Monthly Archives: June 2011

A question of scale

Posted on June 27, 2011 by Jyoti M.. Filed under Paper Trail, Research

Transcriptome and proteome discrepancies highlight the need for integrating information

Any high school biology student is familiar with the central dogma: “DNA makes RNA makes protein.” A new study now questions the unspoken corollary: “Do RNA transcript levels reflect protein levels in mammalian cells?”

Genome studies to identify disease-associated gene variants are based on the implicit idea that changes at the DNA level correspond to changes at the transcript and protein levels. The new research, published this month in PLo S Genetics, finds a surprisingly modest correlation between transcript levels and corresponding protein levels. Of about 7,000 transcripts and nearly 500 proteins in the livers of 97 strains of mice, only half of all proteins had a significant correlation, with an average value of 0.27.
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Q & A with Sepandar Kamvar

Posted on June 23, 2011 by Jyoti M.. Filed under Life at NextBio, Open Science

“In biology, the ability to create information has increased tremendously, faster than the traditional journal system gives the ability to propagate, review, endorse, and remix.”

The Web is an information source to most of us. But it’s also a dynamic, interactive medium, fluid as much in its substance as in its focus. In some ways, the same could be said of scientific data and the trajectory of research, especially in bioinformatics and genomics. As a constantly growing information repository and source, genomic data is constantly re-interpreted to increase our understanding of disease risks, pharmacogenomics, personalized medicine, and much more.

Sepandar Kamvar is no stranger to large amounts of confusing data. After all, he co-authored the book “We Feel Fine: An Almanac of Human Emotion”. Previous head of personalization at Google and currently on the technical advisory board of organizations as diverse as Etsy and NextBio, the assistant professor of Computational and Mathematical Engineering at Stanford University spoke with NextBio about the future of scientific information exchange.
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Networking prescriptions

Posted on June 20, 2011 by Jyoti M.. Filed under Paper Trail, Research

Analyzing electronic medical records uncovers drug interactions

Going paperless with patient records could benefit more than just the trees, according to a new study published in Clinical Pharmacology and Therapeutics. Based entirely on electronic medical records, the research finds an intriguing association between higher blood glucose levels and combining prescriptions for two drugs, pravastatin and paroxetine.

Pravastatin belongs to the statin class of drugs used to treat high blood cholesterol, while paroxetine is of the same class as Prozac, a selective serotonin reuptake inhibitor (SSRI) commonly prescribed to treat symptoms of depression. Depression and hypercholesterolemia are two of the most commonly treated diseases in the US. In 2009, there were at least 15 million prescriptions for pravastatin and paroxetine alone. An estimated 500,000-700,000 people are likely to have been prescribed both these drugs simultaneously in that year.
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Q&A with Aisha Furqan

Posted on June 17, 2011 by Jyoti M.. Filed under Life at NextBio, NextBio

“Everybody knows about genes that are studied. How do you find information about genes that aren’t? Where do you even start looking?”

As a graduate student, I was always amazed by—and a little skeptical of—any software that promised to help my data woes. I’m still curious to know what goes on behind the scenes, so to speak, when a website manages to take my search terms and raw data and turn them into pretty graphs and new correlations. Watch this space to find out about the “behind the scenes” people and ideas that shape NextBio.

We’re excited to bring you “Life @ NextBio”, a series which spotlights our curators, engineers, advisors, and others as they talk about life and work at NextBio. This week, meet Aisha Furqan, associate scientist in Curation, recent graduate from the Biological Sciences Department at Cal Poly Pomona, and enthusiastic NextBio user.
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Bypassing ‘fat’ genes?

Posted on June 15, 2011 by Jyoti M.. Filed under Paper Trail, Research

Growing evidence suggests gene variants may influence the outcome of bariatric surgery

Most people looking to shed a few pounds turn to alternatives like drinking less soda or taking the stairs at work. But for those beyond the reach of dietary and lifestyle intervention, gastric surgery is often the only viable option that presents itself. From 1998 to 2005, the number of weight-loss operations performed in the United States alone rose more than 8-fold, from about 12,000 cases to over 110,000.

There are already several studies that identify so-called ‘fat genes’, or genetic variants linked to obesity and related disorders. Recently, three research groups also published genome-wide association studies (GWAS) identifying obesity-related associations in subjects undergoing some form of gastric surgery* .
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Welcome (back)!

Posted on June 13, 2011 by Jyoti M.. Filed under News, NextBio

More than 8,000 curated studies, a whole new look and thousands more users. If you’ve been wondering where we were, there’s your answer. We’ve had a lot going on, and now we’re back to share it all on this blog. So welcome back to news from NextBio!

Over the next few weeks, we hope to update this space with all the exciting happenings at NextBio. High on that list is the upcoming update of our public site, which will be made freely available to academic, government and non-profit users. Here’s a preview of what it looks like:
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