Researcher

The Simons Electron Microscopy Center (SEMC) is a global leader in cryo electron microscopy (cryoEM) and provides expertise and resources for understanding both molecular and cellular structures. The facilities include 15 transmission electron microscopes and 3 dual-beam scanning electron microscopes and a dedicated high-resolution mass spectrometer. SEMC serves the nine members institutions of NYSBC, provides access and training to the national research community through the NIH National Center for CryoEM Access and Training (NCCAT), provides sample preparation and access and training for in situ cryoET through the NIH National Center for In-situ Tomographic Ultramicroscopy (NCITU), develops and disseminates new technologies through the Simons Resource for Automated Molecular Microscopy (SRAMM), and includes the Simons Machine Learning Center (SMLC) where a team of machine learning, computer vision, and computational biology experts are pushing the boundaries of machine learning and structural biology.

The New York Structural Biology Center (NYSBC) is a global leader in structural biology. The Center’s main facility comprises 50,000 square feet in Upper Manhattan and houses advanced instrumentation in Cryo-Electron Microscopy, Nuclear Magnetic Resonance Spectroscopy, and Protein Production. Its X-ray crystallographic facility is located at the National Synchrotron Light Source II at the Brookhaven National Laboratory. NYSBC is led by world leaders in structural biology and an outstanding staff of 50 researchers.

SEMC is seeking a highly motivated and talented Postdoctoral Researcher with a strong background in computer science and proteomics to join our interdisciplinary research team. This position offers an exciting opportunity to develop and apply cutting-edge computational methods for the analysis of cross-linking mass spectrometry (XL-MS) data, with the goal of integrating these insights with structural biology (cryo-EM) and single-cell analysis data to understand complex biological systems.

List of responsibilities:

The successful candidate will work on a project focused on developing novel computational algorithms and pipelines for the analysis of XL-MS data and its integration with cryo-EM and single-cell proteomics datasets. This includes: ·

• Developing advanced algorithms for the identification and validation of cross-linked peptides from mass spectrometry datasets.
• Creating computational strategies for the integration of XL-MS derived distance constraints with structural models obtained from cryo-EM.
• Developing methods to utilize XL-MS data to inform and validate structural models of large macromolecular assemblies and dynamic protein complexes.
• Exploring the application of XL-MS to understand protein interactions and conformational changes within the context of single-cell heterogeneity, potentially integrating with single-cell proteomics or transcriptomics data.
• Applying machine learning and statistical approaches to improve the accuracy and efficiency of XL-MS data analysis and its integration with other modalities.
• Developing software tools and resources for the broader scientific community to facilitate the integrated analysis of XL-MS, cryo-EM, and single-cell data.

The postdoc will be expected to:

• Design and implement computational algorithms and pipelines specifically for XL-MS data analysis and its integration with structural and single-cell data.
• Analyze large-scale XL-MS datasets, as well as potentially cryo-EM structures and single-cell omics data.
• Develop and validate new computational tools and software for XL-MS data processing, analysis, visualization, and integration.
• Collaborate effectively with experimental proteomics, structural biology (cryo-EM), and single-cell analysis researchers.
• Present research findings at conferences and publish in peer-reviewed journals.
• Contribute to the writing of grant proposals.
• Potentially mentor graduate and undergraduate students

Required Qualifications and Experience:

• A Ph.D. in Computer Science, Bioinformatics, Computational Biology, Chemistry, Biophysics, or a related field. Candidates with a Ph.D. in Proteomics or a related biological science with significant computational experience in mass spectrometry data analysis are also encouraged to apply.
• Strong programming skills in one or more languages (e.g., Python, R, C++). Experience with the analysis of mass spectrometry data, with specific experience in proteomics data analysis being highly desirable.
• Experience with cross-linking mass spectrometry data is a significant advantage.
• Knowledge of statistical modeling, machine learning, and data mining techniques.
• Excellent problem-solving, analytical, and critical thinking skills.
• Strong written and oral communication skills, including the ability to present complex information clearly and concisely.
• Ability to work independently and as part of a collaborative team.

Preferred Qualifications and Experience:

• A track record of authoring peer reviewed publications.
• Familiarity with protein structure, interactions, and structural biology concepts is highly desirable.
• Experience with cryo-EM data or structural modeling is a plus. Experience with single-cell omics data analysis (e.g., scRNA-seq, scProteomics) is beneficial.
• Experience with software development and the creation of user-friendly tools is a plus.

Contact for Inquiries and Applications:

• Alex de Marco [email protected]

E-Verify Statement:

We participate in E-Verify, an electronic employment verification program operated by the Department of Homeland Security in partnership with the Social Security Administration, to verify the employment eligibility of newly hired employees.

Job Types: Full-time, Contract

Pay: $80,000.00 - $90,000.00 per year

Benefits:

• 401(k) matching
• Dental insurance
• Flexible spending account
• Health insurance
• Paid time off
• Retirement plan
• Vision insurance

Work Location: In person