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Bio: Michael Cooke
Posted by Mary Canady August 18th, 2010 .
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Michael P. Cooke received his Ph.D in Biochemistry from the University of Washington, Seattle in 1991 working with Dr. Roger Perlmutter where he studied the role of the src-family kinase, fyn in T cell development and activation. He did postdoctoral work with Dr. Chris Goodnow at Stanford University where he studied molecular mechanism of immune tolerance. From Stanford he went to the hematopoietic stem cell company SyStemix Inc. in Palo Alto, Ca where he was Director of Functional Genomics. He joined the Genomics Institute of the Novartis Research Foundation (GNF) in 1999 and is currently Director of Immunology. He is responsible for oversight of immunology research at GNF leading a team of more than 40 scientists to discover targets and develop therapeutics to treat autoimmunity and boost vaccines. He has published more than 40 papers in top journals including Cell, Science, and Nature and serves as a member of the research management team at GNF. His own research includes the application of genomics tools and chemical screens to study the biology of hematopoietic stem cells and the adaptive immune system and the translation of these findings into novel therapeutics to treat immune disorders and improve HSC transplant outcomes.

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SDBN August 18th Event: The Human Genome 10 Years Later: What Does it Mean for San Diego Biotech?
Posted by Mary Canady July 23rd, 2010 .
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June 2010 marks the 10th anniversary of the sequencing of the human genome. As Francis Collins has pointed out, “we invariably overestimate the short-term impacts of new technologies and underestimate their longer-term effects.” As a member of the community for 14 years, I can tell you that this is true for San Diego, as the expectations in 2000 were likely too high, but the last ten years have brought unexpected progress in many areas.

San Diego has a great ecosystem to take advantage of these exciting longer-term benefits, ranging from our expertise in creating cutting edge research tools, to ground breaking drug discoveries, to new classes of diagnostics, to the exciting new field of synthetic genomics. Of course, Craig Venter has given us a big vote of confidence by relocating here. Let’s bring together experts in an interactive environment August 18th to discuss how we can take advantage of these exciting opportunities. Register here.

Panelists:

Michael Cooke, Ph.D., Director of Immunology Discovery, Genomics Institute of the Novartis Foundation (GNF) (Bio)
Kelly Frazer, Ph.D., Chief of the Division of Genome Information Sciences for the UCSD Department of Pediatrics (more info)
Tom Novak, Ph.D.,, SVP of Research, of Fate Therapeutics (Bio)
Aristides A. N. Patrinos, Ph.D., President, Synthetic Genomics (more info)
Emily Winn-Deen, Ph.D.,, Vice President, Diagnostics Development at Illumina (Bio)

Moderators:

Scott Markel, Principal Bioinformatics Architect, Accelrys, and Paul Flook, Senior Director, Life Sciences R&D, Accelrys

Here are some seed questions for the discussion, and as always feel free to submit your questions as comments below:

• How will the direct to consumer genomics market impact our economy?
• How is genomics being used in drug discovery, and what therapeutic areas have the most promise for San Diego?
• Will the continuing affordability of sequencing affect the landscape of companies?
• What are the best adaptations we can make to take better advantage of the opportunities?

Sponsors

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology August Event: The Human Genome 10 Years Later: What Does it Mean for San Diego Biotech?
When: Wednesday, August 18th, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $25/$20 Academic
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/august

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

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#SBS10 Day 3 – Smart mice and blowing House, M.D.’s mind: Drug discovery in epigenetics
Posted by Dr. Gunn April 14th, 2010 .
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At the afternoon session of the Society for Biomolecular Science in Phoenix, it’s all about epigenetics, the study of heritable changes that don’t involve changes in genetic sequence.  Epigenetics explains why identical twins turn out a little different and even clones won’t be exactly identical.

Manfred Jung from Freiberg kicked off the session giving an overview of recent developments in epigenetics and presented what would become the central theme of the afternoon: Here are some diseases which haven’t received the amount of attention they deserve, here are some enzymes and proteins that cause the diseases when there’s something wrong with them, here’s how to target those enzymes. Go get ‘em, boys! (more…)

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SBS Day Two: A Holistic Approach To Drug Discovery #sbs10
Posted by Mary Canady April 14th, 2010 .
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I’m blogging from the Society for Biomolecular Sciences conference in Phoenix, the organizers were kind enough to offer two of us complimentary passes. I was surprised that the sessions were separated into disease area, technique, or ‘phenomenon’ (e.g., epigenetics) which seemed a bit curious as well, as I had expected the different types of assay technologies would have been the basis (e.g. HTS, Cell-based). It will be interesting to see how this changes if SBS merges with ALA. Nevertheless, I’ve been spending most of my time in the oncology session, and have been looking for trends to share with you, as that is usually the most valuable thing I take away from conferences.

Over the years, I’ve noticed the evolution of different themes each year at drug discovery conferences. In the kinase area alone, I’ve been going to conferences from before the kinome was sequenced, to the era of differing theories of the efficacy of specific targeting, to today’s somewhat routine screening and questions regarding what will be the ‘next big thing’ (but have we figured them out yet?) I think a major theme of this meeting, and something I’ve seen evolving over the past few years, is the idea that a holistic approach to drug discovery, whereby high-throughput screening is seen as part of the process and not the dominant technology.

Peter Simpson of AstraZeneca talked about the need for quality assays across the spectrum, from eliminating error through acoustic liquid delivery, microfluidic methods, and an standardized ‘uber’ kinase assay to utilizing biophysical and fragment-based technologies to round out the information used for lead discovery and optimization. Indeed, a more holistic approach seems to be the norm, perhaps a response to the tightening of belts we’ve all experienced in this economy.

Part of this holistic approach is the the parallel utilization of cell-based assays, which are becoming an essential and more reliable part of the drug discovery process. Perusing the exhibit floor underlines this theme–I didn’t have to walk far to find many great examples of companies pushing the boundaries to improve cell-based assay technologies. SRU Biosystems launched BIND Scanner, a label-free technology and an instrument/software combination which specializes in analyzing data from samples with low cell numbers, such as primary and stem cells. Perkin Elmer has introduced Operetta, ‘bench-top high content screening.’ Fluxion is a South San Francisco company, has married microfluidics with standard 96-well plates to simulate more physiological conditions for live cell assays. Corning continues to make strides with its Epic label-free system, and has a few interesting posters. On the reagents side, Cellular Dynamics is a Madison, Wisconsin based company based on the research and IP from James Thompson of UW, and they aim to create many types of cells for screening utilizing induced pluripotent stem (iPS). Indeed, the confluence of the increased availability of such reagents and improved instrumentation makes this an exciting time for drug discovery.

As a (former?) scientist, one thing really nags me however. From what I’ve seen, most of the cell-based assays still give a binary answer. In other words, the cell reacts to stimuli or doesn’t, and this is plugged into the ‘old’ HTS-type thinking–hit or no hit (correct me if I’m wrong). I can’t help but think that the next wave, after the growing sophistication of the cell-based technologies, will be another wave of informatics/image analysis, whereby cellular responses are deconvoluted further, yielding more important information from these assays.

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SDBN Sept. 22nd Event Featuring Intellikine
Posted by Mary Canady September 1st, 2009 .
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The September San Diego Biotechnology Network (SDBN) event will feature Intellikine, a leader in the development of innovative, small molecule drugs for the treatment of cancer, inflammation and autoimmune diseases, and recently in the news for raising $51M in VC funding. Troy Wilson, Ph.D., CEO, will give a short presentation, and as always there will be plenty of time to ask questions and interact with representatives from Intellikine.

Troy Wilson is the President, CEO and a founder of Intellikine, a biopharmaceutical company focused on the discovery and development of small molecule drugs that target the PI3K/Akt/mTOR pathway for the treatment of cancer, inflammation and other diseases. Dr. Wilson is a serial entrepreneur who previously has co-founded several San Diego based companies, including Ambrx and Phenomix. In his presentation, Dr. Wilson will describe Intellikine’s formation, the scientific and clinical rationale behind its drug discovery programs, its business development and corporate strategy, and how the company was able recently to raise $51 million in venture capital in a very challenging market. The presentation should be of interest to scientists, entrepreneurs, clinicians and anyone interested in how to translate world-class academic science into a leading biotech company.

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology Network’s September Networking Event featuring Intellikine
When: Tuesday, September 22nd, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $20, including appetizers ($15 for Academics) +$5 at door (cash or check only)
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/september

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past Tango del Rey.

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Ali R. Esteghlalian, Ph.D.
Posted by Mary Canady August 13th, 2009 .
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Dr. Ali R. Esteghlalian is a Principal Scientist and Product Manager, Emerging Specialty Enzyme Products at Verenium Corporation (San Diego, California, USA.) He has been involved in enzyme applications research & management, as well as bioproduct development for more than ten years. He specializes in the application of polysaccharide degrading enzymes in natural fiber processing and pretreatment and bioconversion of lignocellulosic feedstocks for biofuels production. Working with major industrial clients worldwide, he currently directs the product management activities for a diverse portfolio of specialty enzyme products with applications in the pulp and paper bleaching operations, textile wet processing, and oil and gas well drilling and hydraulic fracturing operations.

Prior to joining Verenium in 2002, Dr. Esteghlalian was a Research Fellow with the Chair of Forest Products Biotechnology at the University of British Columbia (Vancouver, Canada), where he conducted experimental research to elucidate the interactions between cellulolytic enzymes (cellulases) and lignocellulosic substrates. Specifically, he studied the factors affecting the enzymatic hydrolysis of softwood and hardwood derived pulp and steam-exploded wood during the lignocellulose-to-bioethanol process. Additionally, he has been involved in the assessment of greenhouse gas emissions from a range of agricultural and silvicultural practices for bioenergy production. The results of his R&D studies have been captured in a number of patents, book chapters and peer-reviewed articles.

Dr. Esteghlalian holds degrees in Chemical Engineering (B.Sc., Tehran University, Iran) and Bioengineering (Ph.D., Oregon State University, USA). He will also receive his MBA from the Rady School of Management at the University of California, San Diego in August 2010. He conducted his postdoctoral research/teaching at the University of Georgia (Athens, Georgia, USA), where he focused on how to incorporate environmental and societal factors into engineering solutions. Dr. Esteghlalian is a Senior Member of American Institute of Chemical Engineers (AICHE), American Chemical Society (ACS), Technical Association of Pulp and Paper Industries (TAPPI) and American Society of Agricultural and Biological Engineers (ASABE). He resides in San Diego, California and can be reached by phone at +1 858 526 5108 or by email at ali(dot)esteghlalian(at)verenium(dot)com.

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The Transformation of the Biotech Business Model: Vote on SDBN’s August Event
Posted by Mary Canady July 30th, 2009 .
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San Diego County biotech in 2008 represented the third largest community for developing the next generation of biopharmaceuticals and cutting edge therapies. The impact of the financial crisis and funding shortfall is accelerating trends set by outsourcing and offshoring. Yet there is light at the end of the tunnel. Many companies based in San Diego are making breakthroughs and driving changes with their leading technologies. SDBN and PGC200 are partnering to bring you key people from these companies so that you can hear directly how these changes will help our economy and how we can adapt to prosper.

Vote for the area that you would like to hear about most at our August 18th event, which will be a panel of experts from the area who will focus on the best ways we can grow. As always, this won’t be your grandfather’s panel, we will do our best to involve you in the discussion, turning the event into a brainstorming session which will give you ideas for improving your career and business. Also, there will be plenty of time for networking with the thought leaders on the panel and other biotechnology professionals.

(The poll is now closed, and you can view the results here.)

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Posted by Mary Canady July 12th, 2009 .
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Bloggers Wanted!
Posted by Mary Canady July 7th, 2009 .
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If you attended the Social Media for Scientists Event we had in May, you know that we are aiming to get more of you involved in the SDBN. One of the ways is through inviting you to write blog posts on the SDBN site. You can blog about events you attend, news or trends (any UC postdocs want to blog about the recent unionization?), or scientific topics of interest.

What’s in it for you? You’ll get exposure for yourself and your company/institution to the San Diego Biotechnology community (including hiring managers!) and experience blogging without having to start your own blog. Just submit your ideas to http://sdbn.org/iwannablog and we’ll be in touch to get the content.

Be creative–look for trends, anything newsworthy that you have unique insights on, or amusing things around you. Guides that others may find useful are also good, such as a list of resources. The tone can be amusing or irreverent, but we always want to have the aim of promoting biotechnology in the region.

We’ll look forward to hearing from you!

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Friendfeed: Life Scientists’ Biggest Little Secret
Posted by Mary Canady June 29th, 2009 .
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During our May 28th Social Media for Scientists (SMS) SDBN event, William Gunn talked about friendfeed as a useful tool for discussing science and learning. We polled the attendees before the event and found that they knew almost nothing about it, and had little interest in learning about it. We set up a friendfeed room for the group and frankly have not had much adoption.

So, what’s so great about friendfeed, why do we keep talking about it? Friendfeed aggregates all of your activity on social media, so that when you post anything on twitter, your blog, Flickr, etc. (58 social media applications are available), all of your connections there see it. Now, think of this used with a scientific ‘persona,’ if you will. You can share interesting articles, blog posts, presentations–some people even post data on Flickr–with your colleagues. Every post can be commented on, leading to interesting discussions. See this example of how friendfeed was used to stimulate and manage discussions regarding the conference, and the interest was so high that posts were thought to be spam!

Friendfeed takes it one step further, allowing you to form and join groups which focus on topics (see table below). You can benefit from group members’ posts, ask questions of the group, and take part in the discussions from any post. Scientists have been using the web to interact via forums and mailing list for a long time (we even discussed friendfeed vs. these older ways of communicating there). While someone pointed out that there is ‘nothing wrong with the old forums and mailing lists’ and that ‘you can post longer items using the old methods’ I see real value in the ‘2.0′ forms of communicating such as friendfeed. With these types of social media, as with media such as twitter, often people post interesting observations that lead to unexpected comments and new directions–there is a level of serendipitous discovery that occurs. Also, because the groups are full of like-minded people, there is not much noise, and even discussions that are tangential to your work can be interesting. As William Gunn pointed out in our SMS presentation, you can also search all posts and comments from your friends or groups, leading to one of the most targeted web searches available (bing, eat your heart out).

One thing that I find incredibly interesting is that these groups can also become commentaries on larger issues. See the References Wanted group below–it is a repository for articles that scientists cannot access freely, and thus a commentary on the need for more open access science, paradigms that journals such as PLoS subscribe to. In addition, you’ll find that the scientists on friendfeed are keen to learn about new tools–see the Evernote Addicts group, a group dedicated to software for aggregating information that scientists (and others) find very useful. As with other types of social media, it is not clear what the lifetime of friendfeed’s relevancy will be, but you can be sure that the people here will be ahead of the curve in knowing what the ‘next big thing’ for scientists will be, even if it means moving away from friendfeed or being a ‘force’ to help change it.

As with other social media, the best way to learn is to try it yourself. I suggest signing up and subscribing to the groups below, getting email updates for convenience at first. We realize that some of you are still hesitant to join, and that’s OK. It turns out that Facebook and friendfeed have a lot of similarities, as a fan page can be set up for a group of people, and items can be posted on and discussed among members. We set up a SDBN fan page for this purpose, become a fan and start posting and interacting! We hope that it will give you a ‘taste’ of ’serendipitous scientific social media’ and that you’ll be inspired to participate in tools such as friendfeed. We’ll also continue to help you learn more about the tools for science in social media through blog posts and events. As we mentioned at the SMS event, participating in social media gives you a way to get a ‘leg up’ from your colleagues in real time, and we think that once you start experiencing it, you’ll be as hooked as we are!

P.S. On friendfeed there is even a discussion on this post!

Friendfeed Groups for Life Scientists: Some Examples

Don’t see a group that interests you? Search the friendfeed groups for your research area or anything you’re interested in, or start your own!

Posted by Mary Canady of Comprendia, which helps life scientists and the industry improve communication through social media and marketing strategies. Special thanks to Sally Church of Icarus Consultants & PharmaStrategyBlog for helping with the list of groups, and to the friendfeed life scientists group, who let this ‘marketer in scientist clothing’ participate in the group. Also thanks to William Gunn, for help and convincing me to persist with friendfeed even though I didn’t ‘get it’ at first.