Integrating NGS data into clinical practice
Category Archives: Scientists
Q & A with Russ Altman
“We have to bring “genome-drug” interactions to (physicians’) attention just as we currently bring “drug-drug” interactions to their attention.”
Adverse drug events account for over 700,000 deaths each year, and nearly 30% of these are attributed to interactions of drug combinations. Public databases curate hundreds of thousands of gene variants linked to disease risks every year. Mining these diverse sources could help us learn how genetic variations, drug targets and clinical parameters come together to influence human health. Using computational tools to utilize this wealth of scientific data effectively is something we’ve discussed on the blog earlier as well.
Beginning at the “intersection of molecular biology and medical informatics” over ten years ago, Russ Altman is the founder of PharmGKB (PharmacoGenomics Knowledge Base), a database that curates and disseminates information about gene-drug-disease relationships. The professor of bio-engineering, genetics and medicine at Stanford University is also on the Scientific Advisory Board at NextBio, and spoke to us about genomics and the future of medicine.
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Data Sharing
If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.” But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together? Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.
So why don’t scientist share data well? Nature recently addressed this question in a special issue dedicated to data sharing that is available free of charge online.
Data sharing is an incredibly important issue and I am very happy to see it being addressed by such a respected and widely-read publication. With modern, high-throughput techniques bringing us into an age of data-driven science it may be more important now than ever before. But sharing data has always been central to science, it takes many minds and many perspectives to extract the full value of knowledge from data. As Cambridge professor and Rufus Pollock says : “The best thing to do with your data will be thought of by someone else.” (Voices from the future of science: Rufus Pollock of the Open Knowledge Foundation)
Nature’s special data sharing issue contains:
An editorial titled Data’s shameful neglect
A feature by Bryn Nelson called Data sharing: Empty archives
Two collaboratively written opinion pieces
Prepublication data sharing
Post-publication sharing of data and tools
Any one of them provides a thought-provoking read. Taken together they make a thorough statement on where we are now and where we need to get to in order to take full advantage of the massive amount of experimental data being generated.
by Lisa Green
If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.” But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together? Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.
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The Four Musketeers
- Hope Leman
As I try to grasp the revolution in scientific and medial research that Science 2.0 and Medicine 2.0 are effecting I often find that I am literally being rendered sleepless by trying to keep up on the writings of the leading thinkers on the subject such as Cameron Neylon, Jean-Claude Bradley, Michael Nielsen and the new kid on the block, Steve Koch.
It is quite daunting to try to keep up with the many fascinating things they have to say and the many links they provide to their colleagues in the field such as Bill Hooker and Rich Apodaca (How I wish that the latter two would add “Follow me on Twitter” buttons to their blogs. They have fascinating things to say and I find that the best way by far to keep up with thinkers and doers is via Twitter. RSS is so 2006.)
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Will Francis Collins Be The Next Head Of The NIH?
- Lisa Green
Rumors have been flying about who President Obama will appoint to head the National Institute of Health (NIH). Since the beginning of the Obama administration, Francis Collins has been considered one of the frontrunners for the post, but in the last two weeks the rumor mill seems to think that Collins is as good as appointed.
On Saturday, the LA Times reported that “a source familiar with the selection process” said that Collins was in the final stages of screening. The general consensus of the scientific community is that Collins will pass the screening with flying colors.
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RECOMB 2009 – Notes from May 18th
- Lisa Green
Monday was a great day at RECOMB. The first keynote talk started at 8:45am and at 8:00pm, when the poster ended, people were still energetic and active. At the end of the day, I was tired but not near as I had expected to be. The mental stimulation of all the interesting ideas and conversations was highly effective in counteracting physical fatigue.
It was such a full day that it is hard to pull out just a few highlights, but there were a few presentations that seemed to generate the most interest. Even though it was the first talk of the day and was followed by many excellent talks, people were buzzing about Mark Gerstein’s presentation Large Scale Analysis of Protein Interaction Networks all day long. The Slonim lab’s Evaluating Between-Pathway Models with Expression Data also generated a significant amount of discussion. The Beerenwinkel lab presented a very well-received talk Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction.
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RECOMB 2009 – Notes from May 17th
Yesterday was the first day of RECOMB 2009. The conference started off with a great opening reception. There was a palpable buzz in the room as everyone was excited to be here and very enthusiastic about the upcoming talks and posters.
There are about 300 people at RECOMB 2009 and I think that is an excellent size for a conference. At this size, the conference is small enough that you get a chance to talk with most people and large enough that you are continually finding someone new to talk with. Before the conference started I was hoping to meet and talk with Professors Donna Slonim and Ron Pinter. During last night’s reception, it was easy to find both Professor Slonim and Professor Pinter. It took a little patience to find a time to introduce myself because they were both frequently engaged in lively discussions with a group of people, but I got to meet them both. I also met several other people whose work I found very interesting.
Today is the first full day of the conference and the morning started off with a session on protein interactions chaired by Ron Pinter. No time to blog about it now, I have to get back for the next session – Martin Vingron is the chair and there are three talks on gene expression which I suspect will all be quite interesting.
I will give some details on today’s talk in tomorrow’s blog post. You can find the complete schedule of talks and lists of posters topics on the RECOMB 2009 website.
RECOMB 2009
- Lisa Green
This weekend I am heading off to Tucson Arizona to attend RECOMB 2009. The name RECOMB comes from Research in Computational Biology, and the annual conferences attract many outstanding scientists whose research is at the intersection of computational, mathematical and biological science.
I am really looking forward to this conference! While going over the program I saw some presenters I wasn’t familiar with. I looked into their research to learn more and now I am quite excited about hearing some of these researchers present their work. Two of these are:
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Happy Birthday Rita
- Lisa Green
Today Rita Levi-Montalcini becomes the first Nobel Laureate to reach 100 years of age. Her scientific career is a source of inspiration for many people, scientist and non-scientists alike.
Dr. Rita Levi-Montalcini is a fighter. As a young woman she fought against the Victorian gender stereotypes dictating that women were only suited for domestic roles and should not be permitted to participate in higher education. After graduating from medical school in Turin, she fought against the anti-Semitic laws that barred her from working in a university or a public institution. Working in a makeshift laboratory in her home she did experiments and actively published until Hitler invaded Italy.
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