Snyder's Omics

Host: Marc Pelletier

Co-Host: Andre Nantel, Ph.D.

Our guest published a historic paper less than one month ago (available here), describing the first comprehensive  study of an individual, combining genomic (genome sequence), transcriptomic (genes turned on/off), proteomic (the total complement of proteins - or protein profiles), metabolomic (complete metabolic analysis), and autoantibody profiles. The study was conducted over 14 months through healthy and diseased states, over 3 billion measurements on a single individual over 20 time points. This experiment is an important step toward ushering in the era of personalized medicine. 

Guest: Dr. Michael Snyder

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Host: Marc Pelletier

Co-Host: Markus Veolter

Dr. David Baker explains how the game Foldit uses crowdsourcing to intelligently design artificial proteins never seen before in nature.

Guest: Dr. David Baker

Links

- foldit

- Rosetta@home

- The Baker Labotatory

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6 PhDs Piled High And Deep

Host: Marc Pelletier

In this episode, we talk about the Frontiers of Biotechnology - where the line between science and sci-fi are beginning to blur.

Guests: George Farr, Ph.D. , Mark Gerstein , David Thomas, Ph.D. , Justin Sanchez, Ph.D. and Simon Melov, Ph.D.

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Towards Curing Malaria With Dr. Elizabeth Winzeler

Host: Marc Pelletier

Guest: Dr. Elizabeth Winzeler, Ph.D.; Department Head, Department of Cellular Biology, Genomics Institute of the Novartis Research Foundation, San Diego, CA' Associate Professor, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA

In this episode, Dr. Elizabeth Winzeler shares her strategy to tackle malaria, a disease that affects 250-500 million people per year.

Link to Dr. Winzeler's paper

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Futures in Biotech 88: Cogito, Ergo Sum... Multitasking?

How understanding our mind will shape our futures with Dr. Adam Gazzaley.

Hosts: Marc Pelletier, Ph.D. and Dave Brodbeck, Ph.D.
Guest: Adam Gazzaley, M.D., Ph.D.

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Futures in Biotech 87: Anti-Matter Message In A Magnetic Bottle

Host: Marc Pelletier

We talk with Professor Jeffrey Hangst of the ALPHA Collaboration about the successful trapping of anti-hydrogen to hopefully answer some of our most important questions about the universe.

Guest: Prof. Jeffrey Hangst

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Futures in Biotech 87: Anti-Matter Message In A Magnetic Bottle

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Host: Marc Pelletier

We talk with Professor Jeffrey Hangst of the ALPHA Collaboration about the successful trapping of anti-hydrogen to hopefully answer some of our most important questions about the universe.

Guest: Prof. Jeffrey Hangst 

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Futures in Biotech 86: Biomasses For The Masses

Host: Marc Pelletier

Changing an Amish farm in Ohio into an energy source solution for modern times. The story of the Griswold family and Altoterra Energy.

Guests: John Griswold , Matthew J. Griswold, CFA and Mark A. Griswold, Ph.D.

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Futures in Biotech 85: Modeling Life With The World's Most Powerful Computer System

Host: Marc Pelletier

Dr. Vijay Pande, Stanford's Director of Folding@home, details how the world's most powerful system models Alzheimer's and other human diseases.

Guest: Dr. Vijay Pande

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Futures in Biotech 84: Biotech - Hot in Cleveland

Host: Marc Pelletier

Baiju Shah, President & CEO of BioEnterprise, explains how to transform a regional economy into a thriving biotechnological innovation center.

Guest: Baiju Shah, J.D.

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Futures in Biotech 83: Bioinformatics: Essential Gene names Skewed in a Network of Blame

Host: Marc Pelletier

Guest: Mark Gerstein

Dr. Mark Gerstein from Yale University explains the essence of life through network theory.

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SLIDES HERE: Biological Network Analysis

Futures In Biotech 82: Bionic Brain Symbionts: The Next Phage of Human Slurry

Hosts: Drs. Marc Pelletier, Andre Nantel, and Justin C. Sanchez

We discuss Justin's work on brain machine symbiotic devices, to identifying the key elements in autoimmune disease, to the race between transcription and translation; it's genetics gone wild.

Papers discussed:

1) First cystic fibrosis drug advances towards approval (2011). Nature Biotechnology 29:465-466

2) A symbiotic brain-machine interface through value-based decision making.

Mahmoudi B, Sanchez JC.

PLoS One. 2011 Mar 14;6(3):e14760.

3) Autoantigen discovery with a synthetic human peptidome.

Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Gakidis MA, Church GM, Kesari S, Leproust EM, Solimini NL, Elledge SJ.

Nat Biotechnol. 2011 May 22;29(6):535-41. doi: 10.1038/nbt.1856.

4) Global quantification of mammalian gene expression control.

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M.

Nature. 2011 May 19;473(7347):337-42.

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Futures in Biotech 81: Worm Research: The Buck Starts Here

Hosts: Marc Pelletier and Simon Melov

Guest: Gordon Lithgow, Ph.D., professor at the Buck Institute for Research in Aging

Dr. Gordon Lithgow bridges the science of protein folding and life extenstion. The paper that we discuss:

Amyloid-binding compounds maintain protein homeostasis during ageing and extend lifespan.

Alavez S, Vantipalli MC, Zucker DJ, Klang IM, Lithgow GJ.

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Futures In Biotech 80: Light Up The Brain

Host: Marc Pelletier and Special Guest Host Dave Brodbeck, PhD

Using optogenetics to study learning and cognition.

Guest: Dr. Ann M. Graybiel

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Futures In Biotech 79: Oceans 20

Host: Marc Pelletier and Special Guest Host Mark Gerstein

A test run for the technology that will transition us into the next era of medicine: Proteomics.

Guest: Dr. Tommy Nilsson

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Futures in Biotech 78: TWiV Infects FiB

Hosts: Marc Pelletier and Vincent Racaniello

It's a science mashup. FiB and TWiV together for one big show.

Guests: Dickson Despommiers, Ph.D. , Alan Dove, Ph.D. and Richard Condit , Ph.D.

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Must See: Cassini Images Made into a Film.

5.6k Saturn Cassini Photographic Animation from stephen v2 on Vimeo.

Futures in Biotech 77: How the Environment and a Single Protein Influence Evolution

Hosts: Marc Pelletier 

Drs. Susan Linquist and Daniel Jarosz explain how the environment can drive evolution at the molecular level.

Guests: Susan Lindquist, Ph.D. and Daniel Jarosz, Ph.D.

PAPER PRESENTED:

Science. 2010 Dec 24;330(6012):1820-4.

Hsp90 and environmental stress transform the adaptive value of natural genetic variation.

Jarosz DF, Lindquist S.

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.

Abstract

How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.

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Futures In Biotech 76: It's Time To Proteo Me

Hosts: Marc Pelletier and Vincent Racaniello

How mass spectrometry has become one of the most important technologies in our move toward personalized medicine.

Guest: Prof. Ruedi Aebersold

Sponsored by: Synergy 1.

PAPERS DISCUSSED:

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics.

Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R.

Mol Syst Biol. 2011 Feb 1;7:464.

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.

Sci Signal. 2010 Dec 21;3(153):rs4.

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Futures In Biotech 75: It's Time To Start The Human Proteome

Host: Marc Pelletier

Our guests talk about the next big transition in modern medicine: Human Proteomics.

Guests: Dr. John Bergeron and Dr. Tommy Nilsson

Sponsored by: Synergy 1.

We invite you to read, add to, and amend our show notes. 

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