Current group members

ordered alphabetically by last name

Keith Bettinger, MS (2010-current):  As the Infrastructure Manager at SCGPM, Keith is responsible for the user experience on our genetics cluster, where he designs and implements technical solutions related to data privacy, data commons, and support of various tools and technologies. 

Prior to joining SCGPM, he was Chief Programmer at Stanford Center for Interdisciplinary Brain Science Research (CIBSR) where he developed a multiplatform neuroimaging analysis and MRI visualization application. Prior to joining Stanford, Keith was Technical Lead at Motorola where he led development of software for handwriting recognition on a Chinese cell phone. Keith has a MS in Computer Science from University of New York at Buffalo.


Paul Billing-Ross, MS (2015-current): Paul is an SCGPM software developer who is passionate about building the roads and bridges of genomics research. He broke into computational biology studying models of molecular evolution under Dr. Sudhir Kumar at Arizona State University and then transitioned to studying mitochondrial genetics as an NSF Graduate Research Fellow at Cornell University. At SCGPM, he migrated Stanford sequencing pipeline on DNAnexus, and is now using cloud technologies to open and streamline the process of biomedical innovation for our collaborator VA Palo Alto Health Care System.


Somalee Datta, PhD (2012-current): As Director of Bioinformatics at SCGPM, Somalee is responsible for Stanford’s Bioinformatics Service Center, a Core facility that provides comprehensive computational solutions to enable large scale genomics research and clinical projects.  

Prior to joining SCGPM, Somalee worked at various start-ups in Silicon Valley as well as large organizations such as Life Technologies (now Thermo Fisher) and Gen-Probe (now Hologic). Among her start-ups is Verseon, a drug design company, where she was founding team member responsible for building the platform that brought together multiple innovations in molecular modeling, library design, large scale computation and data mining. Verseon is backed by one Nobelist (Steven Chu, Prof of Physics at Stanford & Former Secretary of Energy) and multiple heads of R&D at large pharmaceutical companies and has produced several novel pre-clinical candidates in Thrombosis. Somalee has a PhD in Statistical Physics from Boston University, and MS in Physics from Indian Institute of Technology Madras.


Priya Desai, MS

Priya is a Biomedical Engineer at SCGPM responsible for technologies and applications at Genetics Bioinformatics Service Center. Priya has a background in Physics and Astronomy and started her career at the Harvard Smithsonian Center for Astrophysics in Cambridge, MA where she was part of the Chandra X-ray Center and involved in analyzing spectral data of sun like stars. As the PI of her own NASA grant she continued working in the field of xray spectroscopy at the Space Science Labs at UC Berkeley. It was while working on a project to predict solar flares at the Stanford Solar Center that she got interested in machine learning and data science. Most recently she was part of Pritchard Lab at in the Genetics department at the Stanford where she helped develop SciReader- a recommendation engine for biomedical literature. She has a blog

Priya has a MS in Physics from Indian Institute of Technology, Bombay and completed her graduate coursework in Math from UT Austin. 


Vandhana Krishnan, MS (2016 - current): As a software developer at SCGPM, Vandhana is working on Stanford Clinical Genomics Service, and is responsible for implementing computational pipelines on the cloud and conducting benchmarking for clinical data. Prior to joining SCGPM, she was an Associate in Research at Washington State University managing the bioinformatics research and services in the Western Regional Small Grains Genotyping Laboratory, USDA-ARS where she built the lab’s computational facilities and helped develop a computational pipeline used for variant calling mainly from wheat genotype data.

Vandhana has a MS in Computer Science from Washington State University and a MS in Bioinformatics and Computational Biology from University of Idaho. Previous research experience includes fruit genomics, archaea genomics and human microbiome.

 


Greg McInnes (2014-present): As a part time Software Engineer at SCGPM, Greg is responsible for streamlining our data mining infrastructure on our Cloud (a dbGaP-compliant gateway to Google Cloud Platform). He is currently responsible for VCF mining for VA's Million Veteran Program. Prior to joining SCGPM, Greg was a Bioinformatics Scientist at Illumina.

Greg has a BS in Biological Sciences from Arizona State University and is pursuing his PhD in Biomedical Informatics at Stanford University.

 


Isaac Liao, PhD (2014-current): As Software Engineer at SCGPM working on Stanford Clinical Genomics Service (CSGS), Isaac is responsible for implementing the software stack on Cloud. Prior to joining SCGPM, Isaac was post-doctoral researcher at UC Davis where he developed an interactive plankton exhibit at SF Exploratorium in collaboration with MIT Darwin group. He has a PhD in Neuroscience at UC Davis. Prior to his graduate studies, he was a Research associate at VA Medical Center where he conducted MRI experiments and analyzed data.


Ramesh Nair, PhD (2014-current): Ramesh, Associate Director of Bioinformatics at SCGPM, 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.


Denis Salins, BS (2013-current): As a part time Software Engineer at SCGPM, Denis is responsible for Information Data Management in several projects including ENCODE ChIP-SeqiPOP, HMP2, and NASA Twin Astronaut Study. Prior to joining SCGPM, Denis managed a 10 person software development team responsible for complete lifecycle development of First Medical Solution’s flagship EMR product. He has a BS in Computer Science from Florida Atlantic University.


Nathaniel Watson, MS (2013-current): As a Bioinformatician at SCGPM, Nathaniel is responsible for bioinformatics for ENCODE ChIP-Seq lab informatics. In an earlier role, he was responsible for Stanford Sequencing Center informatics. Prior to joining SCGPM, Nathaniel was Research Associate at Bayer Vegetable Seeds. He has a MS in Bioinformatics from the University of North Carolina at Charlotte.

Yue (Wendy) Zhang, PhD (2016-current): Yue is a Bioinformatics Data Scientist dedicated to analyzing the data which comes into the GBSC Bioinformatics-as-a-Service resource. Prior to joining the SCGPM, Yue was a postdoctoral scholar with Prof Mark Kay in the Departments of Pediatrics and Genetics. She has a PhD in Theoretical Physics from Xiamen University in China.

Yue has broad  knowledge and solid experience in different bioinformatics fields, especially in next-generation sequencing data including RNA-seq, single cell RNA-seq, small RNA-seq, Ribosome profiling, ChiP seq, PAR-CLIP seq, ATAC-seq and other cutting-edge sequencing type. She has expertise in statistical modeling, library normalization, classification, programming and visualization. Yue has developed active and close collaboration with dozens of labs at Stanford and is continuing to bring her interdisciplinary knowledge and professional skills to help Stanford researchers achieve their goals.  

 


Ex-members

Philip Cayting, BS (2010-2013): As a Software Engineer at SCGPM, Philip developed high-throughput pipeline for scoring chromatin IP genomic sequencing (ChIP-Seq) results for one of the largest production centers of ENCODE consortium (then in phase 2) and performed standardized analysis. Prior to joining SCGPM, Philip was Programmer at at Gerstein Lab at Yale where he analyzed, mined and wrangled pseudogenes. Philip has a BA in Applied Mathematics from UC Berkeley.

After SCGPM, Philip joined Syapse as a Software Engineer. 


Nathan Hammond, PhD (2013-2016): As Software Engineer at SCGPM, Nate was responsible for development of the pipeline framework, Loom. Prior to joining SCGPM, Nathan worked as Quality Engineer and Application Support Engineer with Computational Biology group at Matlab Mathworks where he was responsible for Bioinformatics Toolbox (Next-Generation Sequencing, Microarray Analysis, Visualization Tools) and SimBiology (Modeling tool for Systems Biology, Pharmacokinetics/Pharmacodynamics). He has a PhD in Mechanical Engineering from MIT where he designed peptide scaffolds with tailored mechanical properties for tissue engineering applications. He holds two patents for medical devices.

After SCGPM, Nathan joined Stanford Health Care as a Staff Scientist with Clinical Genomics Service team.


Mingjie Wang, PhD (2015-2016): Mingjie was Microbiome Bioinformatician at SCGPM embedded with Ami Bhatt's lab. Mingjie received his PhD in Bioinformatics from Indiana University Bloomington, where he worked with Prof. Yuzhen Ye on metagenomics and next generation sequencing. Prior to joining the SCGPM, he worked at Stanford with Dr. Michael Snyder and his iPoP team to analyze accuracy of some of the best practice tools and methods for various types of metagenomic samples. 

After SCGPM, Mingjie joined Synthetic Genomics as a bioinformatics scientist.


Amin Zia, PhD (2013-current): As a Sr. Bioinformatician at SCGPM, Amin was responsible for development of “best-in-class” variant discovery pipeline for DNA-Seq data. This pipeline served Stanford Clinical Genomics Service (CSGS) pilot. 

Prior to joining SCGPM, Amin was post-doctoral researcher at Ontario Institute for Cancer Research (OICR) working on prostate cancer biomarker discovery. Prior to OICR, Amin was post-doctoral fellow at University of Toronto where he focused on annotations of genetic variations. Prior to his bioinformatics stint, he was a pukka Signal Processing engineer. He was (Sr.) R&D Engineer at Evertz Microsystems and Digital Rapids Corp working on video compression and codec technologies. He has a PhD in Electrical and Computer Engineering from McMaster University, Canada.


Introduction

The bioinformatics team at the Stanford Center for Genomics and Personalized Medicine (SCGPM) is a group of passionate and highly skilled individuals who like solving big problems that face today’s researchers in genomics-driven health care. The team works with a large number of researchers (grads, post-docs, faculty), and industry partners, and is responsible for several prestigious genomics projects. The solutions are often developed in an open source general purpose manner so that it can benefit the larger biomedical community at Stanford and elsewhere.

SCGPM bioinformatics team volunteers their expertise via office hours to GBSC community.

Our code highlights

In alphabetic order of repository name

HugeSeq

Latest iteration of variant detection pipeline that was first published in Nature Biotechnology in 2012.

Loom

Loom is a platform-independent tool to create, execute, track, and share workflows. Now supporting Stanford Clinical Genomics Service.

mvp_aaa_codelabs

This codelab goes over methods to do large-scale genomic analysis on Google Cloud.

Pre-prints and Publications

Relevant publications in reverse chronological order

Secure cloud computing for genomic data

Nature Biotechnology 34, 588–591 (2016)

Interactive Analytics for Very Large Scale Genomic Data

doi: http://dx.doi.org/10.1101/035295

Conference Poster Sessions & Talks

In reverse chronological order

Videos

In reverse chronological order

Stanford Clinical Genomics Service Engineering Team presents on Genomics Information Management System on Oct 24th, 2016. Director of Bioinformatics, Sowmi Utiramerur, presents platform overview and Sr. Scientist, Nathan Hammond, PhD, gives demo of Loom. Introduction by host and Head of infrastucture at SCGPM, Keith Bettinger, who provides a brief overview of SCGPM biomedical services.

Bioinformatics for the Microbiome conference. This video presents Ramesh Nair, PhD, co-host of the conference, moderating a panel session titled "The Future of Microbiome Research: Prospects, Translation, and Horizons". Panelists include: Elhanan Borenstein, Associate Professor, Dept. of Genome Sciences, University of Washington, George Weinstock, Professor and Director of Microbial Genetics, The Jackson Laboratory, Michael Snyder, Professor & Chair of Genetics, Stanford University and Nick Greenfield, Founder, One Codex.