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Bio Saga

Thursday, January 31, 2013

Interesting story about Nicholas Tatonetti & his New Computational Tools to Study Drug Effects

Courtesy Genomeweb & Julia Karow
 
Studying for a dual degree in mathematics and molecular biology, Nick Tatonetti became interested in using computational models to study biology and make sense of its massive datasets. As a bioinformatics PhD student at Stanford, he developed new statistical models and computational approaches for analyzing drug effects and drug-drug interactions.

At Columbia, Tatonetti is now focusing on molecular mechanisms of drugs. "We can actually think of each time a patient is being given a drug as an experiment," he says. "When the drug goes into the human system, it interacts molecularly, and then phenotypes come out of this system," which can be connected to molecular mechanisms in new ways.

In particular, he is developing techniques that use clinical data to develop networks that highlight interactions between different systems in the human body, such as two organs. "And once we know that certain gene products or pathways are working together at a systems level, we can start integrating all of the molecular data we know to fill out a complete picture" and to predict phenotypes from, for example, RNA expression data or genotypes, he adds.

Paper of note

A study revealing a new drug-drug interaction by using a machine learning algorithm Tatonetti designed that scanned through millions of adverse event reports from the Food and Drug Administration appeared in Science Translational Medicine this year. That is his favorite paper, he says, "because it represents the most comprehensive innovations on both the algorithmic side and the evaluation side."

Looking ahead

Tatonetti says that over the next five years, there will be major advances in using genetic data in medicine. "It may not be that we need to store lots of genetic data in the clinical record, but that we need to understand the genetic data better so that we can provide results and suggestions to physicians," he says. Personalized medicine will not only involve genotypes, though, but also environmental exposures. Putting genetics into the context of these, he says, will increase its clinical impact.

And the Noble goes to…

If he were to win the Nobel, it would be for developing a new scientific approach, based on informatics methods and computational methodologies, that discovers a fundamental biological or medical truth. "Where that truth may be, in what system, in what disease, I could not say, but I love the idea that we're in the midst of changing the way that we do science," Tatonetti says. "That's what informatics is about, advancing the tools of the scientific method itself."

Tuesday, January 29, 2013

NextBio Teams Up with Emory, Aflac, to Locate Biomarkers for Pediatric Brian Tumors


NextBio said this week that it is partnering with Emory University’s Winship Cancer Institute and the Aflac Cancer Center to work on identifying biomarkers that can predict brain cancer metastasis in children, which will help clinicians determine which patients should receive radiation therapy.

The partners will use NextBio Clinical software to analyze and interpret molecular and genomic data collected from children with medulloblastoma, a childhood brain tumor that affects around 500 children in the US every year and accounts for 20 percent of all brain cancers in children below the age of 19.

Specifically, “this study will look at clinical and genomic data from real patients, as well as data from mouse models and frozen human tissue samples, and then will correlate these data sets with other data from the public domain,” Alpana Verma-Alag, NextBio’s head of clinical development, explained in a statement.

Tobey MacDonald, director of Aflac’s brain tumor program and associate professor of pediatrics at Emory, noted that there is currently no way to tell which patients have a higher risk of metastasis and as such all children suffering from medulloblastoma receive radiotherapy even though “it causes long term side-effects and toxicity in young growing brains.”

“[The] ability to perform genomic studies on patients and then to use NextBio Clinical’s correlation engine to compare the genomic profile of primary tumors with that of metastatic tumors, both across our data and across the large amount of data that NextBio has curated from the public domain, makes achieving our goal of improving outcomes for people with medulloblastoma seem nearer in sight,” he said in a statement.

Do you wish to know more?

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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