analytical tools  (both sequencing- and array-based technologies) interrogating  molecular attributes such as expression (mRNA, miRNA, lncRNA), copy number, CpG methylation, sequence variations (mutation, SNPs), and  DNA-protein interactions, have led to discovery of:  a)  genes crucial to cancer progression; and b) molecular biomarkers of cancer progression, early detection, prognosis, predisposition, and therapeutic response, as well as new targets for drugs. In addition to ushering  in new discoveries, genomics data have also validated (and at times corrected)  much of  our prior knowledge regarding cancer (such as   functionalities, pathways, regulatory mechanisms, and diagnostic values  associated with  a given gene). Fortunately,  there are now tens of thousands of  cancer-related genomic datasets  which are  publicly available (e.g. TCGA, GEO, ENCODE).  TCGA datasets are particularly interesting since the molecular profiling data are integrated, and are accompanied by very comprehensive clinico-pathological information. I strongly believe that many of the important, clinically-relevant, but yet-to-be- discovered knowledge regarding cancer are just buried in the depths of publicly available cancer genomic datasets.

B. Current projects and interests

Having been previously involved in a wide range of cancer-related research (chemical carcinogenesis and DNA repair, therapeutics and drug resistance, diagnostics, molecular genetics), I am currently interested in employing  predictive approaches that can be applied to various topics in cancer. The eventual aim is  for these bioinformatic observations to be experimentally validated, clinically translated (for some), and IP protected (for some).  Below are some of the ongoing (and recent) projects.

1.  Cancer biomarker prediction.

● Bionformatic identification of CpG methylation  markers for blood-based early cancer detection.  We then develop highly sensitive assays, based on technologies   invented  in Francis Barany’s group (Weill Cornell). Although markers have been identified for almost every cancer type, the assays under development are intended for early detection of colorectal cancer, breast cancer, and ovarian cancer.  The projects received support from Acuamark Diagnostics and Earlier.org.