Job Description:
Job Description Computational Biologist I/II: Spatial transcriptomics and proteomics The Broad Institute of MIT & Harvard is looking for two Computational Biologists to join the Optical Profiling Platform (OPP) directed by Dr. Sami Farhi to advance large-scale analysis efforts in the Human Tumor Atlas and Brain Initiative Cell Census Network. OPP seeks to translate advances in optics and imaging to the broader biological community to impact pressing problems in biology and human health. We do this by: - Inventing developing onboarding and refining new methods from our lab and others.
- Operating an in-house research program looking to generate high-resolution multi-modal portraits of biological systems.
- Partnering with an increasingly large set of labs to disseminate these tools.
Our current tool palette is focused on in situ transcriptomics in situ proteomics optical pooled screening and optical electrophysiology. Each of these data modalities generates multi-parametric multi-Terabyte imaging data sets. We apply these data sets to problems in neuroscience oncology and immunology focusing on the construction of tissue atlases and on the integration with orthogonal data and information types. In these efforts OPP works especially closely with the Broads Klarman Cell Observatory (Dr. Ramnik Xavier Dr. Alex Shalek) and Stanley Center for Psychiatric Disease (Dr. Paola Arlotta Dr. Steve McCarroll). In this position the Computational Biologist will become an expert in the analysis of in situ -omics data particularly CODEX and MERFISH; implement and further develop computational pipelines for parametrizing data types; and integrate with other data sets to answer questions about the forces driving tissue organization both within our lab and in collaborations with Broad core faculty. The role will be primarily computational but the candidate will be strongly encouraged to understand the full data generation process through interaction with experimental colleagues. The candidate will be supported by computational collaborators from both the academic and professional scientific communities at the Broad including Drs. Yonina Eldar Brian Cleary Mehrtash Babadi and the Data Sciences Platform. As the candidate expands their role they will take on leadership and mentorship responsibilities of junior students and associate computational biologists. We actively seek to advance scientists from under represented backgrounds. We believe that a team composed of diverse educational or demographic backgrounds is essential for driving discovery. Our work takes place at the interface between disciplines and these interactions spark new ideas. We are most interested in candidates with a desire to work on emerging technologies; a curiosity that spans across fields; and a strong belief in open and collaborative science. Both OPP and the Broad as a whole know that the ongoing COVID-19 pandemic presents challenges to balancing caregiving and professional responsibilities and we will be flexible to help candidates find arrangements that work for their situation. Characteristic duties: - Implement distributed computational pipelines for in situ omics data.
- Identify cell states and construct spatially resolved tissue atlases from high-dimensional imaging data.
- Lead collaborations and serve as a resource to for scientists at the Broad
- Develop working relationships with major data analysis efforts and consortia efforts
- Work closely with multidisciplinary teams to provide technical expertise training and to develop specific protocols. Train experimental biologists in execution of low-level data analysis.
- Attend and present at team meetings to share results plan projects and experiments and ensure that projects support team goals
Qualifications: Requirements. - PhD or equivalent industry experience in machine learning computer science image processing digital pathology cartography earth science or related field.
- Experience with developing robust pipelines for distributed computing. Strong command of Python and acquaintance with workflow languages.
- Experience with imaging data processing possibly including segmentation feature detection or classification
- Strong written and oral communication skills
Nice to haves. An ideal candidate would have one or more of these but we dont expect anyone to have all of them. Particular projects will be chosen to match candidates skills. - Experience with single cell data analysis
- Experience with transfer learning approaches
- Experience with hyperspectral/multicolor imaging data
- Experience with digital pathology data
- Experience managing or mentoring junior personnel
- Experience working on large-scale collaborative projects
"All computational scientists at Broad are encouraged to continue developing their expertise by engaging with the wider computational community through Broad's vibrant Models Inference & Algorithms Initiative (broadinstitute.org/mia)." All Broad employees regardless of work location must be fully vaccinated for COVID-19 by Tuesday October 12 2021. Requests for exemption for medical or sincerely held religious beliefs will be considered. #LI-POST All qualified applicants will receive consideration for employment without regard to race color religion sex sexual orientation gender identity national origin disability or protected veteran status. EEO is The Law - click here for more information Equal Opportunity Employer Minorities/Women/Protected Veterans/Disabled Check out this video for a look into our community! |
