Arash Alavi, PhD

2019-present: Arash is a Software Developer at SCGPM. His research interests are in the areas of software engineering, software analysis, computer security and privacy, and smartphone side of systems/security. Arash received his PhD in computer science from University of California, Riverside under the supervision of Prof. Rajiv Gupta. He worked on building a scalable and secure platform for real-time health management when he was working as an intern at SCGPM, and then he fully joined the team to continue the development of PHD (Personal Health Dashboard). He also collaborates on data management projects at Metabolic Health Center (MHC). Here is his personal homepage.


Amir Bahmani, PhD

2017-present: Amir Bahmani is our Research and Development Lead at the SCGPM. He has been working on distributed and parallel computing applications since 2008. Amir received his PhD in computer science from North Carolina State University under the supervision of Prof. Frank Mueller. He collaborates with different universities (e.g., NC State, Duke University, University of North Carolina, Stanford University) on several computationally intensive applications. In the past, he has also worked on industry cloud computing projects with Impulsonic and Illumina. He served as the vice-president of the Computer Science Graduate Student Association at NC State, and received the graduate student leadership award in 2016. He enjoys taking walks in nature, and studying cancer biology in his spare time. Here is his personal website.


Keith Bettinger, MS

2010-present:  As the Director of the GBSC, 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 the support of various tools and technologies. 

Prior to joining SCGPM, he was Chief Programmer at the 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 the State University of New York at Buffalo.


Paul Billing-Ross, MS

2015-present: 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 the Stanford sequencing pipeline on DNAnexus, and is now using cloud technologies to open and streamline the process of biomedical innovation for our collaborator, the VA Palo Alto Health Care Center.


Daniel Cotter, MS

2020-present: Daniel manages biomedical data on a variety of projects for the SCGPM.  He comes to us after gaining a wealth of experience managing clinical data with the University of Kentucky Healthcare system, which included leading an effort to create an enterprise-wide data warehouse for patient data.  Daniel earned his MS degree in Computer Science also from the University of Kentucky, but, if you want to elicit a knowing laugh from him, ask him about his BA degree from Transylvania University.


Vandhana Krishnan, MS

2016-present: Vandana is currently working as a bioinformatician on the VA's Million Veterans Project.  As a software developer embedded within Stanford Health Care, Vandhana also worked on the Stanford Clinical Genomics Service, and was 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.

 


Ramesh Nair, PhD

2014-present: Ramesh, the Acting 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 the 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 Senior 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.


Pratima Nallagatla, MS

2020-present: Pratima solves research problems for labs as a bioinformatician for the BaaS team.  Prior to joining us, she was a Senior Product Care Engineer for Roche Molecular Systems, participating in many phases of the product development cycle, from pre-launch preparations to post-rollout issue investigations.  Pratima received her MS in Bioinformatics from Johns Hopkins University and her BS in Bioengineering from UC Riverside.


Jina Song, PhD

2018-present: Jina Song is a Bioinformatics Data Analyst at SCGPM. Her research interests are in the areas of statistical analysis, mathematical modeling and machine learning in computational systems biology. Prior to joining SCGPM, Jina worked as a postdoctoral researcher in Biostatistics & Computational Biology Branch in National Institute of Environmental Health Science (NIEHS/NIH), where she analyzed ChIP-seq data in cancer research. She was also responsible for the computational modeling parts of various projects related to plant systems biology at North Carolina State University (NCSU). Jina has a Ph.D in Systems Biology Research lab. In Electrical and Computer Engineering from NCSU.

 


Yan Yang, PhD

2019-present: Yan is a Bioinformatician at SCGPM dedicated to BaaS. She has a broad range of research interests in big data, bioinformatics, population genomics, and statistical genomics. Her postdoctoral work at the DOE Joint Genome Institute, a division of Lawrence Berkeley National Lab, focused on population genetics using various types of NGS data to reveal molecular mechanisms underlying adaptive strategies in sorghum. Yan received her PhD in Plant Breeding and Genetics from Texas A&M University in 2018.


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.

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.