Arnaout Laboratory for Immunomics
Now hiring!

We use experiments, mathematics, and machines
to decipher the human immunome.

Our mission

Your billions of B and T cells play pivotal roles in vaccination, infection, inflammation, autoimmunity, aging, and cancer. Our goal is to find signals and signatures that describe what each cell is doing, to better prevent, diagnose, and treat disease.

Selected publications

Kaplinsky J and Arnaout R. Robust Estimates of Overall Immune-Repertoire Diversity from High-Throughput Measurements on Samples. bioRxivHTML | PDF

Kaplinsky J et al. Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells. Proc Natl Acad Sci U S A 111(25):E2622-9 2014 HTML | PDF

Lakhani KR et al. Prize-based contests can provide solutions to computational biology problems. Nat Biotechnol 2013 31(2):108 HTML | PDF

Arnaout R et al. High-resolution description of antibody heavy-chain repertoires in humans. PLoS One 2011 6(8):e22365 HTML | PDF

Tsibris AMN, Korber B†, Arnaout R† et al. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 2009 4(5):e5683 †Contributed equally HTML | PDF

Dostie J, Richmond TA, Arnaout RA et al. Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res 2006 16(10):1299 HTML | PDF

Our team

We are biologists, physicians, computer scientists, physicists, mathematicians, and engineers of many backgrounds, career paths, and interests united in unlocking the secrets of the immunome—and having fun doing it. We are also now hiring. If you'd like to apply to one of the open positions below, send a CV or resume to rarnaout at gmail dot com together with a brief (~200-word) statement about why you'd like to join the lab and what you'd like to accomplish while here.

Open positions

02.16 | Bioengineer

The Arnaout Laboratory for Immunomics uses experiments, mathematics, and machines to decipher the human immunome. We are looking for a postdoctoral-level bioengineer to devise and refine novel methods relating to high-throughput sequencing.

Responsibilities:

Design, program, build, and troubleshoot electromechanical/robotic devices for high-throughput sample handling

Design, refine, and troubleshoot nucleic-acid amplification protocols (e.g. PCR)

Contribute to the generation of standard protocols and intellectual property

Qualifications:

Advanced undergraduate or graduate degree in mechanical engineering, biomedical engineering, chemical engineering, physics, or equivalent practical experience

Hands-on experience designing and building simple electromechanical/robotic devices, including programming using (ideally) Arduino or Raspberry Pi environments

Hands-on experience with PCR or similar nucleic-acid amplification methods, ideally in micro- or nanofluidic contexts

Ideally, hands-on experience in nucleic-acid synthesis and/or synthetic chemistry

Ideally, Fluency in Python and ideally other standard bioinformatics tools (e.g. R, Perl)

Excellent creativity, decision-making, troubleshooting, and English-language communication skills

Comfort with and excitement about working in a startup-type atmosphere

02.16 | Computational/systems biologist

The Arnaout Laboratory for Immunomics uses experiments, mathematics, and machines to decipher the human immunome. We are looking for a postdoc-level computational/systems biologist to operate and contribute to the informatics infrastructure required to make this happen.

Responsibilities:

Design, develop, and execute high-throughput sequencing and analysis projects

Devise, test, and implement computer algorithms for high-throughput data

Contribute to the generation of standard protocols and intellectual property

Qualifications:

PhD degree in physics, mathematics, computational/systems biology, bioinformatics, or related field, or equivalent practical experience

Hands-on experience designing and implementing computer algorithms, ideally including machine learning

Hands-on expertise with statistical descriptions of complex systems (e.g. energy, entropy, moments, etc.) and their theoretical underpinnings

Fluency in Python and ideally other standard bioinformatics tools (e.g. R, Perl, Arduino), ideally including hands-on experience with parallel processing

Demonstrated expertise in computational analysis of large data sets, ideally biological and/or sequence-based data sets

Excellent creativity, decision-making, troubleshooting, and English-language communication skills

Comfort with and excitement about working in a startup-type atmosphere

Current and former members

Ramy Arnaout, MD, DPhil is director of the lab, Assistant Professor of Pathology at BIDMC and Harvard Medical School, and Associate Director of the Clinical Microbiology Laboratories at BIDMC. 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.

Rohit Arora, PhD is a postdoctoral fellow working on immunomics in the lab. He received his doctorate in computational biology with highest honors from the Ecole Normale Superieure where he studied the origin and mechanism of resistance to the inhibitors of HIV-1 integrase. Previously he received his MS summa cum laude as an Erasmus Mundus scholar.

Anthony Li, MS 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.

Joseph Kaplinsky, PhD is former a postdoctoral fellow studying immunomics 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.

Fahim Mohammad, PhD is a former 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.

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®.

Paulvalery Roulette, MD is an 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 resident in radiation oncology in California. 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.

Our lab

Our laboratory is part of the Department of Pathology at the Beth Israel Deaconess Medical Center (BIDMC) and Harvard Medical School (HMS) and is affiliated with the Division of Clinical Informatics in the Department of Medicine at BIDMC and the Department of Systems Biology at HMS. We are supported through generous gifts and grants from the National Institutes of Health, the American Heart Association, and others.

Contribute

We study immunomics because of its great potential to improve people's health. We are only able to do that because of you: through your grants and gifts, and through your personal commitment to and involvement in scientific research. If you believe in our mission, here are two ways you can help. Thank you!

Support the lab

One way is to make a gift to the lab through a donation to our parent institution. Other options may be available. Please direct inquiries to us at rarnaout at gmail dot com.

Get involved

Immunomics today is where genomics was a decade ago: we have lots to learn. One of the best ways to help is by letting us sequence your immunome, following the precedent set by the the Personal Genomes Project, the Million Veterans Program, and other citizen science projects. Speaking with or involving other people, from students to policymakers, are also helpful things to do. If you are interested, or can think of other ways to help, please write us at rarnaout at gmail dot com.

© 2011-2016 Ramy Arnaout

Arnaout Laboratory for Immunomics · BIDMC · 330 Brookline Avenue · Boston, MA 02215

Contact us at rarnaout at gmail dot com