At the Center of the Bioinformatics Universe with Atul Butte

This podcast originally aired on April 3, 2012

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Atul Butte, MD,PhD, Associate Professor of Pediatrics, Medicine, and Computer Science, Stanford Bio and Contact Info

Listen (0:58) How did you get to the center of the bioinformatics universe?

Listen (2:06) 99% of our work is coming up with great questions

Listen (1:59) When will we have a new molecular based classification for disease?

Listen (2:54) What are you most passionate about?

Listen (3:45) iPOP - Integrated Personal Omics Profiling

Listen (2:07) Biggest challenge to clinical sequencing

Listen (1:57) Bioinformatician - the new hybrid

Listen (6:05) Thoughts on entrepreneurship

Listen (2:22) The dry researcher

Listen (3:32) Looking ahead

As part of our series, 'Finding Meaning in the Data,' we’re pleased to have Dr. Atul Butte to the program. He is Chief of the Division of Systems Medicine and Associate Professor of Pediatrics, Medicine, and Computer Science, at Stanford University and Lucile Packard Children's Hospital. The Butte Lab at Stanford has received a good amount of press as one of the leading labs worldwide focused on converting billions of molecular and clinical data into meaningful new insights into disease. Atul trained in Computer Science and received an MD at Brown University, worked as a software engineer at Apple and Microsoft, trained in Pediatrics at Children's Hospital Boston, then received his PhD in Health Sciences and Technology from Harvard Medical School and MIT. He’s the co-founder and scientific advisor to several start-ups, including NuMedii and Personalis.

Appistry Brings Their Cloud Computing to Bio, Sultan Meghji


Sultan Meghji, VP Product Strategy, Appistry Bio and Contact Info

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Listen (3:01) Formative years with geneticist father

Listen (4:55) Appistry, new to life science

Listen (7:17) Regulation and security issues

Listen (4:43) Roche move on Illumina

Listen (7:26) We haven't scratched the surface of genomics

Listen (8:12) Human de novo sequencing

Listen (0:46) Emerging sequencing technologies

Listen (6:24) Sequencing still the bottleneck, not analysis

Listen (1:53) No more blockbuster drugs

Sultan Meghji is the Vice President of Product Strategy at Appistry, a company working to develop the infrastructure needed to deliver medically actionable genetic data that can be applied to individual patients. Meghji has spent more than 20 years studying the technical aspects and business applications of high performance computing. He started his career at the National Center for Supercomputing Applications (NCSA), where he developed artificial intelligence systems and Internet technologies. From there, Meghji moved into several IT leadership positions at ABN AMRO, American Express, Monsanto, United Airlines, as well as in academia.

On the Front Lines: Frank Schacherer, BIOBASE

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Frank Schacherer, CTO, BIOBASE Bio and Contact Info

Listen (4:12) Products and databases

Listen (1:32) Over 70 curators on staff

Listen (4:42) Why go to BIOBASE over public databases?

Listen (2:40) Customers don't have to be bioinformaticians

Listen (5:46) Example of clinical project

Listen (7:03) Where is the field at now?

Listen (3:40) A lot of human work involved

Listen (8:41) Lots of requests from clinics, but genomic medicine not routine

Listen (1:50) In school couldn't study informatics and biology at the same time

Frank Schacherer is the CTO of BIOBASE, a company headquartered near Hannover, Germany which provides a genomics data analysis service. Their product is built on a vast comprehensive database and super powerful algorithms. These are combined into a user interface for over 600 customers including pharma, clinical and academic researchers.

Breathing Life into Complex Data: Doug Bassett, Ingenuity

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Doug Bassett, CSO & CTO, Ingenuity Systems Bio and Contact Info

Listen (2:28) Breathing life into complex data

Listen (1:14) Where exactly is the bottleneck?

Listen (4:56) New products

Listen (4:33) Curating the Knowledge Base for 14 years

Listen (5:10) Working with clinical customers

Listen (3:17) Why come to Ingenuity?

Listen (6:12) Are arrays dead?

Listen (:48) Is there a preferred sequencing platform?

Listen (2:01) Personal path to Ingenuity

Listen (1:31) Looking ahead

Today we’re coming to you from Redwood City, CA at the office of Ingenuity Systems. Founded in 1998 by Stanford graduate students, Ingenuity Systems is taking on the challenge of next-generation knowledge management for the life sciences community. Today, Ingenuity's products are used by thousands of researchers at hundreds of leading pharmaceutical, biotechnology, and academic research institutions worldwide. Joining us to talk about the company and what they do is the CSO and CTO, Doug Bassett.

Google Invests in Bioinformatics: Andreas Sundquist, DNAnexus

Podcast Sponsor: Appistry- Delivering the most cost-effective and the highest quality analytics for your NGS data. Jumpstart your analysis with runs beginning at just $99. Appistry, complex analytics made simple. Guest: Andreas Sundquist, CEO, DNAnexus Bio and Contact Info Listen (9:28) An instant online genomics data center Listen (2:31) Moving bioinformaticians to more interesting work Listen (3:49) From exomes to whole genomes Listen (5:38) Using the cloud Listen (4:35) Mirror of SRA Listen (6:00) Google's investment and the future of bioinformatics Listen (6:12) Is there something in the water at Stanford that creates entrepreneurs? Listen (2:50) Recruiting engineers in Silicon Valley Listen (1:31) Are you the next Sergey Brin? Andreas Sundquist is here to talk about his exciting new company. He’s the CEO and co-founder of DNAnexus, a company receiving a fair amount of buzz since catching a chunk of cash from Google Ventures and TPG Biotech. The company offers cloud based storage and analysis of next-gen sequencing data. Receiving his Ph D in computer science from Stanford, Andreas has published methods for whole-genome mammalian assembly, metagenomics, and population genetics. Andreas talks about his company platform and looks to a time when everyone will have their genome sequenced.

BlueSEQ's Michael Heltzen

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Michael Heltzen, CEO, BlueSEQ Bio and Contact Info

Listen (2:26) Why BlueSEQ?

Listen (5:20) How does the service work?

Listen (3:53) Platform agnostic

Listen (1:47) Who are the providers?

Listen (2:35) Thoughts on Roche action

Listen (2:22) Will you add bioinformatics?

Listen (1:54) Being an entrepreneur

Listen (5:03) Bio in Denmark

To wrap up our series on Sequencing and Genomic Medicine, we’d like to welcome Michael Heltzen. He’s the founder and CEO of BlueSEQ, a new start-up based in Arhus Denmark, serving as an online sequencing exchange, matching providers and researchers. Michael has served as Director of Partner Sales at CLC Bio, a bioinformatics company also based in Denmark and as VP at BGI Europe. Michael is a board member of both Startup City Denmark and the Copenhagenomics Foundation.

Drug Repositioning: Joel Dudley of NuMedii

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Guest: Joel Dudley, Ph D, Co-founder, NuMedii Bio and Contact Info

(Place marker at the following time markers.)


1:12 - What is drug repositioning?

4:51 - A few guys and a computer can be a pharma company

8:00 - Model of service

13:25- First company set up to do this

20:25- Spin-off from Stanford

27:24- Personal journey to Silicon Valley

33:24- 'Open science'

40:04- Exploring Personal Genomics

41:54- How far can computers take us?

Joel Dudley is a co-founder of NuMedii, a spin-off from Atul Butte's lab at Stanford. The new bioinformatics company has developed proprietary software to find new uses for existing or retired drugs. The company accesses a great amount of public and private data on both drug compounds and disease targets to come up with a Network of Efficacy.

Joel is from a small town in Wisconsin. He talks about his journey to Silicon Valley.

Joint Summit on Bioinformatics


Dr. Neil Sarkar, Director, Biomedical Informatics, University of Vermont

Listen Listen (17:00) - Bio and Contact Info

Dr. Philip Payne, Dept. Chair, Biomedical Informatics, The Ohio State University

Dr. Philip Payne Listen (21:14) - Bio and Contact Info

Dr. Russ Altman, Dept Chair, Bioengineering, Stanford University

Dr. Russ Altman Listen (25:34) - Bio and Contact Info


The field of Biomedical informatics has been around for a long time. But with the great output of genetic and genomic data and the recent push to create electronic medical records, the world of bioinformatics is greatly expanding and gaining in popularity. In early March we attended the Joint Summit for Translational Bioinformatics and Clinical Research Informatics. At the show, I sat down with the conference chairs for each of these sides of the show to discuss this exciting and emerging field.