Job Title: Post-Doctoral Fellow in Image Processing for Spatial Proteomics
Location: Stanford School of Medicine, Stanford, CA
Department: Canary Center for Cancer Early Detection
Position Type: Post-Doctoral Fellowship

About Us:

The Stanford School of Medicine is a leading institution dedicated to advancing biomedical research and improving patient care. Our team is committed to exploring innovative technologies that enhance our understanding of biological processes at single-cell resolution. The Mallick Lab, is focused on the development of approaches to understand diseases like cancer and Alzheimer’s Disease from a multi-scale systems perspective that integrates novel technologies with advanced experimentation and computation to understand disease origins and progression.

Project Overview:

We are collaborating with the Zavaleta lab at USC developing a novel imaging modality aimed at enhancing our ability to visualize and analyze protein expression in single cells within their spatial context in pathomic samples. This research opportunity will be focused primarily on the development and application new image processing and machine learning techniques to enable high-resolution interpretation of single-cell, spatial proteomic data.

The successful candidate will be responsible for leveraging insights from single-cell and spatial data to ask an answer systems biology questions about cellular functions and interactions and cellular heterogeneity in complex tissue environments, such as cancer and Alzheimer’s disease.  This role involves working in a dynamic environment and conducting integrative analyses of multidimensional datasets.

Key Responsibilities:

• Develop and optimize image and signal processing techniques to improve data quality and data acquisition for single-cell analysis.
• Analyze and interpret spectral and image data, providing statistical insights that contribute to the optimization of the imaging methodology.
• Contribute to the design and execution of experimental protocols, ensuring the integration of imaging and proteomics methodologies.
• Develop and implement computational and systems biology approaches for microenvironment analysis from spatial omics and single-cell omics data.
• Mentor graduate students and contribute to the overall educational environment of the laboratory.
• Collaborate with interdisciplinary teams to apply developed algorithms to real-world datasets and generate valuable biological insights.
• Perform integrative analyses of multidimensional datasets within the context of cancer and Alzheimer’s disease.
• Communicate research findings through presentations, publications, and conferences.
• Contribute to the development of grant proposals and funding applications.

Qualifications:

• Candidate must have a strong quantitative background, with a PhD in computational biology, bioinformatics or related field including bioengineering, computer science, statistics, mathematics, electrical engineering, physics, or a related field with a focus on image and signal processing.
• Strong knowledge in bioinformatics, machine learning, statistics and programming skills (Python, or C++) are required.
• A strong background in quantitative imaging techniques and proficiency in computational analysis of imaging data and image processing algorithms.
• Familiarity with proteomics or spatial biology methodologies is a plus but not required.
• Excellent communication skills, both written and verbal, with the ability to work collaboratively in a team-oriented environment.
• A strong publication record in peer-reviewed journals is desirable.
• Excellent verbal and written communication skills are essential.

Application Process:

Interested candidates should submit a cover letter, CV, and contact information for three references to spatialbio_applicants@mallicklab.org. In your cover letter, please include a brief statement of research interests and how your background aligns with the goals of the project.

Join us at Stanford to advance the frontiers of spatial proteomics and make impactful contributions to the field of biomedical research!

Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.

POSITION/TITLE: Core Senior Research Specialist – Mass Spectrometry
COMPANY: The Salk Institute for Biological Studies
LOCATION: 10010 N. Torrey Pines Road, La Jolla, CA, USA 90037

Summary of Position:

This position serves as a senior technical expert to provide core/lab management support of Salk Institute Mass Spectrometry Core services. The incumbent, with limited input from the Core Director, will independently conduct experiments related to LC/MS technologies for proteomics. Responsibilities include independent development and execution of specific workflows for sample preparation including protein fractionation, sample cleanup (precipitation, SPE, and affinity column), in-gel and in-solution protein digestion, lyophilization, stable isotope peptide labeling (i.e. TMT), and enrichment of post-translationally modified peptides.

Responsibilities also include preparation of capillary LC columns, operation of instrument software for data acquisition by LC/MS and usage of bioinformatics software for protein identification and quantification. The position will support the Core Director with management of core operations, including its resources, executing administrative duties, supporting grant writing and training programs, and maintaining lab protocols. Secondarily, the position will engage in sample preparation and analysis for metabolomics and lipidomics applications.  

Who We Are

The Salk Institute is an internationally renowned research institution that values diversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.

Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Salk's vibrant community comprises a diverse and talented group of individuals, each playing a crucial role in driving our mission forward. From visionary leaders to dedicated administrators and brilliant faculty members, the Institute is united by a shared passion for scientific exploration and innovation.

What Your Key Responsibilities Will Be

• Works with Salk researchers to achieve targeted research goals utilizing mass spectrometry (MS) technology platforms for proteomics analysis. Performs procedures associated with protein/peptide identification and quantitative analysis, including sample preparation, instrument operation and data analysis. Provides collaborative support to experiment design and implementation for new and existing approaches to using MS technologies for proteomics analysis. Collaborates and assists Salk researchers on application and development of advanced MS methods for proteomic analysis.   60%
• Supports the Core Director with sample preparation and analysis for metabolomics and lipidomics applications. 15%
• Maintains core facility to include mass spectrometry equipment and instrumentation maintenance and scheduling repairs, oversight of inventory and ordering, instrument QA/QC, data management and record keeping, and overseeing lab safety protocols and practices. 10%
• Reviews current MS-based technologies, particularity in the fields of proteomics by review of relevant literature and attendance at scientific meetings. Reviews the latest in technology (hardware, software and networking) and ensure that recommendations for changes or upgrades will integrate well with existing MASS core technologies. 5%
• Participates in teaching, training and instruction to a broad spectrum of researchers and core users. 5%
• Provides relevant support for grant applications, progress reports, and support for the development and design of training programs, workshops, and seminar series when appropriate. 5%

SUPERVISORY RESPONSIBILITIES:

May provide supervision, training and guidance to lower-level personnel.

What we Require

• Bachelor’s degree in relevant field with 7+ years’ experience, OR graduate degree (M.S. or Ph.D.) with 5+ years’ experience.
• 5+ years of experience in mass spectrometry, to include experience in the design, execution and analysis of mass spectrometry-based experiments for proteomic analysis on current technology platforms, especially Orbitrap systems.
• Experience and detailed understanding of a range of methodologies utilizing MS technology including protein and peptide identification and quantitative analysis, protein pull down experiments, tandem mass tag labeling for multiplexed quantitative analysis. Analysis of post-translational modifications on complex proteomic and peptidomic samples, and other current techniques relevant to proteomic analysis via MS.
• Demonstrated experience in the development, optimization and execution of complex experiments and techniques with reliability and accuracy while working within time constraints.
• Demonstrated experience establishing and managing efficient workflows for various mass spectrometry-based analysis platforms.
• Demonstrated ability to develop, execute and optimize cutting-edge mass spec-based methods.
• Well versed in using analysis software and downstream data analysis of complex mass spec data sets, including use of Proteome Discover, MaxQuant, or other similar programs.

What We Can Offer

The expected pay range for this position is $67,500 to $88,750 per annum. Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, department budget availability, internal equity, geographic location, and external market pay for comparable jobs.  

Benefits

Salk Institute offers competitive benefits, including medical, dental, vision, retirement, paid time off, tuition reimbursement, patient advocacy services, and transit/parking program.

Salk Values

The Salk Community, both scientists and administrators, worked together to define values that we believe support Salk’s pursuit of excellence. To be truly the best scientific institution requires not only incredible discoveries, but a common understanding of how we should work together to enable those discoveries.

The acronym “I CARE” provides a simple way to remember each of the values and reminds each of us of the importance of what we do each day.

Equal Employment Opportunity Statement

The Salk Institute for Biological Studies is an Equal Opportunity Employer and is committed to providing equal access to opportunities for students, employees, applicants for employment and other visitors. Salk has also adopted and maintains a policy to encourage professional and respectful workplace behavior and prevent discriminatory and harassing conduct in our workplace.

Accordingly, the Institute prohibits harassment and discrimination in employment on the basis of, and considers all qualified applicants for employment without regard to, actual or perceived race, color, religion, religious creed (including religious dress and grooming practices), national origin, ancestry, citizenship, physical or mental disability, medical condition (including cancer and genetic characteristics), genetic information, marital status, age, sex (including pregnancy, childbirth, breastfeeding, or related medical conditions), gender, gender identity, gender expression, sexual orientation, veteran and/or military status (disabled veteran, veteran of the Vietnam era, other covered veteran status), political affiliation, and any other status protected by state or federal law.

Candidates should apply through the website (deadline for the Fall 2025 admissions is December 2, 2024)

More information on the position and application details: https://recruiting2.ultipro.com/SAL1013SIBS/JobBoard/e9f055e1-a105-4f91-9a67-21aea61655fa/Opportunity/OpportunityDetail?opportunityId=850c809a-da7b-48fc-948a-abf58f5b7b88 

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