single cell genomics


A Great Time to Be in Biology: Steve Quake, Stanford

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

Guests:

Steve Quake, PhD, Professor, Bioengineering, Stanford
Bio and Contact Info

Listen (4:45) Bringing physics to biology

Listen (6:28) New technology driving the study of single cells

Listen (4:30) A great time to be in biology

Listen (4:32) Thoughts on privacy and incidental findings

Listen (4:05) What is holding back the adoption of genomic medicine?

Asked about how he comes up with so many inventions, today's guest, Steve Quake, replies that he is "impatient." It's a quick answer that leaves a lasting sting. Last year when Steve won the Lemelsen-MIT award for being such a mad-inventor, Jim Plummer, dean of the Stanford School of Engineering, wrote of Steve: “It is important to remember that, at just 43 years old, Steve Quake has introduced a number of inventions, any one of which most people would consider a lifetime achievement — and there’s more to come. The true measure of the man, however, is less in his remarkable productivity, but in the profound reach of his inventions".

Beginning with a discussion about the technology Steve developed and commercialized to drive the study of single cell genomics, our interview continues on into the realm of genomic medicine and and the future of biology. Is Steve a believer that we'll be living to 200 yrs old anytime soon? And what are his thoughts on the issue of incidental findings? Listen to Steve's latest ideas in today's program.

NOTE: Since this interview was taped, Steve was elected to the National Academy of Sciences. http://engineering.stanford.edu/research-profile/quake-elected-national-...

Garry Nolan: Trailblazing Single Cell Analysis

Podcast brought to you by: Fluidigm - The leader in single-cell genomics and maker of the C1™ Single-Cell Auto Prep System. The path less traveled just go easier.

Guests:

Garry Nolan, PhD, Professor of Microbiology and Immunology, Stanford University School of Medicine Bio and Contact Info

Listen (6:41) Why is the focus on the single cell so important?

Listen (5:18) Low hanging fruit from bulk analysis already picked

Listen (6:29) What has been the response to your work?

Listen (6:25) Commercializing work as diagnostics at Nodality

Listen (6:38) Biggest challenge is to simplify

Making a big decision several years ago that his lab would have the single focus on the single cell, Gary Nolan has become a global leader in a new discipline. In today's show, he shares his conviction that the next frontier in biology is to expand the number of parameters wherein the individual cell can be studied. "The low hanging fruit from bulk analysis has already been picked," he says. Gary is a founder of two companies, Rigel Pharma (publicly traded) and Nodality, wherein his research is being commercialized. Is 2013 the year of single cell genomics, we ask this trailblazer.

Democratizing Single Cell Genomics with Gajus Worthington, Fluidigm

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

Guest: Gajus Worthington, CEO, Fluidigm Bio and Contact Info

Chapters: (Advance the marker)

0:39 Looking at heterogeneity

6:18 How is your technology driving the study of single cells

13:35 Overcoming skepticism

18:29 The promise of IPS dependent on looking at cells separately

21:11 Single cell genomics will expand to every area of cell biology

25:31 Are you the next big Illumina?

30:01 BONUS: Chip holds as much plumbing as a one-thousand-room hotel

Gajus Worthington has a message. Molecular biologists have been studying the genetics of individual cells (single cell) for a long time. But the amount of manual labor required has been prohibitive to achieving sufficiently large data sets. Fluidigm, a tools company in South San Francisco, co-founded by Worthington, is changing that. Now a single micro fluidics chip that contains as much plumbing as a one-thousand-room hotel is driving the adoption of single cell genomics research. In today's interview, Worthington, also CEO of Fluidigm, explains the company's technology and some of its applications.

We've heard a lot lately about the heterogeneous nature of cancer tumors. But there is heterogeneity everywhere, including stem cells. "Some iPS (induced pluripotent stem) cells are more "gifted" than others," Worthington explains. "To make iPS achieve its promise, and the promise is amazing, you have to understand the mechanism by which these "gifted" cells go from one type to another." One assumes the company's name comes from the two words "fluidics" and "paradigm." Fluidigm's technology is enabling researchers to make a shift in paradigm necessary to go ever deeper into the complexity of biology. Will they be the next Illumina?

Tumor Heterogeneity and Personalized Medicine

My recent blog post, Tumor heterogeneity, revealed…, discussed the New England Journal of Medicine article by Gerlinger and colleagues describing the genetic heterogeneity found both within a patient’s individual tumor nodules and between spatially separate nodules. There has been a substantial amount of discussion of this work and angst about how it might signal the end of personalized medicine even before it really got started.



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