bioinformatics


Christophe Lambert Tackles the Bioinformatician Bottleneck

Guest:

Christophe Lambert, Professor at MSU, Founder, Golden Helix

Bio and Contact Info

Listen (6:00) Not nearly enough bioinformaticians?

Listen (7:23) Are students customers or products of the university system?

Listen (2:40) Computer Science not a science?

Listen (3:47) Are biologists becoming mere technicians?

Listen (7:17) Theory of Requisite Organization

Listen (6:02) Applying cybernetics to biology

We can always count on Christophe Lambert to come on the show and raise some tough questions and even make a stab at answering them. Christophe is one of those early pioneers of bioinformatics. Getting an undergraduate in Computer Science at Montana State and then a PhD in the same at Duke back in the 90's, Christophe was intrigued early on by biology. This led him to found Golden Helix in 1998, one of the oldest bioinformatics companies around.

This year Christophe hired a new CEO to replace him at Golden Helix which allowed him to transition back into academia at Montana State. He's currently developing the computer science program there, and this has him questioning not only how we go about education, but also how we are bringing information science to the complexity of biology.
After a few questions to get him warmed up, such as "Is Computer Science really science?" Christophe goes on a run, tackling some difficult topics. Are biologists in the IT age becoming mere technicians? Christophe turns to the Theory of Requisite Organization, saying there are many different kinds and levels of biologists. There are those doing classification, or naming, all the way up to those working on universal laws. What universal laws about biology has he probed, we ask.

For more in-depth presentation on the ideas Christophe presents here, we suggest his Vimeo channel.

Podcast brought to you by: Roswell Park Cancer Insititute, dedicated to understanding, preventing and curing cancer for over 115 years.

How Much Bioinformatics for the New Biologist, Asks Educator Moray Campbell

Guest:

Moray Campbell, PhD, Assoc. Professor, Roswell Park Cancer Institute

Bio and Contact Info

Listen (5:35) How much bioinformatics does the new biologist need?

Listen (7:51) Biologists need to be asking smarter questions

Listen (4:28) The right ratio of dry lab to wet lab

Listen (5:48) Going back to school for the bioinformatics degree

Attend any conference on genomic medicine today and you’ll hear about the $1,000 genome and the $100,000 analysis. What must happen for the interpretation of genomic data to keep up with the output?

Moray Campbell is an associate dean at Roswell Park Cancer Institute, one of the nation's oldest cancer research centers. Through an alliance with the University at Buffalo and other regional colleges, the institute offers training to the next generation of cancer researchers. Moray is part of the team responsible for designing the curriculum and is wrestling with the question of how to keep up with all the biological data. Furthermore, if the answer to this lies in the education of the next generation of research scientists, what should be the ratio of dry lab to wet lab work for the new biologist?

As the study of biology becomes ever more complex in the world of big data, this question is a critical one. We will explore it in a new series beginning today, The Bioinformatics Bottleneck.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

The Very Angry Evolutionary Biologist

Guest:

Dan Graur, PhD, Professor, University of Houston Bio and Contact Info

Listen (3:09) Study of biology overtaken by hype

Listen (4:55) Scientist vs. technician

Listen (6:34) Public unaware that all they eat are GMOs

Listen (3:58) Do you have a role as a scientist to reach out to the lay audience?

Listen (2:27) What was your reaction to gene patent decision?

Listen (1:43) Thoughts on clinical genomics

Listen (2:04) Twitter and the Very Angry Evolutionary Biologist

We're happy to welcome Dan Graur, Professor of Biology and Biochemistry at the University of Houston, back to the program. Dan and his colleagues caused a stir in the world of genetics with their publication "On the Immortality of Television Sets," a sarcastic and witty criticism of the ENCODE Project and ensuing claims about the death of "junk DNA."

In today's interview, Graur says that he's always been a critic of bad science. He sees a trend where technicians and tools folks are masquerading as scientists.

"What happened in recent years," he says, "is that we have a huge influx of people who are not versed in the basics of population genetics and molecular evolution, and such. They are all essentially people who know how to write computer programs, who believe that science is not driven by questions, but it's driven by a sort of high tech natural history--the data will tell us what is in there."

Is not biology an information science? Does not the new biologist need to be a bioinformatician as well? Graur says we do not need to reinvent the wheel when it comes to basic science. (We'll be pursuing this question in an upcoming series, "The Bioinformatician Bottleneck")

Graur is currently working on a book about GMOs for the lay audience. He also shares his thoughts on gene patents, clinical genomes, and that marvelous "time waster", Twitter.

Podcast brought to you by: See your company name here. - Promote your organization by aligning it with today's latest trends.

Quality Is the Key, Says Veteran of Personalized Medicine

Guest: Dr. Larry Marton, Program Chair, PMWC

Bio and Contact Info

Chapters: (Advance the marker)

0:40 Building one of the first molecular diagnostics labs at UCSF

6:47 Where are we at with personalized medicine today?

11:27 What can we do to better quality assurance in the industry?

19:01 Using PMWC as a neutral place for dialogue between disparate groups

23:47 If you practice medicine better than the community, you can be in trouble

29:14 What can those in the industry do to better engage the medical community?

Our guest today has been focused on personalized medicine since before it was called that. Larry Marton is the former chair of the Department of Laboratory Medicine at UCSF. Helping to form the department back in the late 70's, Larry and his colleagues set out to transform a standard clinical laboratory into a place for cutting edge molecular research, a place where basic research could be done and translated into medical practice.

Today he's retired from UCSF, but "busier than ever before." He serves on various boards and is the program chair for the Personalized Medicine World Conference which takes place each January in Mountain View, CA. Anyone who has been to this conference knows the depth and breadth of Larry's contacts and influence in the industry. He says the PMWC is an important conference because it plays the role of "neutral broker" between the various stakeholders in the field: entrepreneurs, researchers, investors, regulators, physicians, and patients.

Larry's core message is that we must improve the quality of new clinical tests which have been translated from research. It is the key to demonstrating clinical relevance, he says. There are issues with sampling, with analytics, and with compliance. What can those in the industry do to better the quality assurance? And how can the industry better engage the medical community? A veteran shares his insights.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Joel Dudley Discusses New Book, "Exploring Personal Genomics"

Guests:

Joel Dudley, Co-Author, Director of Biomedical Informatics, Mt. Sinai School of Medicine Bio and Contact Info

Listen (1:46) The bet on computation and genomics at Mt. Sinai Hospital

Listen (2:32) A new handbook, Exploring Personal Genomics

Listen (6:34) Who is the audience for the book?

Listen (4:05) What did you learn from the project?

Listen (3:25) How can the book help clinicians?

Listen (6:58) NuMedii and drug repurposing

One of the major obstacles to personalized medicine is that today's generation of clinicians are not up on the latest in genomics. Today's guest is a rising star in the world of genomic medicine who has written a book to address this issue. Coming from Atul Butte's lab at Stanford, then co-founding a company to commercialize algorithms for repurposing drugs, Joel Dudley is now working with Eric Schadt at Mt. Sinai Medical Center in New York. Joel was an author on one of the first papers to interpret a genome which put him on the front lines of genomic medicine. He's now taken this journey as a genomics hacker and put it into a handbook with co-author Konrad Karczewski, "Exploring Personal Genomics."

The book reviews the various sequencing technologies as well as the emerging bioinformatics platforms for analyzing the sequence data. Though full of technical detail and many images, some of which have never been seen in print, the two authors aimed for an audience such as clinicians who don't know that much about informatics or "Google and Facebook hackers" with little knowledge of biology. "We wanted to make it as accessible as possible," says Dudley in the interview, "but what we did not want it to be was a stuffy textbook . . . that would only be given out at universities."

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

Dietrich Stephan Hits the Refresh Button with SV Bio

Guests:

Dietrich Stephan, Founder, CEO, SV Bio Bio and Contact Info

Listen (5:24) What makes this the right time for SV Bio?

Listen (6:03) What does the SV Bio product look like?

Listen (2:38) Healthcare IT behind by several decades

Listen (6:52) How are you selling your product?

Listen (6:11) Whole genome pricing level still uncertain

Listen (5:02) The big ambition

On January 15th of this year a new company, Silicon Valley Biosystems, or SV Bio, was launched in the clinical genome interpretation space. And just this past week the company's lab gained CLIA certification. Founder and CEO, Dietrich Stephan was the creator several years back of Navigenics, a direct-to-consumer approach to personalized medicine. Navigenics was acquired by Life Technologies in the summer of last year. Stephan is quoted in Bio-It World as saying he “wanted to hit the refresh button and do the necessary inventing around rare variants now that the time is right.” Today he joins us to share his ambition for what he considers THE scalable platform and tell us why the time is right for SV Bio and genomic medicine.

Podcast brought to you by: Myraqa Clinical Research: The CRO for Point of Care and PMA Diagnostics.

and by: Roche Molecular Systems: A proud sponsor of today's podcast.

UCSC Up To More than Bioinformatics

UC Santa Cruz is well know in our field for their part in the Human Genome Project.  Led by David Haussler, the bioinformatics group there released the first working draft of the human genome sequence on the web, leading shortly to the UCSC Genome Browser, an essential open resource for biomedical science.  This was followed up last year by the launch of the  Cancer Genomics Hub (CGHub), a large-scale data repository for the National Cancer Institute. 

Big Data Takes the Stage at Stanford

We're currently developing a series on big data here at Mendelspod.  So we jumped at the chance to attend the first 'Big Data in BioMedicine Conference' put on at Stanford in conjunction with the University of Oxford.  The conference gave a great overview of the topic, reaching not only into all that omics data, but health IT and public health as well.  

Open Source or Commercial? Lasse Goerlitz, CLC Bio, Talks Bioinformatics

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

Guests:

Lasse Goerlitz, VP of Communications, CLC Bio
Bio and Contact Info

Listen (5:16) Highest demand coming from agro

Listen (3:06) What is holding back the adoption of genomic medicine?

Listen (4:03) A commercial platform with plug-ins

Listen (3:37) Open source vs commercial software

Listen (4:40) The all-in-one guys

Listen (5:56) Genomics in Europe

The repeating trend from industry to industry is for software to go from fragmented, custom applications toward larger dominant platforms. It's still the early days for bioinformatics, and just who the dominant platforms of the future will be remain unknown. Will they be open source, public platforms or commercial platforms?

CLC Bio, a bioinformatics company has been working on the solution for eight years now and hopes that their platform which works with many different plug-ins will become number one for biologists around the world. In today's show, CLC's VP of Communications, Lasse Goerlitz, talks about their platform and trends in genomics. Currently their heaviest users are in ag bio, but the demand from the clinic is rising. We conclude with a discussion of differences between Europe and the US in the genomics space.

Bioinformatics 3.0: an App Economy with Matt Landry, Biomatters

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

Guest: Matt Landry, CTO, Biomatters
Bio and Contact Info

Chapters: (Advance the marker)

0:37 What is the focus of Biomatters?

4:32 Hack or bioinformatician?

8:52 Are you seeing the commoditization of bioinformatics?

10:38 Bioinformatics 3.0: an app economy

16:49 The state of genomic medicine in New Zealand

21:59 Have you started thinking beyond the cloud?

Matt Landry calls himself a hack rather than a bioinformatician. He's the Chief Technology Officer at Biomatters, a bioinformatics company based in New Zealand that provides an easy-to-use desktop application for biologists. In today's show, Landry explains that coming up with a user friendly platform called Geneious has been the main driver for the company. If you're looking to write your own command line, Geneious is probably not for you, says Matt. He believes that the next phase for bioinformatics will go the user friendly direction and be based on an app model similar to the Apple platform. This makes him very interested in the two cloud based platforms offered by Illumina and now the new one released in beta by DNAnexus.

New Zealand is a country with a small population and a national health service, and Matt comments on the opportunities for genomic medicine in such a country. How do we change the culture of the medical ecosystem, and what comes after the cloud? Matt works out on the front lines and tackles these questions head on.



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