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An NCI-designated Comprehensive Cancer Center, affiliated with the University of Pittsburgh School of Medicine
Research
Finding the right member is just a click away.
I direct the Genomics Analysis Core, a Health Science shared resource and co-direct the Cancer Bioinformatics Services (CBS) for UPMC Hillman Cancer Center. The GAC and CBS’s aims are to 1) provide genomics data analysis, 2) support team science projects such as consortia projects with computational infrastructure for analysis, storage and sharing of large genomics datasets, 3) assist with University of Pittsburgh initiatives for genomics education. GAC and CBS are an interdisciplinary collaboration between my team, the Department of Biomedical Informatics faculty with bioinformatics expertise, UPMC Hillman Cancer Center, the Institute for Personalized Medicine, the Pittsburgh Supercomputing Center (PSC) and the University of Pittsburgh’s Center for Research Computing (CRC). My team and I have experience working with all genomic platforms and applications RNA Seq, Whole Exome Seq (WXS) and Whole Genome Seq (WGS), single cell seq and digital spatial profiling (DSP). We support both cancer and non-cancer studies and from cell culture, model organisms and human datasets such as The Cancer Genome Atlas Project (TCGA).
My team contributes to team science projects by providing expertise in data analysis, metadata annotation, FAIR principles of data sharing and high performance computing. Examples of such projects include the Breast Cancer Research Foundation’s multi-institution AURORA metastatic breast cancer project in which CBS and PSC collaborate in hosting the data coordination center (DCC). My group also plays a key role in the Breast Cancer Research Foundation’s Data Hub for all 250 BCRF sites.
In the area of genomics education, I teach bioinformatics lectures for DBMI’s Intro to Biomedical Informatics course. My team and I also work closely with the CRC’s genomics education initiative funded by a Pitt seed grant. We have taught hands-on workshops in RNA Seq, metagenomics, single cell genomics and next flow (nf-core) pipelines. The courses are archived and are available through the CRC course website.
