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SCGPM Seminar: Ramesh Nair and Wendy Zhang, SCGPM/GBSC
Mon, September 19, 2016, 12:30 PM – 1:30 PM PDT
This month, we are doing a special SCGPM/GBSC showcase of some of the work in our group.
Monday, Sept 19th
12:30 - 1:30PM
“Can Bioinformatics-as-a-Service help your lab?”
Ramesh Nair, Associate Director of Bioinformatics, SCGPM / GBSC
Abstract: This talk will provide an update on Bioinformatics-as-a-Service (BaaS) activities over FY 2016. In particular, we will examine summary statistics in terms of labs and projects served during this period including the various NGS data types handled. The talk will further highlight examples of the diverse levels of support offered by BaaS in terms of sophisticated tertiary analysis, analysis pipeline development, and training/consulting efforts.
“RNAseq and single cell RNAseq tertiary analysis - WGCNA and SCDE”
Wendy Zhang, Senior Bioinformatician, SCGPM / GBSC
Abstract: Correlation networks are increasingly being used in RNA-Seq tertiary analysis and provide a systems biology approach to describing the correlation patterns among genes across samples. In this talk, we are going to demonstrate the use of the Weighted Gene Co-expression Network Analysis (WGCNA) R package to perform co-expression network analysis of gene expression data. Single-cell RNA-Seq provides an unbiased higher resolution of cellular differences and a better understanding of the function of individual cells. A high level of inherent technical noise poses a big challenge for tertiary analysis. In this talk, we are going to show the use of the Single Cell Differential Expression (SCDE) R package for analyzing single-cell RNA-Seq data, including differential expression analysis and pathway and gene set overdispersion analysis (PAGODA).
Ramesh's Bio: Ramesh Nair heads up the Bioinformatics-as-a-Service resource for the GBSC, and is the bioinformatician-in-residence for the CIRM-initiated Stem Cell Center of Excellence (CESCG). He is responsible for diverse bioinformatics needs for the Center Initiated Projects and its extensive collaboration network. Prior to joining SCGPM, Ramesh was a Bioinformatics Analyst at Center for Cancer Systems Biology (CCSB) where among other things, he was sole developer of next-generation sequencing (NGS) pipelines for genome sequencing (Exome-Seq) applied to follicular lymphoma and transcriptome sequencing (RNA-Seq) applied to lung cancer tumor microenvironment. Prior to joining Stanford, he was a Sr. Scientist at various Biotech firms in Bay Area including Cobalt Biofuels, Iconix BioSciences (now Entelos), Lynx Therapeutics (now Illumina) and DuPont. Ramesh has a PhD in Chemical Engineering from Northwestern University and MTech in Biochemical Engineering and Biotechnology from Indian Institute of Technology Delhi.
Wendy's Bio: Wendy Zhang is a Staff Bioinformatician dedicated to analyzing the data which comes into the GBSC Bioinformatics-as-a-Service resource. Prior to joining the GBSC, Wendy was a postdoctoral scholar with Prof Mark Kay in the Departments of Pediatrics and Genetics. As part of her postdoctoral work, she developed and applied statistical and computational methods to analyze and interpret high-throughput genomic data, including RNA-Seq, small RNA-Seq, CLIP-Seq, Ribosome-Seq, IcShape, targeted sequencing for adeno-associated virus (AAV) evolution, et al. Wendy received her PhD in Thermodynamics and Statistical Physics from Xiamen University, China.
ABOUT THE SCGPM: The Stanford Center for Genomics and Personalized Medicine (SCGPM) seeks to advance genomic technology so that someday both genetic and molecular profiling will become powerful and routine tools for predicting disease risk and monitoring and treating a wide range of pathologies. Towards this mission, the SCGPM serves to centralize and develop collaborative intellectual and technological resources that promote genomic research and analysis, predict drug response, educate physicians, and examine the ethics of personalized medicine. This includes large basic science projects such as ENCODE that decipher the human genome as well as clinical research projects such as the sequencing of cancer genomes and individuals with inherited diseases. Through these efforts, the Center aims to bring genomics to the clinic.
For more information about the SCGPM, go to http://scgpm.stanford.edu.
The SCGPM supports the Genetics Bioinformatics Service Center, a SoM core facility for genomics research that provides a secure on-premise computing infrastructure, Google Cloud gateway, and bioinformatics consulting. The facilities are available to all faculty members at Stanford University.
More @ http://gbsc.stanford.edu. Send inquiries to firstname.lastname@example.org .