IS Programmer/analyst II/ 40 hrs/ Day/ Pathology Partners Healthcare
Boston, MA

Job Description

GENERAL SUMMARY:

Position available immediately to assist in developing novel computational models for analyzing microbiome time-series data using advanced statistical and machine learning methods. In this position, you will implement new methods being developed in the Gerber lab. You will have the opportunity to work on real, clinically relevant biomedical problems as well as help develop advanced machine learning methods. There will also be an opportunity to publish and pursue independent research projects. This could be a good fit for a very talented recent B.S. or M.S. graduate seeking to gain more research experience. Techniques we use, and you would have an opportunity to learn more deeply, include Bayesian nonparametric models, dynamical systems inference from sparse data, interpretable machine learning models, and approximate inference methods.

The Gerber lab (http://gerber.bwh.harvard.edu) develops novel Bayesian statistical/machine learning models and high-throughput experimental systems to understand the role of the microbiota in human diseases, and applies these findings to develop new diagnostic tests and therapies. A particular focus of the Gerber lab is understanding dynamic behaviors of host-microbial ecosystems. Our work in this area includes the MCTIMME, MDSINE and MITRE algorithms, for discovering temporal patterns in microbiome data, inferring dynamical systems models from microbiome time-series data, or predicting host status from microbiome time-series data. We have applied these methods to a number of clinically relevant questions including understanding dynamic effects of antibiotics, infections and dietary changes on the microbiome, and designing bacteriotherapies for C. difficile infection and inflammatory bowel disease. We also apply our methods to synthetic biology problems, to engineer consortia of bacteria for diagnostic and therapeutic purposes.

The Gerber lab is located in the Division of Computational Pathology, which Dr. Gerber directs, at Brigham and Women's Hospital (BWH) at Harvard Medical School (HMS) and the Massachusetts Host-Microbiome Center (http://metagenomics.partners.org), which Dr. Gerber co-directs. BWH, an HMS affiliated teaching hospital is adjacent to the HMS main quad and is the second largest non-university recipient of NIH research funding. The broad mandate of the BWH Division of Computational Pathology is to develop and apply advanced computational methods for furthering the understanding, diagnosis and treatment of human diseases. The Division is situated within the BWH Department of Pathology, which houses over 40 established investigators, 50 postdoctoral research fellows, and 100 research support staff. In addition, BWH is part of the greater Longwood Medical Area in Boston, a rich, stimulating environment conducive to intellectual development and research collaborations, which includes HMS, Harvard School of Public Health, Boston Children's Hospital and the Dana Farber Cancer Institute.

PRINCIPAL DUTIES AND RESPONSIBILITIES:

* Under general supervision of the Principal Investigator, applies, researches, and develops statistical, mathematical, or computer science models for analysis, inference, and prediction from microbiome data sources.


* Develops software for use in the Principal Investigator's laboratory and for general use in the research community, for analyzing microbiome data. Software must be well-documented and maintained, including appropriate version control, internal documentation, and user manuals.


* Contributes to scientific literature, reports, journals and presentations.


* Assists in orientation and training of graduate students, post-doctoral fellows, and other personnel as needed.



Qualifications:

* Minimum of a Bachelor's degree in computer science, applied mathematics, statistics, or other highly quantitative discipline


* Strong Python development skills and experience implementing machine learning algorithms; TensorFlow or Pytorch experience desirable


* Formal coursework in algorithms, software design, machine learning, and probability/statistics required; you will need to understand quite a bit of theory


* Some experience modeling biological systems required; microbiome experience desirable, but not required


* Superior communication skills; you will be expected to contribute to writing scientific papers


* U.S. citizen, permanent resident, or valid visa allowing you to work in the U.S.



Skills/Abilities/Competencies Required:

* Strong Python development skills and experience implementing machine learning algorithms; TensorFlow and Pytorch experience desirable


* Formal coursework in algorithms, software design, machine learning, and probability/statistics required; will need to understand quite a bit of theory


* Some experience modeling biological systems required; microbiome experience desirable, but not required


* Superior communication skills; will be expected to contribute to writing scientific papers


* Excellent time management/organizational skills.


* Ability to work well in a multidisciplinary, team setting.


* High degree of initiative and ability to persevere on research problems.