Technical Research Assistant I – Gibson and Walt Labs

A position is open for a full-time research assistant (RA) in the Department of Pathology at Brigham and Women’s Hospital. Under the supervision of Dr. David Walt and Dr. Travis Gibson, the selected candidate will provide technical assistance for research pertaining to the human gut microbiome and its interactions with the host immune system. This position will provide the opportunity to work with histologic, immunohistochemical, molecular cytogenetic, and in situ protocols in a state-of-the-art lab environment.

Among other responsibilities, the selected candidate will perform multiplexed error-robust fluorescence in situ hybridization (MERFISH). The RA will perform all stages of the MERFISH protocol, including tissue fixation, permeabilization, hybridization, embedding, and clearing, in addition to imaging using a custom-built semi-automated robotic system built by a team at BWH. The selected candidate will primarily work independently to prepare and process tissue samples while optimizing the respective protocols, and will work closely with the surrounding research team to interpret the resulting data. Previous experience with protocols involving RNA is considered a strong asset. Other responsibilities of the selected candidate include assistance with the execution of the ultrasensitive single molecule array (Simoa) assay. Research conducted by the candidate in collaboration with the research team will provide new insights into the dynamics of the gut microbiome and will address underlying biological questions.

The responsibilities of the selected candidate may include:

  1.  Independently performing routine and non-routine experimental protocols of moderate to high complexity. Experimental work will include preparing buffers and reagents without RNase contamination and evaluating the reagents for viability.
  2.  Performing literature searches relevant to the execution of the required protocols.
  3. In collaboration with the PIs or Research Manager, modifying existing research techniques and potentially establishing new techniques.
  4. Communicating progress professionally with collaborators and with the scientific community.
  5. Coordinating and scheduling tests and procedures, and documenting experimental work accurately and in detail.
  6. Ordering laboratory supplies related to their assigned tasks.
  7. Following all lab safety protocols.

BA/BS in biological/physical science required.  Some prior research preferred but not essential.

Skills/Abilities/Competencies Required:

  • Sound analytical and organizational skills.
  • Requires good oral and written communication skills.
  • Must be able to logically and effectively structure tasks and set priorities.
  • Ability to identify potential problems and troubleshoot solutions.

About the lab environment

The Gibson Lab is located in the Division of Computational Pathology at Brigham and Women’s Hospital (BWH), a Harvard Medical School teaching hospital, which is the second largest non-university recipient of NIH research funding. The broad mandate of the 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 the Harvard Medical School quad, Harvard School of Public Health, Boston Children’s Hospital, and the Dana Farber Cancer Institute. Many of our lab members also have appointments at the Massachusetts Institute of Technology and the Broad Institute.

Applications Process

Submit: (1) cover letter; (2) curriculum vitae to: Utkarsh Sharma, usharma1@bwh.harvard.edu

Postdoctoral Fellow, Microbiome-Host Immune System Interactions – Gerber Lab

The Gerber Lab (http://gerber.bwh.harvard.edu) is a multidisciplinary group at Brigham and Women’s Hospital/Harvard Medical School that develops novel computational 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. The director of the lab, Dr. Georg Gerber, MD, PhD, MPH, uses his unique expertise, combining advanced machine learning method development, medical microbiology, and human pathology, to leverage cutting-edge technologies to tackle scientifically and clinically important problems.

We are looking for an exceptional researcher who will play a major role in a new initiative in the lab to investigate systematically how commensal microorganisms interact with the host immune system. Although host-bacterial interactions have been extensively characterized for some pathogens, much less is known about how commensal bacteria in the microbiome interact with us. The lab will use both experimental systems (e.g., gnotobiotic animals and cell culture) and computational approaches to study various aspects of immune host system-microbiome interactions, including influence on infection/inflammation and immune repertoire development/diversity.

The successful candidate will be highly motivated and creative, taking a lead role in experimental design, execution of experiments, and interpretation of results. This position is a fantastic opportunity for an individual with strong experimental skills to learn about and apply computational techniques, enriched by extensive collaborations with top computational researchers.

Qualifications:

  • PhD in Immunology, Microbiology, or related discipline.
  • Excellent publication track record.
  • Proficiency in cell and molecular techniques including cell culture, flow cytometry, qPCR, and ELISA assays.
  • Proficiency in mouse studies including animal handling, blood collection, necropsy and cell isolation.
  • Superior communication skills and ability to work on multidisciplinary teams.
  • Experience in cellular immunology, including immune cell proliferation is highly desirable.
  • Experience in microbiology, including culture of anaerobic bacteria is highly desirable.
  • Experience with next-generation sequencing library preparation and data analysis is highly desirable.

Environment:  the Gerber Lab is located in the Division of Computational Pathology (http://comp-path.bwh.harvard.edu), which Dr. Gerber heads, at Brigham and Women’s Hospital (BWH) at Harvard Medical School (HMS), and the Massachusetts Host-Microbiome Center (MHMC) (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 Division is situated within the BWH Department of Pathology, which houses over 40+ established investigators, 50+ postdoctoral research fellows, and 100+ research support staff. The MHMC has extensive facilities to support microbiome research, including the largest not-for-profit gnotobiotic mouse facility in New England, a microbiology unit with advanced anaerobic culturing systems, and a molecular unit with next generation sequencers and robotic liquid handlers. 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 and Boston Children’s Hospital.

To apply: email a single PDF including cover letter, CV, brief research statement and a list of at least three references to Dr. Georg Gerber (ggerber@bwh.harvard.edu). In your CV, indicate whether you are a U.S. citizen/permanent resident or visa holder (and list visa type). Incomplete applications will be considered non-responsive and unfortunately cannot be considered.

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law.

Postdoctoral Fellow, Deep Learning for Microbiome – Gerber Lab

The Gerber Lab (http://gerber.bwh.harvard.edu) is a multidisciplinary group at Brigham and Women’s Hospital/Harvard Medical School that develops novel computational 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. The director of the lab, Dr. Georg Gerber, MD, PhD, MPH, uses his unique expertise, combining statistical machine learning method development, medical microbiology, and human pathology, to leverage cutting-edge technologies to tackle scientifically and clinically important problems.

We are looking for an exceptional researcher who will play a major role in new initiatives in the lab to develop novel deep learning (DL) approaches to further understanding of the microbiome–the trillions of microbes living on and within us. This fascinating, complex and dynamic ecosystem is crucial for human health, and when disrupted may contribute to a variety of diseases including infections, arthritis, allergies, cancer, heart and bowel disorders. Over the past decade, sequencing and other high-throughput methods have provided data about the microbiome at unprecedented scale. Applications include forecasting microbial population dynamics in the gut for rational design of therapies, predicting the impact of the microbiome on the onset or progression of human diseases, predicting interactions with the host immune system, elucidating host-microbial metabolic interactions, and discovering functions of uncharacterized microbial metabolites and proteins.

The successful candidate will be highly motivated and creative, taking a lead role in developing new deep learning-based methods, analyzing data, and interpreting results. The position is a fantastic opportunity for an individual with either a strong machine learning background who wants to get domain-specific research experience, OR someone with a strong mathematical background who wants to get more machine learning experience. Although some experience modeling biological or other complex systems is required, microbiome specific knowledge is not required.

Qualifications:

  • PhD in Computer Science, Computational Biology, Ecology, Mathematics, Physics, Statistics, or other highly quantitative discipline.
  • Excellent publication track record.
  • Experience with deep learning methods; experience developing DL models for biological sequencing data is highly desirable.
  • Experience modeling biological or other complex systems is required; microbiome experience is desirable, but not required.
  • Strong mathematical background with track record developing novel models and methods.
  • Solid programming skills in Python, including PyTorch.
  • Superior communication skills and ability to work on multidisciplinary teams.

Environment:  the Gerber Lab is located in the Division of Computational Pathology (http://comp-path.bwh.harvard.edu), which Dr. Gerber heads, at Brigham and Women’s Hospital (BWH) at Harvard Medical School (HMS), and the Massachusetts Host-Microbiome Center (MHMC) (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. With a recent grant from the Massachusetts Life Science center, the Division has built the Lab for AI/Deep Learning for the Microbiome, which has a state-of-the-art GPU cluster for model development, training and deployment. 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 and Boston Children’s Hospital.

To apply: email a single PDF including cover letter, CV, brief research statement and a list of at least three references to Dr. Georg Gerber (ggerber@bwh.harvard.edu). In your CV, indicate whether you are a U.S. citizen/permanent resident or visa holder (and list visa type). Incomplete applications will be considered non-responsive and unfortunately cannot be considered.

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law.

Graduate Students – Gerber Lab

I am always excited to work with talented graduate students with interests relevant to my lab, which focuses on developing novel machine learning/computational biology/wet lab approaches to further understanding of the microbiome–the trillions of microbes living on and within us. This fascinating, complex and dynamic ecosystem is crucial for human health, and when disrupted may contribute to a variety of diseases including infections, arthritis, allergies, cancer, heart and bowel disorders.

In general, I can only be a primary advisor (and provide financial support) for students enrolled at Harvard or MIT. However, I am open to co-advising students at other institutions.

If you’re interested, email me at ggerber#bwh.harvard.edu. Please include your CV and a brief description of your research interests.

Students should have a high level of interest in:

  • Developing and applying new technologies to biomedical problems.
  • Advancing knowledge of the microbiome and its role in human health and disease.
  • Having your work make an impact on healthcare outcomes.
  • Working on an interdisciplinary team and collaborating with computational, wet lab and clinical scientists.

About the lab: the Gerber Lab develops novel 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 Bayesian statistical machine learning methods 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 with human interpretable rules. 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 food allergy. We also apply our methods to synthetic biology problems, to engineer consortia of bacteria for diagnostic and therapeutic purposes.

Environment:  the Gerber Lab is located in the Division of Computational Pathology, which Dr. Gerber heads, at Brigham and Women’s Hospital (BWH) at Harvard Medical School (HMS), and the Massachusetts Host-Microbiome Center, 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.

Computational Biology (ML4Bio) Postdoctoral Fellow – Gibson Lab

Opening for a Postdoctoral Research Fellow to join the Gibson Lab https://gibsonlab.io at Harvard Medical School and Brigham and Women’s Hospital. We leverage tools from machine learning and control theory to understand biological systems. Control theoretic concepts are integrated both in the design of our optimization schemes and statistical machine learning models, as well as in the design of our in vitro and in vivo experiments. Our main area of focus is the microbiome and microbial dynamics more specifically. Applications include the design of bacteriotherapies (bugs-as-drugs), developing methods to learn microbial dynamics at ecosystem-scale, studying the impact of phages on microbial communities, methods for tracking low abundance pathogens, and methods for integrating multiple data modalities and prior knowledge (from other studies or databases) in time-series models. We focus on Bayesian methods that propagate measurement uncertainty throughout the model so that we can access confidence in model parameters and to help prioritize follow-up experiments. ML techniques applied include variational inference, Bayesian non-parametric models, and relaxation techniques (for making discrete models differentiable).

The specific project(s) you will be working on will fall under one of the following grants. Follow the links below for more details:

The candidate will also be encouraged to design their own experiments as well, which would then be carried out by staff in the germ-free mouse facility or in a collaborating wet lab. In addition to addressing our biological questions we also include key experimental components that can aid in validating our methods that would otherwise not be included in a purely hypothesis driven experiment. For a candidate wanting some wet lab experience we are looking to develop new single-molecule enzyme-linked immunosorbent assays (digital ELISA) to measure low abundance host inflammatory markers in feces (please mention this explicitly in your cover letter if interested).

Qualifications

  • PhD in computer science, applied mathematics, ecology, computational biology, systems biology, statistics, or other quantitative discipline
  • Excellent publication track record
  • Strong mathematical background with track record developing novel models and methods
  • Solid programming skills in Python; this isn’t a software engineering job, but you will need to be able to develop efficient implementations and apply your work to real biomedical data
  • Ability to reside in the U.S. and legally work in the country.

About the lab environment

The Gibson Lab is located in the Division of Computational Pathology at Brigham and Women’s Hospital (BWH), a Harvard Medical School teaching hospital, which is the second largest non-university recipient of NIH research funding. The broad mandate of the 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 the Harvard Medical School quad, Harvard School of Public Health, Boston Children’s Hospital, and the Dana Farber Cancer Institute. Many of our lab members also have appointments at the Massachusetts Institute of Technology and the Broad Institute.

Applications Process

Submit: (1) brief research statement (not to exceed 2 pages); (2) curriculum vitae; (3) two most relevant publications; (4) names and contact information of three individuals who can serve as references to: Travis Gibson, tegibson@bwh.harvard.edu. If you wish to chat briefly over Zoom before submitting materials to learn more details about our ongoing work, please inquire about this possibility.

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law.