CRC Spring 2021 NGS workshop trainer
Uma Chandran, Director, Genomics Analysis Core and Cancer Bioinformatics Service, and research associate professor, Department of Biomedical Informatics
Dr. Chandran provides bioinformatics support for RNA Seq, Exome Seq, Whole Genome Seq, ChiP Seq, ATAC Seq and other emerging genomic applications. Research Interests: Genomic data mining, Next Generation Sequencing data analysis, Integrative analysis of The Cancer Genome Atlas Project (TCGA), Development of computing infrastructure for large genomics datasets
Dr. Mu manages the HTC cluster. The cluster is designed to efficiently run high throughput computing jobs. He maintained a set of bioinformatics software tools on the cluster. He also computational developed workflows with researchers to use these tools under the HTC cluster to support bioinformatics research.
Dhivyaa Rajasundaram, research assistant professor in Pediatrics and core lead, Bioinformatics Core, UPMC Children’s Hospital
Dr. Rajasundaram has a scientific background in the field of computational and systems biology. She leads the Bioinformatics Core at UPMC Children’s Hospital of Pittsburgh. Research Interests: Next-generation sequencing data analysis, Integrative multi-omics data analysis, Single-cell systems biology, Statistical methods for host-pathogen interactions, Predictive Analytics.
Riyue Bao, Co-Director, UPMC Hillman Cancer Center Cancer Bioinformatics Services, Research Associate Professor, Department of Medicine
Dr. Bao provides support for data from Next Generation Sequencing (NGS) platforms for ChIP Seq, cancer variants and RNA Seq, integrative TCGA analysis, single cell RNA Seq, analysis of immunogenomic markers, immune/stroma cell deconvolution, neoantigen prediction, analysis of microbiota composition, taxonomy, and metabolic pathways, and integration of microbiome data with transcriptomics data.
Silvia Liu, Assistant Professor, Department of Pathology
Dr. Liu has been working in the area of biotechnology, biostatistics and bioinformatics. She have been one of the key members in the team to analyze whole genome sequencing, methylation sequencing, ChIP sequencing and transcriptome sequencing. Research Interests: High throughput genomic data analysis by machine learning and statistical methods, Next Generation Sequencing (NGS) and Long-read Sequencing data analysis
Amanda Poholeka, Director, Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh, Assistant Professor, Department of Pediatrics
Amanda Poholek’s interest in immune-mediated disease and how transcription factors contribute to T cell differentiation and function began while pursuing her doctorate degree at Yale University. She expanded her understanding of how transcription factors contribute to differentiation at the chromatin level during her post-doctoral training at the National Institutes of Health, where she learned how NextGen Sequencing can be used to interrogate chromatin accessibility, epigenetics and transcriptome analysis
Robert Lafyatis, Director, Single Cell Core, Professor, Department of Medicine
The Single Cell Core performs cutting edge assays in single cell technologies using the 10X Genomics Chromium platform to facilitate university researchers projects. Services include: 3’ and 5’ Gene Expression assays, TCR and BCR coupled with gene expression, Single Cell ATAC seq, CITE Seq cell surface protein expression coupled with mRNA gene expression, and Perturb Seq is expected to be available winter 2019. The Single Cell Core also performs experimental design consultations and data analysis.