bioinformatics


Ingenuity Nabs Genome Scientist, Nathan Pearson

Podcast brought to you by: Chempetitive Group - Who for more than a decade has helped science-based companies build and execute innovative marketing campaigns. "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Guest:

Nathan Pearson, PhD, Principle Genome Scientist, Ingenuity Systems Bio and Contact Info

Chapters: (Advance the marker)

0:42 What does it mean that you left Knome for Ingenuity?

7:02 How important is it that we have common ontologies?

13:00 What is your first goal at Ingenuity?

15:24 What will it take to get the ultimate end user buying?

18:54 Is sequencing good enough?

20:48 Where will Ingenuity make most headway going forward?

26:50 Thoughts on ENCODE and junk/not junk?

31:35 BONUS A student of Jonathan Eisen

Long time player in bioinformatics and database cultivation, Ingenuity Systems recently announced a new Principal Genome Scientist, Nathan Pearson. Nathan is known for joining Ozzy Osbourne and his wife on stage for a TED talk after interpreting the rock star's genome at Knome. What does this move mean for Ingenuity and for Knome? As I wrote in a recent blog, Pearson feels he'll make more headway moving to a platform further upstream. "For me," he says in the interview, "it's a chance to put my shoulder behind a platform that has a really high ceiling for bringing genomes into everyone's life in a more substantive way". Though new on the job, Pearson is comfortable explaining his first goal at Ingenuity, and tackling the big question of what will it take to get the end user, i.e., patients in the clinic, buying genomic medicine. At the end we catch Nathan talking about the person who influenced him to be a scientist, evolutionary biologist, Jonathan Eisen.

Editor of Bio-IT World Shares Overview of Bioinformatics in 2013

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

Guest:

Kevin Davies , Editor-in-Chief, Bio-IT World Bio and Contact Info

Listen (3:41) What must we all know about bioinformatics?

Listen (12:30) The explosive genome interpretation space

Listen (3:27) What will success in this space look like?

Listen (3:38) The Clinical Genome Conference expanding

Listen (6:18) What does it mean that CHI bought out the Genetic Conference?

Kevin Davies is the founding editor and current Editor-in-Chief of Bio-IT World. Reporting regularly on all things bioinformatics, he joins us to share his thoughts on the field. This last year has seen a flowering of new companies offering genome interpretation and reporting, a space Davis says is "the most interesting to me personally." But what will success for these early entrants look like?

DTC genomics has changed drastically since Davies covered the field in his 2010 book, The $1,000 Genome. Is the world of DTC genomics over? And what does it mean that CHI, conference producer and owner of Bio-IT World, bought out the Consumer Genetics Conference last year?

Looking at the Big Picture in Bioinformatics with Christophe Lambert, Golden Helix

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing

Guest:

Christophe Lambert, PhD , CEO, Golden Helix, Inc Bio and Contact Info

Listen (6:56) Beware the lure of solving tough problems for a small market

Listen (8:32) Is Illumina competing with their customers?

Listen (9:37) If the end user isn't buying, no one is selling

Listen (6:36) Learning from our GWAS mistakes

Listen (4:14) Where has Golden Helix found success?

Today we transition from our series on sequencing to one on bioinformatics. Christophe Lambert is the CEO of Golden Helix, a bioinformatics company based in Bozeman, Montana. With some degrees in computer science, Lambert saw early on the potential for IT in bio and began Golden Helix back in 1998, the same year Ingenuity Systems was founded. A research internship led to some funding from Glaxo Welcome and Lambert says he "started writing code in his bedroom" with no one to talk to but his wife.

Lambert's fourteen years in the business combined with his ability to think systematically has given him an insightful perspective on the industry. He's one of the few in this exploding field who acknowledges that the industry is quite small, not yet really making it to the clinic. "When the end user is not buying, no one is selling," he says in today's show. Lambert's impulse is to always look at the macro picture, probing why the science isn't there yet and what societal issues are holding back genomic medicine. I tried to pull him back a bit and get more information on Golden Helix, but half way through the interview, I just went with him. I highly recommend his blog at http://blog.goldenhelix.com/?author=5. This Montana Canadian has something to say.

Speeding Data Transfer with Dawei Lin, UC Davis

Podcast Sponsor: Ingenuity - iReport, the fastest and most accurate way to get biological meaning from your expression data. www.ingenuity.com/get iReport/

Guest:

Dawei Lin, PhD, Director of the Bioinformatics Core at UC Davis Genome Center Bio and Contact Info

Chapters: (Advance the marker)

0:50 Set up first bioinformatics server in China

3:15 From 26 hrs to 30 seconds: a new high speed connection with China

11:52 Training the next generation of bioinformaticians

25:47 Empowering the masses to understand their own biological data

30:02 BGI and genomics in China

35:15 Know thyself

37:43 EXTRA: Molecular modeling with legos

Dawei Lin set up the first bioinformatics server in China back in 1995. And things have come full circle this past summer, as he was involved in setting up a new high speed connection between China and the Genome Center at UC Davis where he is Director of the Bioinformatics Core. Dawei worked with BGI to set up the connection. We ask him about the company and about genomics in China.

It's Dawei's passion to know himself that brought him to working with biological data.

$1,000 Genome No Good

There comes a time when powerful memes that have become widespread begin to lose their value. Is it that time for ‘The $1,000 Genome?’ Mark Boguski thinks so. At the first annual Clinical Genome Conference in San Francisco this week, Dr. Boguski from Harvard Medical School said that the term is actually fallacious. The price of sequencing has come down.

India's Rising Star in Bio-IT: Prahalad Achutharao

Podcast Sponsor: Ingenuity - iReport, the fastest and most accurate way to get biological meaning from your expression data. www.ingenuity.com/get iReport/

Guest:

Prahalad Achutharao, CEO Geschickten Biosciences Bio and Contact Info

Listen (4:51) How is the genomics revolution progressing in India?

Listen (2:51) Geschickten providing knowledge of knowledge

Listen (4:15) First to talk about cloud computing for life sciences

Listen (7:34) Leveraging big data experience outside of biology

Listen (4:01) IT has given India a great push as a nation

Listen (1:04) What should Americans know about India and the future?

Recently awarded the 2012 Indian Leadership Award for Industrial Development, Prahalad Achutharao is one of India's rising stars in IT. Particularly in bio-IT. The first to talk about cloud computing in the life sciences, Prahalad and his colleagues at Geschickten are leveraging deep experience handling big data for bioinformatics. We talk to Prahalad about what Geschickten brings to the table in NGS data storage, analysis and interpretation and also about the progress of the genomics revolution in India.

At the Center of the Bioinformatics Universe with Atul Butte

This podcast originally aired on April 3, 2012

Podcast Sponsor: Audacity - Building health and science brand supremacy through disruptive marketing and advertising. Download "4 Secrets to Brand Supremacy," for free www.audacityhealth.com/approach

Guest:

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

Guest:

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

Podcast Sponsor: Ingenuity - iReport, the fastest and most accurate way to get biological meaning from your expression data. Upload your data and get a free iReport analysis summary at www.ingenuity.com/get iReport/

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.



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