Keeping it simple (for a bioinformatician)

Alumnus strikes delicate balances in big data — helping define the future of health care.

There is a “deluge of information” at the intersection of biology and computation, says Gaurav Bhatia PhD '14, a graduate of the Harvard-MIT Division of Health, Science and Technology (HST). However, Bhatia seeks to “push complexity away, and solve problems in the simplest incarnation possible.” Using newly developed statistical methods and computer models, he is accomplishing just that, with some of modern biology’s largest and most challenging data sets — those involving the human genome.

HST Graduation 2014

Friday, May 30, 2014

MIT Media Lab
MIT Campus, Building E14, 6th floor
Corner of Amherst and Carleton Streets
Cambridge, Massachusetts




Patty Cunningham Honored with 2014 Gillis Award


The 2014 Gillis Award is presented to Patty Cunningham (center) by Jane Neill (left) and Jules Dienstag, MD.


Patricia Cunningham, Academic Programs Administrator for IMES and HST, was honored with the 2014 Richard A. Gillis Award for Excellence in Medical Education at Harvard Medical School’s annual Teaching Awards Ceremony on May 5. 

This phenomenally well-deserved award recognizes Patty’s very long tenure as an HST administrator and her dedication and devotion to the HST program, students, faculty and staff. Patty is widely admired for her amazing can-do spirit, positive attitude, even temperament, and consummate teamwork, which she exercises uniformly both within HST and in the broader MIT and Harvard communities. As her colleagues explained:

"Patty has been integral to the lives of literally generations of HST students and faculty. In her typical understated and diplomatic manner, Patty works her magic in just about every aspect of the workings of HST at HMS. What she does is always in the best interests of the students and the program, as she shies away from taking credit."
"Patty is simply the heart and soul of HST. Beyond herding all the HST cats and insuring that the trains run on time (something she seems to do almost effortlessly), Patty also functions as the institutional memory of the program. She knows every student past and present, and is a loving mother/sister/aunt to each and every one of them. She is also a wise and experienced observer of the human condition; her insights, reflections, and broad shoulders (to cry on) have salved many a bruised ego, and salvaged many a difficult situation.”
The Richard A. Gillis Award for Excellence in Medical Education was established in 2012 in memory of Rick Gillis (1953-2011), Executive Director of Curriculum Programs, whose 27 years of contributions to the MD program at Harvard Medical School exemplify the standards of excellence and the work ethic he inspired in those who were privileged to know him and to work with him. The award is given to a member or members of the HMS staff for their outstanding contributions to the educational mission of the School. This award serves as a reminder of Rick’s legacy and the critical role of staff in facilitating, in the words of his hero, President John F. Kennedy, “the infinite potential of the human mind that can be realized through education … [and that] can be translated into benefit for everyone and greater strength for our Nation.”


Martha Gray Prizes for Excellence In Research Given to Students at HST Forum

The “Martha Gray Prizes for Excellence in Research" were named to honor former MIT director Martha Gray.  Under Dr. Gray's leadership, HST's faculty, graduate programs and community outreach grew—underscoring her focus on developing connections among individuals. 

Her passion for bringing together the diverse, yet interconnected, parts of the HST universe is part of her abiding legacy, and bears fruit in the breadth of HST student research.

In the context of an impressive array of student research, the 2014 Martha Gray Prize Winners selected at the Forum were:

Bioinformatics and Integrative Genomics
Michael S. Rooney, “The Mutational Landscape of Immune-Infiltrated Tumors”    

Physiology and Systems Biology
Jared Mayers, “Elevated circulating branched chain amino acids are an early event in pancreatic adenocarcinoma development”

Imaging and Optics
Sheldon J.J. Kwok, “Multiphoton photoconvertible probe for in situ labeling of circulating cells”

Biomedical Devices
Andrew Warren, “Point-of-care diagnostics for cancer using synthetic urinary biomarkers and paper microfluidics”

Cell and Molecular Biology
Priya Srikanth, “Identifying critical functions of DISC1 disrupted in major mental illness”

Regenerative Medicine
Steven Castleberry, “Self-Assembled Wound Dressings Silence MMP-9 and Improve Diabetic Wound Healing In Vivo”

Pictured left to right: Michael Rooney, Andrew Warren, Priya Srikanth, Sheldon J.J. Kwok and Steven Castleberry (not pictured - Jared Mayers).
Photo by David Barron

Nanopores underlie our ability to tune in to a single voice

David L. Chandler, MIT News Office

Even in a crowded room full of background noise, the human ear is remarkably adept at tuning in to a single voice — a feat that has proved remarkably difficult for computers to match. A new analysis of the underlying mechanisms, conducted by researchers at MIT, has provided insights that could ultimately lead to better machine hearing, and perhaps to better hearing aids as well.

Our ears’ selectivity, it turns out, arises from evolution’s precise tuning of a tiny membrane, inside the inner ear, called the tectorial membrane. The viscosity of this membrane — its firmness, or lack thereof — depends on the size and distribution of tiny pores, just a few tens of nanometers wide. This, in turn, provides mechanical filtering that helps to sort out specific sounds. Read more...

This optical microscope image depicts wave motion in a cross-section of the tectorial membrane, part of the inner ear. This membrane is a microscale gel, smaller in width than a single human hair, and it plays a key role in stimulating sensory receptors of the inner ear. Waves traveling on this membrane control our ability to separate sounds of varying pitch and intensity.   



A Paper Diagnostic for Cancer


Photo: Bryce Vickmark

MIT professor Sangeeta Bhatia has developed a new paper diagnostic that can detect cancer by identifying biomarkers in the patient's urine.

Cancer rates in developing nations have climbed sharply in recent years, and now account for 70 percent of cancer mortality worldwide. Early detection has been proven to improve outcomes, but screening approaches such as mammograms and colonoscopy, used in the developed world, are too costly to be implemented in settings with little medical infrastructure.  

To address this gap, MIT engineers have developed a simple, cheap, paper test that could improve diagnosis rates and help people get treated earlier. The diagnostic, which works much like a pregnancy test, could reveal within minutes, based on a urine sample, whether a person has cancer. This approach has helped detect infectious diseases, and the new technology allows noncommunicable diseases to be detected using the same strategy.

The technology, developed by MIT professor and Howard Hughes Medical Institute investigator Sangeeta Bhatia, relies on nanoparticles that interact with tumor proteins called proteases, each of which can trigger release of hundreds of biomarkers that are then easily detectable in a patient’s urine.

Robert Langer wins 2014 Breakthrough Prize in Life Sciences


Institute Professor Robert Langer was one of six scientists honored with the 2014 Breakthrough Prize in Life Sciences, which recognizes excellence in research aimed at curing intractable diseases and extending human life. Each award included a $3 million prize, with the “aim of providing the recipients with more freedom and opportunity to pursue even greater future accomplishments.”

“Scientists should be celebrated as heroes, and we are honored to be part of today’s celebration of the newest winners of the Breakthrough Prize in Life Sciences,” said Anne Wojcicki and Sergey Brin, two of the award founders. Other founders include Silicon Valley entrepreneurs Jack Ma, founder of Alibaba Group, and his wife, Cathy Zhang; technology investor Yuri Milner and his wife, Julia; and Mark Zuckerberg and his wife, Priscilla Chan. Langer was honored for his “discoveries leading to the development of controlled drug-release systems and new biomaterials," according to the prize. Read more...



Encapsulate This


Arturo Vegas hits the play button on his tablet computer. A video pops up showing the inside of a monkey's abdomen. “You see this blistering?” asks Vegas, a chemist at the Massachusetts Institute of Technology (MIT) in Cambridge. He points to the lining of the abdominal cavity onto which hundreds of tiny balls resembling semi-translucent fish eggs are attached. “Those are all capsules, and what we're trying to do here is wash them out with a saline solution.” A large needle comes into view and squirts the capsules with fluid in an effort to retrieve them for analysis. They don't budge.

Insulin-producing islet cells could hold the secret to curing type 1 diabetes—if only scientists could figure out a way to encapsulate and transplant them into the body. But first, the right biocompatible material must be found to hold these precious cells. A team of bioengineers thinks it has discovered one. Elie Dolgin reports.

A new way to monitor induced comas
  Automated system could offer better control of patients’ brain states. After suffering a traumatic brain injury, patients are often placed in a coma to give the brain time to heal and allow dangerous swelling to dissipate. These comas, which are induced with anesthesia drugs, can last for days. During that time, nurses must closely monitor patients to make sure their brains are at the right level of sedation — a process that MIT’s Emery Brown describes as “totally inefficient.”  

Emery Brown Photo: Bryce Vickmark

Wyss Study Could Be Genetics Breakthrough

A recent study from Harvard’s Wyss Institute for Biologically Inspired Engineering has uncovered features of the genetic code that may end a long-standing controversy in molecular biology and revolutionize the way many drugs and biofuels are currently produced.

Daniel B. Goodman, a graduate student in the HST program, and George M. Church, the Robert Winthrop Professor of Genetics at HMS, led the study.

When rare “words” (codons) are present near the start of bacterial genes, working copies of the gene don’t fold as readily into structures that block protein production. To find out whether the rare words themselves or lack of roadblocks increased protein production, Wyss Institute researchers synthesized 14,000 snippets of DNA with rare codons, roadblocks, both, or neither (individual pixels in this diagram), inserted them into genes, and measured how much protein they produced. Those with rare codons and roadblocks no longer made more protein (green pixels). That showed that rare codons work by removing roadblocks. (Credit: Wyss Institute for Biologically Inspired Engineering at Harvard University)