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. Before joining Stanford, Keith was a Technical Lead at Motorola where he led the 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.


Lyong Heo, MS

2022-present: Lyong is a staff bioinformatician for the BaaS team whose interests are in population genomics, machine learning, and NGS analysis.  Prior to joining the GBSC, he was a Computational Biologist at the Van Andel Institute (VAI) in Grand Rapids, MI, where he performed bioinformatic analyses on patients with pediatric acute myeloid leukemia (AML).  Prior to that, he was a Research Assistant in GWAS projects on metabolic diseases in population-based cohorts and Korean Reference Genome (KRG) at Korea National Institute of Health.  He also managed multi-omics data at the Center for Genome Science in South Korea.  Lyong received his Master’s Degree in Computer Science from Chungbuk National University.


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.


Joe Sarro, MS, PhD

2021-present: Joe is a Bioinformatics Engineer currently working on the VA’s Million Veteran Program. Prior to joining Stanford, he served as the Bioinformatics Senior Analyst for the Genomics and Bioinformatics Core Facility at The University of Notre Dame, where he developed software and pipelines for Next Generation Sequencing projects. He also worked with VectorBase, where he served as a consultant, administrator of their Galaxy instance, and a curator of mosquito trap abundance data.

Joe received his Bachelor’s in Computer Science from Iona College, his MS in Bioinformatics from New York University, and his PhD in Biological Sciences from The University of Notre Dame under the supervision of Prof. Molly Duman-Scheel. Joe is also a certified Carpentries Instructor and has instructed several workshops in bioinformatics and coding.


Meng Wang, PhD

2022-present: Meng is a senior bioinformatician for the BaaS team whose interests are in developing statistical methods and computational tools to better understand the complexity of biology.  She was most recently a research scientist with the Snyder Lab and led the algorithm development in several projects.  In the GTEx project, she was in charge of proteomics data analysis and integration, and developed several new algorithms in robust normalization and data-adaptive quantification of tissue-specificity (AdaTiSS).  In the project to predict the onset of COVID-19 from wearable device data, she developed both offline and online detection algorithms to detect infection-associated heart rate anomalies from smartwatch data.  Meng received her PhD in Mathematical Statistics from the University of California, San Diego.


Tao Wang, PhD

2020-present: Tao Wang (王韬) is a researcher with multi-disciplinary interests in high performance computing (HPC), large-scale storage, and statistical machine learning-based analysis for precision medicine and human genomics. Currently, he works closely with biologists in the Mike Snyder Lab and is in charge of data submissions to ENCODE (Encyclopedia of DNA Elements). He is a computer science alumnus of College of William and Mary and North Carolina State University, and a former intern at Argonne National Laboratory, Lawrence Livermore National Laboratory, and MediaTek.


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.

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

Pre-prints and Publications

Relevant publications in reverse chronological order

Trellis for efficient data and task management in the VA Million Veteran Program

Nature Scientific Reports 11, Article number: 23229 (2021)

Secure cloud computing for genomic data

Nature Biotechnology 34, 588–591 (2016)

Cloud-based interactive analytics for terabytes of genomic variants data

Bioinformatics, Volume 33, Issue 23, 01 December 2017

Conference Poster Sessions & Talks

In reverse chronological order

Videos

In reverse chronological order

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.