NEWS | OCTOBER 2015
Arnaout Lab Wins Jackson Labs Pilot Grant
Working with the Jackson Laboratories, Dr. Arnaout and his team will be investigating the adaptive immune response to breast cancer and to treatment with cutting edge chemotherapeutics known as checkpoint blockade inhibitors.
NEWS | AUGUST 2015
Arnaout Lab Team Releases Recon, v1.0
Sampling from immune repertoires and other very large populations introuces bias, even when samples are large. The species frequencies and diversity measures in the sample can misrepresent those of the overall population. To solve this problem, the Arnaout Lab built Recon (reconstruction of estimated communities from Observed clones) and shared it on GitHub.
NEWS | DECEMBER 2014
Arnaout Lab Team Receives American Heart Association Award
The American Heart Association has announced Dr. Arnaout as winner of its groundbreaking Cardiovascular Genome-Phenome Study Pathway Grant. Through this generous support, Dr. Arnaout will lead a multi-institutional, multi-disciplinary team to study how the immune system might be harnessed to help prevent heart disease, the nation's leading killer.
NEWS | SEPTEMBER 2014
Dr. Arnaout Wins 2014 Dvorak Award
Named in honor of cancer research pioneer Harold Dvorak, MD, whose novel investigations helped launch the field of angiogenesis, the award was created in 2013 through a gift from BIDMC donors Sheldon Simon and Ruth Moorman, whose generous support is helping to train the next generation of outstanding biomedical researchers.
NEWS | JUNE 2014
Arnaout Lab Discovers New Form of B-Cell Selection
Antibody repertoires are known to be shaped by selection for antigen binding. Unexpectedly, we now show that selection also acts on a non–antigen-binding antibody region: the heavy-chain variable (VH)–encoded “elbow” between variable and constant domains. Thus, deep sequencing reveals a previously unidentified mode of B-cell selection. Out now in Proceedings of the National Academy of Sciences.
NEWS | MAY 2014
CAP Profiles Underuse in Laboratory Testing
Misuse of laboratory testing is rife. Until recently the focus has been on overuse. In November, the lab showed that underuse was at least as important. Now, the College of American Pathology has published an in-depth feature picking up this story. The lab's work is quoted. Out now in the May 2014 issue of CAP Today.
NEWS | APRIL 2014
Team Predicts Blood Test Results Using Big Data
Lab testing is the single highest-volume medical activity, making it valuable for doctors to be able to predict results without having to order the actual tests. The team uses big data from electronic medical records to show when this might be possible—and when it might not. Out now in PLoS One.
NEWS | DECEMBER 2013
Lab joins the Dana-Farber/Harvard Cancer Center (DF/HCC)
Dr. Arnaout has joined the faculty of the Dana-Farber/Harvard Cancer Center. The lab looks forward to closer ties with the extraordinary community of the DF/HCC regarding B- and T-cell immune repertoires in cancer and in cancer immunotherapy.
NEWS | NOVEMBER 2013
Team charts the dollars and sense behind blood tests
Doctors order too many blood tests, conventional wisdom goes, and repeat blood tests are helping bankrupt medicine. But is it true? A surprising new 15-year study by Dr. Arnaout and colleagues finds widespread underuse, as well as overuse, of this single highest-volume medical activity, with repeat tests just the tip of the iceberg. The team discusses the implications for patients, doctors, and the $3-trillion US healthcare economy. Out now in PLoS One.
NEWS | JUNE 2013
Lab joins HMS Systems Biology PhD program
Dr. Arnaout has joined the faculty of Harvard Medical School's Systems Biology Program. The lab looks forward to closer ties with the amazing students, fellows, and faculty of the Department of Systems Biology at HMS.
NEWS | MAY 2013
Statistics help pundits plan big science
"Statistics Crush Pundits" ran the headlines when Nate Silver predicted the 2012 presidential election using mathematical models. A brief comment following up on our own recent work predicting the cost and pace of pharmacogenomic advances using models was just published in Nature.
NEWS | FEBRUARY 2013
Crowdsourcing big-data bioinformatics
Informatics expertise is in short supply in biology, including in immunomics. Teaming up with the medical school, business school, and industry, we show that competitive crowdsourcing can help. Joy's Law says "no matter who you are, most of the smartest people work for someone else." Through competitive crowdsourcing, maybe more of them can work for biologists. Out now in Nature Biotechnology.
NEWS | JANUARY 2013
Team prices out genomic medicine
You've heard it before: genomic medicine will change everything. But how exactly, when, and how much will it cost to get there? Using mathematical forecasting techniques like those used to predict presidential elections, the Arnaout Lab offers numbers and a roadmap in a first-of-its-kind evidence-based study just published in Clinical Chemistry.
NEWS | JULY 2011
Turning resident calls into clinical insights
Clinical pathology residents handle thousands of calls each year on every topic imaginable, but most institutions lack an easy way to keep track of them all. So we built one—CallWall—and have now published on our trainees' initial experience using this web-based system to track their calls.
Want to use CallWall for resident training and test utilization where you are? Contact Dr. Arnaout.
We use computational biology, math, physics, and engineering to understand complex systems in biology, genomics, and medicine.
Immune repertoires and genomics
B and T cells are important in vaccines, infections, autoimmunity, aging, and cancer. There are millions of these cells in a typical blood sample. High-throughput sequencing and big-data computational biology make it possible to investigate how this unique set of cells carries out its functions—and raise the possibility of using them as early diagnostics and biological therapeutics for a range of conditions. In our lab, we are sequencing and analyzing antibodies and T cell receptors across species and medical conditions to understand this complex system.
Medicine has a genome. This genome is made up of the health data of the millions of people who interact with doctors, nurses, and others at hospitals and clinics around the world. This includes the results of diagnostic blood tests, the single highest volume medical activity, as well as procedures, diagnoses, and more. Within this genome is knowledge for better patient care and the basis for a nationwide learning health system. We are using big-data analytics and traditional techniques to reveal useful patterns, trends, and features of conventional medical care and of genomic medicine and use real-world hospital data to give structure to problems in clinical medicine that are commonly talked about but not well understood.
Working with us
Are you a physicist, mathematician, bioengineer, or computational biologist looking for awesome, game-changing problems to work on in biology, big data, or medicine, or some combination of the three? Let us hear from you. We also collaborate with Harvard and MIT researchers looking for RNAseq or microarray analysis.
Ramy Arnaout, MD, DPhil is Assistant Professor of Pathology at BIDMC and Harvard Medical School, Associate Director of the Clinical Microbiology Laboratories at BIDMC, and cofounder of the Department of Pathology's Genomic Medicine Initiative. An alumnus of MIT, he received his doctorate in mathematical (systems) biology from Oxford University on a Marshall Scholarship and his MD from Harvard Medical School as a Soros Fellow. He completed residency in pathology at Brigham and Women's Hospital and postdoctoral work at the Broad Institute of MIT and Harvard.
Joseph Kaplinsky, PhD is a postdoctoral fellow studying immunogenomics in the lab. He received his doctorate from Imperial College, where he built microfluidic systems for single-cell analysis. Trained in theoretical and experimental physics as well as biology, he is interested in applying physical and quantitative systems approaches to biological problems.
Anthony Li is a research assistant studying immunomics in the lab. He received his MS in Pharmaceutical Sciences from the Massachusetts College of Pharmacy and Health Sciences where he helped develop of liposomal techniques to specifically target mitochondria in malignant murine glial cells. He is interested in the use of microfluidics as a high throughput method of analysis and quantification. He moonlights at the circus.
Alumni and Friends
Thomas Buck, MD is a hematopathologist in Connecticut. He completed his pathology training at the Beth Israel Deaconess Medical Center. He is interested in promoting an empirical approach to the practice of laboratory medicine and in finding ways to apply this directly to patient care. In the lab he helped build models and analyzed data on the pace of pharmacogenomic advances to forecast when they will affect patients in the clinic, and how much this is likely to cost.
Eric L. Ding, ScD is an epidemiologist, nutritionist, and research faculty at the Harvard School of Public Health. His research focuses on obesity and nutritional risk factors for chronic diseases, social networks on health, and social media technology for health. In 2006, he was noted for his key role in leading a two-year-long investigation into the controversial drug safety and adverse metabolic risks of Vioxx®.
Fahim Mohammad, PhD is a postdoctoral fellow studying the bioinformatics of complex diseases, computational biology, and systems medicine in the lab. He received his doctorate from the University of Louisville, where he devised a systems-based approach for detecting and predicting molecular interactions across tissues.
Paulvalery Roulette, MD is a second-year orthopedics resident at Carolinas Medical Center and an alumnus of Harvard Medical School and Cornell University. In the lab he compiled and analyzed data on the pace of pharmacogenomic advances to forecast when they will affect patients in the clinic, and how much this is likely to cost.
Ming Zhi, MD is a first-year resident in radiation oncology in Palo Alto, CA. He is an alumnus of Harvard Medical School and of Stanford University, where he majored in biology. His interests lie at the intersection of medicine, design, and technology. In the Arnaout Lab he studied the utilization of laboratory diagnostics across medicine. He has been known to school Dr. Arnaout on the basketball court and prefers to be paid in Gatorade.
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