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    Featured announcements
    Opportunity: Staff Associate III @ Columbia University -- New York, NY (US)
    Submitted by VPS HR; posted on Thursday, September 30, 2021

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    Lawrence Berkeley National Lab (LBL, lbl.gov) Joint Genome Institute (JGI, biosciences.lbl.gov/area[...]jgi) Division has an opening for a Postdoctoral Fellow (Biological Sciences) to join the Vogel lab.

    RESPONSIBILITIES

    In this exciting role, you will perform research on plant-microbe interactions with an emphasis on developing and using novel high-resolution ultra-sensitive label-free nonlinear optical microscopy imaging techniques to characterize interactions at cellular and subcellular resolution. The work will be conducted in close collaboration with the Ji lab at UC Berkeley which is developing the microscopy techniques. Responsibilities include identifying applications for these new techniques that will inform our understanding of the interaction between plants and their microbiomes. The main experimental platform will consist of small, enclosed ecosystems (EcoFABs, eco-fab.org) that allow for complete control of the microbiome, non-destructive imaging, and media sampling. This position will store and organize results for presentation and viewing by project team members and the wider scientific community and prepare results for publication in scientific journals. For more information contact John Vogel jpvogel[at]lbl.gov.

    What You Will Do:
    • Identify use cases that use the new microscopy techniques.
    • Perform experiments that provide insight into the interaction between plants and the root microbiome and/or beneficial microorganisms.
    • Work with members of the Ji lab to image the interaction to provide insight into mechanisms.
    • Use other techniques (e.g. 16S community profiling, metabolomics, transcriptomics, modeling) as necessary to provide a more complete picture of the interactions.
    • Store and organize results for presentation and viewing by JGI staff, collaborators, and the wider scientific community.
    • Interact with a multi-institution project team to ensure efficient communication and completion of * Write results up for publication.
    Additional Responsibilities as needed:
    • Work with group members and/or outside collaborators on additional plant-microbe projects.

    REQUIREMENTS

    What is Required:
    • Ph.D. in life sciences with relevant research experience.
    • Strong background in microscopy, molecular biology, plant biology and/or microbiology.
    • Strong organizational and record keeping skills to record experimental results and analyze data.
    • Laboratory experience in microscopy, molecular biology, plant biology and/or microbiology.
    • Effective oral and written communication skills to present findings at group meetings and conferences and publish results.
    • Ability to interact with a variety of technical and scientific personnel including Research Associates, Scientists and Software Engineers.
    Desired Qualifications:
    • Experience using bioinformatics tools.
    • Experience with beneficial plant-microbe interactions.

    TERMS & COMPENSATION

    • This is a full-time 3 year postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 2 years of paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.
    • This position is represented by a union for collective bargaining purposes.
    • Salary will be predetermined based on postdoctoral step rates.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

    LOCATION

    Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]10785 and follow the on-line instructions to complete the application process.

    ABOUT US

    JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest
    They say it's all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class multidisciplinary science within a diverse and respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Genome Institute (JGI) addresses the most pressing energy and environmental challenges using integrative genome science approaches. JGI takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of our next ground-breaking discoveries?

    POLICY

    Equal Employment Opportunity:
    Based on University of California Policy – SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit covid.lbl.gov for more information.

    Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, diversity.lbl.gov/ideaberkeleylab/) and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

    Equal Opportunity and IDEA Information Links:
    Know your rights, click here (www.dol.gov/ofcc[...]t.htm) for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision (www.dol.gov/ofcc[...].html) under 41 CFR 60-1.4.

    BACKGROUND

    We are seeking a highly motivated and experienced scientist to join the research group of Peer Bork within the Structural and Computational Biology Unit to contribute to and coordinate activities both within the research group and in the German National Research Data Infrastructure consortium "NFDI4Microbiota" (nfdi4microbiota.de). This consortium will create a new core national infrastructure for microbial research through training and community building activities, as well as through the development of an online analysis and integration system which will prioritise FAIR, open and reproducible research.

    Our bioinformatics research group works on a wide range of research topics with a current focus on microbiome analysis in ecosystems like the human gut or the ocean. We are involved in various national and international projects and also engage in the development, improvement and implementation of standards for microbiome data and metadata in other consortia, including the German Human Genome-Phenome Archive (GHGA, ghga.dkfz.de) and the International Human Microbiome Coordination and Support Action (IHMCSA).

    RESPONSIBILITIES

    Your role will be to coordinate NFDI4Microbiota activities within the Bork group and coordinate and contribute to the creation of data and metadata standards within the consortium. In collaboration with software engineers, you will also lead the creation of an online resource that will centralise and make accessible existing experimental standards in microbiology, with a focus on microbiome approaches and reproducibility. You will develop and implement strategies to support the long-term stability of NFDI4Microbiota and its connection to other consortia. To this end, you will work with producers of microbiome data to identify obstacles and challenges to data sharing, with consumers of such data to identify their needs and encountered problems, and with existing repositories of microbiome data. You will work with colleagues both from the Bork group and other members of the consortium, and therefore have the opportunity to help shape a new national infrastructure for microbiota analysis and collaborate with microbiologists across Germany.

    REQUIREMENTS

    • A university degree in Biology, Bioinformatics, Medical Informatics or a related field; a doctorate is a plus
    • Experience in wet lab microbiology, preferably including in the microbiome field (16S and metagenomics), and in writing experimental protocols (SOPs)
    • Experience using and/or developing data standards
    • Excellent organizational skills and a high motivation to interact and discuss with stakeholders and key players in the fields of experimental, computational, and clinical microbiological research
    • Familiarity with office suites and online collaboration tools
    • Ability to work both independently and in a team at the interface between life sciences and informatics
    • Willingness to learn new skills as projects require
    • Good communication, interpersonal and English language skills
    You might also have:
    • Experience in project management and coordinating research grants (e.g. tracking and fulfilling milestones and deliverables)
    • Experience in generating or curating microbiological and/or microbiome data and metadata
    • Experience in generating online training materials and/or documentation
    • Experience in community development and organising workshops or conference sessions
    • Experience in working with public ontologies, mapping between resources, and data analysis
    • Familiarity with the concepts of analysis pipeline management (e.g. Common Workflow Language, NextFlow, Snakemake)

    COMPENSATION

    Why join us:
    EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus.

    What else you need to know:
    We are Europe's flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with approximately 2000 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

    HOW TO APPLY

    Please follow the link below to apply:
    www.embl.org/jobs[...]02062

    DEADLINE

    19 November 2021

    BACKGROUND

    We are seeking a highly motivated computational biologist to join the research group of Peer Bork within the Structural and Computational Biology Unit as a postdoctoral fellow. This bioinformatics group works on a wide range of topics with a current focus on microbiome analysis in ecosystems like the human gut and the ocean. We are offering this position within the context of the newly established National Research Data Infrastructure consortium "NFDI4Microbiota", which aims to support microbiology researchers across Germany by offering open data analysis and integration services as well as training and data standardisation.

    RESPONSIBILITIES

    Your role would be to develop and run approaches for multi-omic data integration and the analysis of large-scale microbiomics data (metagenomes, metatranscriptomes, metabolomes etc.) for biological discoveries. For the development of these approaches, data will mostly come from various internal and external human microbiome projects, but also from ocean and soil. Within the NFDI4Microbiota consortium, you will develop data integration services that will put researchers' data in context using relevant public data sets and databases, and expand the biological questions they can answer through multi-omic integration. Throughout the project, workflows you set up with the help of software engineers will be made available to outside scientists through a web-portal. The work will comprise both methodological development and applied aspects, and also aims at biological discoveries. You will work with colleagues both from the Bork group and other members of the consortium, and therefore have the opportunity to help shape a new national infrastructure for microbiota analysis and collaborate with microbiologists across Germany.

    REQUIREMENTS

    • A PhD degree in Biology, Bioinformatics, Computer Science, or a related field
    • Proven biological background knowledge and bioinformatics skills related to the group's research
    • Experience in data integration, statistical analysis and visualisation, e.g. in Python or R
    • Experience developing new strategies, workflows or tools for data analysis
    • Competence in processing large microbiomics and/or multi-omics datasets
    • Ability to work both independently and in a team
    • Willingness to learn new skills as projects require
    • Good communication, interpersonal and English language skills
    You might also have:
    • Familiarity with processing next-generation sequencing data and performing metagenomic analysis
    • Experience working with the Linux command line and compute clusters
    • Experimental experience in microbiology
    • Experience working in large consortiums

    COMPENSATION

    Why join us:
    EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus.

    What else you need to know:
    We are Europe's flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with approximately 2000 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

    HOW TO APPLY

    Please follow the link below to apply:
    www.embl.org/jobs[...]02064

    DEADLINE

    19 November 2021

    One postdoctoral research associate position is available for motivated candidates in the Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte. The successful applicant will work on an NSF funded project to investigate protein-DNA interactions and to develop novel algorithms for protein-DNA complex model assessments.

    REQUIREMENTS

    An ideal candidate shall have a Ph.D. degree in bioinformatics, computational biology, computational chemistry, biophysics, computer science or a related field. The candidates should have good communication skills and can work independently and as a team member.

    PREFERENCES

    Good programming skills. Experience in structural bioinformatics and machine learning.

    TERMS

    Up to three years.

    LOCALE

    Charlotte, NC, USA

    COMPENSATION

    Competitive salary based on experience.

    HOW TO APPLY

    Send a copy of recent CV, three references, and a brief research statement to Dr. Jun-tao Guo (jguo4[at]uncc.edu)

    DEADLINE

    Until the position is filled.

    DESCRIPTION

    At Regeneron, we are known for our scientific excellence, our biomedical innovations, and our commitment to publishing important basic science findings – often leading the way in discovering and communicating important mechanistic insights. We are a leading science-based biopharmaceutical company that discovers, invents, develops, manufactures, and commercializes medicines for the treatment of serious medical conditions. We have a long-standing postdoctoral fellow program and are committed to training the next generation of leading scientists.

    The postdoctoral fellow position is for early career scientist trainees who have finished graduate school, and received their PhDs (or MDs, DVMs, etc), to receive a rigorous scientific postdoctoral training at Regeneron under the auspices of a scientist mentor. The program spans up to four years. Fellows will be expected to conduct creative mechanistic exploratory research that results in publication. The program is academic in nature - the goal is to ask fundamental questions - not to work on Regeneron therapeutic agents.

    The program consists of:
    • Up to four years of formal postdoctoral training in a program co-Directed by award-winning and published Regeneron scientists, committed to training postdoctoral fellows
    • Exposure to the biotechnology industry's most successful and innovative scientists
    • Opportunities to pursue ground breaking, creative biomedical research in a prestigious, well- resourced, and dynamic industry environment
    • Weekly postdoctoral scientist meetings to cultivate scientific rigor, creative thinking, critical reasoning, and career advancement
    • Support of scholarly productivity such as publications and conference presentations
    As part of your Postdoctoral Training Program, you will:
    • Conduct forward-looking and innovative research to address a novel scientific question of your choice with the guidance of a mentor
    • Publish and disseminate data via external conferences and peer-reviewed publications
    • Have the opportunity to assist with mentoring and guiding interns and other more junior trainees
    • Participate in postdoctoral program activities such as weekly meetings and the annual research conference
    • Present data internally, including at lab meetings, trainee meetings, and company-wide seminars
    • Provide reports of research progress to supervisors and program staff

    REQUIREMENTS

    Experience and Required Skills:
    • Doctoral degree in a relevant subject area
    • Scientists looking for their first postdoctoral training (or those with less than one year of postdoctoral training)
    • Outstanding scientific skills including critical and analytical thinking
    • Demonstrated publication success as evidenced by peer-reviewed publications
    • Good written and oral communication skills
    • Ability to interact dynamically and constructively with peers, and cross-functionally when applicable
    Note: Occasional travel

    HOW TO APPLY

    Apply online: careers.regeneron.com/job/[...]nings

    Applications Accepted: October 1, 2021 – December 1, 2021

    Required Documents:
    • A full academic CV
    • At least two letters of recommendation
    • Responses to two essay questions
    Within one business day of applying you will receive an email with instructions on how to complete your essay questions and upload documents.

    DEADLINE

    All documents are required to be submitted no later than December 1, 2021.

    Applications received after December 1, 2021 may not be considered.

    Following the close date, please allow 3-4 months for review and interviews.

    Targeted Start Date: Summer 2022, but the start date is flexible – depending on when you finish defending your graduate thesis or finish up prior manuscripts.

    If you have an issue submitting or any questions, please email: postdoctoral[at]regeneron.com.

    Does this sound like you? Apply now to take your first steps toward living the Regeneron Way! We have an inclusive and diverse culture that provides amazing benefits including health and wellness programs, fitness centers and stock for employees at all levels!

    POLICY

    Regeneron is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion or belief (or lack thereof), sex, nationality, national or ethnic origin, civil status, age, citizenship status, membership of the Traveler community, sexual orientation, disability, genetic information, familial status, marital or registered civil partnership status, pregnancy or maternity status, gender identity, gender reassignment, military or veteran status, or any other protected characteristic in accordance with applicable laws and regulations. We will ensure that individuals with disabilities are provided reasonable accommodations to participate in the job application process. Please contact us to discuss any accommodations you think you may need.

    Submitter

    DESCRIPTION

    Genomics Data Scientists investigate and develop solutions to extract more information from the genome (alignment and variant calling) and to interpret the genome in the context of a persons clinical features.

    They work as part of squads building and translating state of the art analytics into clinically-fit production quality solutions.

    Key Accountabilities Include:
    • Benchmarking and fine-tuning tools for quality control, processing and analysis of whole genome sequence data, e.g., alignment, variant callers for types of variants
    • Develop algorithms for variant prioritisation / classification to improve their diagnostic potential or actionability
    • Performing custom computational analysis for a range of projects in rare disease/germline or cancer/somatic samples and carefully document results using reproducible computing principles
    • Developing, prototyping, and validating new features for genome analysis in collaboration with internal and external stakeholders
    • Work with other squad members to ensure that solutions are implemented in a robust, scalable, fit for clinic, accredited, production ready for converting prototypes to production pipelines
    • Continuously scan the scientific literature to identify new approaches to genome analysis that can be implemented to improve our capabilities
    • Contribute to the publication and dissemination of our learnings in the form of scientific papers, white papers, conferences, etc.
    • Establishing general bioinformatics resources for day-to-day use by colleagues
    • Know and understand the meaning behind our virtues of Empathy, Integrity, Focus, Connection, Speed, Curiosity, Impact and embody them in all aspects of your role

    REQUIREMENTS

    Key Skills Include:
    • Excellent knowledge in cancer genomics, approaches to call somatic variation and interpret cancer genomes
    • Strong knowledge of statistics and/or machine learning
    • Strong knowledge of high throughput sequencing algorithms and available resources. Experience with full cycle of analysing NGS data from sequencing QC to annotation and prioritization of variants.
    • Strong programming skills (Python, R)
    • Excellent technical writing skills
    • A decent publication record demonstrating their ability to conceive and carry to conclusion scientific investigations
    • Excellent ability to represent and visualise data to derive insights
    • A demonstrable ability to cope under pressure and deliver to deadlines
    • Experience in handling large data sets
    • Ability to communicate effectively within a multidisciplinary team
    • Flexible and co-operative approach to colleagues
    • Experience and flexibility to collaborate on code with others including good working knowledge of Git
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Rare, Disease, Analyst, Cancer, WGS, WES, Genomics, Bioinformatics, Germline, Somatic, Mutations, Clinical, Python, Pipelines, Statistics, Testing, Writing, Variants, Alignment, Statistical, Genetics, NGS, London

    BACKGROUND

    We are:
    The Bioinformatics Core (BIC) at Memorial Sloan Kettering Cancer Center (MSK). We facilitate scientific discoveries by supporting basic and translational research groups. BIC is responsible for research project support, web-based applications, computational training programs and the development of tools to facilitate analysis and integration of genomic, pathway and clinical information. For more information about the team, click here.

    We are seeking a Bioinformatics Engineer to perform next-generation sequence data processing and analysis. Our environment is dynamic and exciting in an academic setting that is at the nexus of cancer biology, computer science, statistics, and clinical research. We work in small groups, collaborating with other Bioinformatics and Software Engineers throughout the institution. We are dedicated to reproducible research and open source communities.

    We are looking for someone to develop, maintain and operate computational pipelines for the analysis of next-generation sequencing data. This work will include both large-scale projects and custom jobs tailored to individual research efforts. They will span a wide variety of analysis problems. The Core remains on the cutting edge of computational biology. We have several R&D engineering efforts in areas including large scale image analysis, machine learning and smart phone application development. Are you interested in working on the cutting edge of computational biology? Then our group will provide numerous opportunities to learn and grow.

    RESPONSIBILITIES

    You are:
    • Self-Motivated and able to apply your skills to translational research
    • Someone who enjoys working in teams but also enjoys independence
    • Interested in learning and applying new technologies

    REQUIREMENTS

    You have:
    • Extensive experience in bioinformatics software development working with both large and complex datasets
    • Strong experience with Python plus one of the following languages: Java, C++, Swift
    • Solid experience with NGS computational tools
    • Experience with R for data and statistical analysis

    COMPENSATION

    Competitive compensation packages | Sick Time | Generous Vacation + 12 holidays to recharge & refuel | Internal Career Mobility & Performance Consulting | Medical, Dental, Vision, FSA & Dependent Care | 403b retirement savings plan match | Tuition Reimbursement | Parental Leave & Adoption Assistance | Commuter Spending Account | Fitness Discounts & Wellness Program | Resource Networks | Life Insurance & Disability | Remote Flexibility

    We believe in communication, transparency, and thinking beyond your 8-hour day @ MSK. It's important to us that you have a sense of impact, community, and work/life balance to be and feel your best.

    HOW TO APPLY

    For more details and to apply, please click this link: careers.mskcc.org/jobs[...]er-v/

    DESCRIPTION

    We are looking for an experienced bioinformatician to be responsible for the informatics and data infrastructure, and perform research analyses, for major ongoing translational genetics studies focusing on rare developmental disorders, within the research group of Matthew Hurles, working closely with our clinical collaborators.

    This role will involve opportunities to identify and feedback much-needed diagnoses for children who do not currently have a known cause for their severe condition, as well as to make important research discoveries.

    About the Research:
    These translational genetics studies include the Deciphering Developmental Disorders (DDD) study (www.ddduk.org) which is resulting in the diagnosis of thousands of previously undiagnosed children and is having major translation (PMID: 25529582) and research (PMID: 25533962) impact. These studies also include working with the 100,000 genomes project (www.genomicsengland.co.uk/abou[...]ject/), coordinated by Genomics England in partnership with the UK National Health Service, which includes over 70,000 genome sequences from rare disease families. This partnership is continuing to sequence rare disease families as part of routine diagnostic practice, and make these data available to researchers.

    About the Role:
    The vast amount of data generated by these translational genetics studies require careful data management, robust data processing pipelines and sophisticated research analyses. You will work with the wider group to maintain and develop the existing informatic and data infrastructure. You will also have the opportunity to lead on specific research projects befitting your interests and expertise, leveraging these incredibly rich and powerful datasets, as an integral part of the analytical team of post-docs and students working on these studies. The Hurles group at the Sanger Institute includes experimental human geneticists as well as bioinformaticians and statistical geneticists.

    REQUIREMENTS

    Essential Skills:
    As detailed in the job description, of particular note are strong skills and experience in UNIX/LINUX and scripting languages (e.g. Perl, Python) and expertise in bioinformatics.
    • Experience in genetics research, bioinformatics or a related field
    • Advanced degree (MSc or PhD) in a quantitative field (e.g. computer science, bioinformatics, etc) or equivalent experience
    • Experience with developing and managing analytical pipelines
    • Strong UNIX/LINUX/systems skills
    • Experience programming in scripting languages (e.g. Perl, Python)
    • Excellent communication skills, including written and spoken English and ability to understand and implement workflow specifications
    • Ability to work independently and as part of a larger team
    • Excellent attention to detail and problem solving skills
    • Effective interpersonal skills and the ability to work with the team and with collaborators
    • Efficient time management
    • Demonstrates inclusivity and respect for all

    HOW TO APPLY

    Apply online: jobs.sanger.ac.uk/vaca[...].html

    BACKGROUND

    The section of Bioinformatics, DTU Health Tech is world leading within Immunoinformatics and Machine-Learning. Currently, we are seeking a highly talented and motivated postdoc to advance the prediction of T cell receptor (TCR) specificities. TCRs scrutinize the surface of cells for foreign peptides presented in complex with MHC (Major histocompatibility complex) molecules. Only a minor proportion of the MHC presented peptides are recognized by T cells. Finding out the rules and properties defining this peptide subset has large implication for our understanding of immunity and the development of novel immune treatments such as vaccines.

    If you are looking for the best possible foundation for establishing your scientific carrier and fulfilling your dreams and ambitions, this position could be your opportunity. The postdoc project will be focused on forefront cutting edge research to gain novel insights and advance our understanding of the rules associated with the T cell receptor (TCR) specificity with the aim of developing improved methods for rational epitope discovery and vaccine design. This we envision can be achieved by use of structural modeling of the interaction surface between the TCR and its target combined with refined deep neural network methods including variants of transformers and CNNs. The project will be conducted in the inspiring environment at the section of Bioinformatics at DTU Health Tech as part of the IML research group led by Professor Morten Nielsen.

    RESPONSIBILITIES

    As a postdoctoral fellow, your focus will be on continuing the work on expanding our understanding of the rules that define T cell receptor recognition of its cognate epitope targets. The work will be conducted as part of the IMI2 project Inno4Vac in collaboration with academic and industrial partners.

    REQUIREMENTS

    You hold a PhD degree or equivalent in one or more of the following areas: Bioinformatics, Biology, Engineering, Computer science or related fields, and have experience doing research within Bioinformatics.

    The successful candidate must moreover exhibit the following professional and personal qualifications:
    • Strong background within machine learning, and bioinformatics is a requirement
    • Experience in structural biology and protein structure modeling and knowledge of the basic concepts of the cellular immune system would be a plus
    • Interest in engaging in supervision of project students
    • Capability of taking personal responsibility for your work and your results
    • Flexibility and a general positive attitude to changes
    • Motivation by both individual and team accomplishments
    • Strong communication skills in both written and verbal English

    TERMS & COMPENSATION

    We offer:
    DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

    Salary and terms of employment:
    The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

    The period of employment is 2 years with a starting date of 1 December 2021 or as soon as possible hereafter.

    You can read more about career paths at DTU here: www.dtu.dk/engl[...]paths

    FOR MORE INFORMATION

    Further information may be obtained from Morten Nielsen, morni[at]dtu.dk and at "Immunoinformatics and Machine Learning (IML)" (www.healthtech.dtu.dk/engl[...]rning).

    You can read more about DTU Health Tech at www.healthtech.dtu.dk/english.

    HOW TO APPLY

    If you are applying from abroad, you may find useful information on working in Denmark and at DTU at "DTU – Moving to Denmark" (www.dtu.dk/engl[...]nmark).

    Application procedure:
    Your complete online application must be submitted no later than 12 November 2021 (Danish time).

    Apply online here: "Postdoc in Immunoinformatic Methods for Prediction of T Cell Receptor Specificity" (www.dtu.dk/engl[...]1ea3e)

    Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:
    • Application (cover letter)
    • CV
    • Academic Diplomas (MSc/PhD)
    • List of publications

    ABOUT US

    Section of Bioinformatics:
    The section of Bioinformatics within DTU Health Tech has its main research and teaching activities in bio-medical and bio-technological informatics, metagenomics, epidemiology, integrative systems biology and machine learning. The research at DTU Bioinformatics is focused on bioinformatics and computational analyses of large amounts of data generated within biological, biomedical and biotechnological and life sciences area. We strive to gain new knowledge and drive innovation in human, animal, plant and food science and collaborate with all relevant industries. A cornerstone in achieving this is the dedicated effort within DTU Bioinformatics to develop bioinformatics, immuno-informatics, metagenomics and systems biology methods and solutions to the challenge of handling and interpreting large scale and heterogeneous big data. We run projects combining big data and laboratory research via the national supercomputing center (Computerome) and molecular genomics laboratories.

    DTU Health Tech engages in research, education, and innovation base on technical and natural science for the healthcare sector. The Healthcare sector is a globally expanding market with demands for the most advanced technological solutions. DTU Health Tech creates the foundation for companies to develop new and innovative services and products which benefit people and create value for society. DTU Health Techs expertise spans from imaging and biosensor techniques, across digital health and biological modelling, to biopharma technologies. The department has a scientific staff of about 210 persons, 130 PhD students and a technical/administrative support staff of about 160 persons, of which a large majority contributes to our research infrastructure and related commercial activities.

    Technology for people:
    DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN's 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

    POLICY

    All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

    SUMMARY

    Seeking a Bioinformatics Scientist for the Research Technology group, part of Tufts Technology Services at Tufts University, who will support bioinformatics research and education for Tufts University faculty, staff and students. The ideal candidate has excellent ability to present and interpret scientific data, is enthusiastic about both research and teaching and enjoys working in a collaborative environment.

    RESPONSIBILITIES

    • Developing `omics data workflows and curating reference data for the support of bioinformatics research on the Tufts High Performance Compute Cluster (HPC) and Tufts Galaxy Server
    • Providing consulting services and technical support to faculty, post-docs, and students from a wide range of academic backgrounds
    • Providing training in analysis and visualization methods for `omics data in the form of workshops and modules in semester courses
    • Evaluating commercial bioinformatics software and managing renewals for site licenses

    REQUIREMENTS

    • Knowledge and experience typically acquired through a BA/BS in Computer Science or a related quantitative science (Biology, Engineering, Math, Physics)
    • 1-2 years of work experience in Bioinformatics in industry or research
    • Significant hands-on experience with:
      • Bioinformatics methods for Next Generation Sequencing (NGS) analysis, such as bulk and single-cell RNASeq, ChIPSeq, variant calling, de novo genome assembly
      • Functional annotation and pathway analysis
      • High-Performance Computing (HPC), analytics and visualization platforms, including extensive experience with UNIX/Linux based systems.
      • One or more programming languages: Python, R, C, Perl
      • One or more database language: SQL, MongoDB
    • Demonstrated ability to visualize and present bioinformatics data using relevant programming and visualization tools
    • Interest in teaching and outreach
    • Excellent oral and written communication skills

    PREFERENCES

    • MA/MS in Bioinformatics, Computer Science, Computational Biology or a related quantitative science
    • 2+ years of work experience in Bioinformatics industry or research
    • Consulting experience for interdisciplinary projects
    • Experience in teaching and outreach
    • Experience developing NGS pipelines
    • Experience with cloud computing and development (e.g. AWS, Google Cloud)
    • Experience teaching workshops and/or semester courses
    • Experience with presenting biological results to scientific audiences, such as research publications or conference presentations
    • Experience with web server development

    TERMS

    This is a two-year limited term appointment with possibility of renewal.

    LOCATION

    Medford and Boston MA, USA

    HOW TO APPLY

    Apply online: tufts.taleo.net/care[...]27501

    ABOUT US

    Tufts Technology Services (TTS) is a university-wide service organization committed to delivering technology solutions in support of Tufts' mission of teaching, learning, research, innovation, and sustainability. With staff across all of Tufts' campuses, as well as a 24x7 IT Service Desk, we collaborate with schools and divisions to meet the demands of a global, mobile community. We promote a collaborative, flexible work environment, embrace diversity and inclusion, and encourage personal and professional development. Learn more about TTS on our website.

    Submitter

    BACKGROUND

    The Pinello Lab at Harvard Medical School/Massachusetts General Hospital/Broad Institute of MIT and Harvard is looking for Research Scientists/Postdoctoral Candidates/ Computational Biologists and Programmers excited about computational challenges in modeling biological data coming from CRISPR genome editing, chromatin biology and single-cell experiments.

    Massachusetts General Hospital is a teaching hospital for Harvard Medical School and one of the top ranked hospitals nationwide. We are located in Boston, Massachusetts with close proximity to numerous other top-notch medical and research institutions including Harvard School of Public Health, Massachusetts Institute of Technology (MIT), The Broad Institute of MIT and Harvard, Boston Children's Hospital, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Beth Israel Deaconess Medical Center, which fosters close interactions among faculty and fellows and a strong and rich network of collaborations and intellectual exchange.

    The focus of the Pinello laboratory is to use innovative computational approaches and cutting-edge experimental assays to systematically analyze sources of genetic and epigenetic variation and gene expression variability that underlie human traits and diseases. The lab uses machine learning, data mining and high-performance computing technologies such as parallel and GPU computing to solve computationally challenging and Big Data problems associated with next generation sequencing (NGS) data analysis. Our mission is to use computational strategies to further our understanding of gene regulation in development and disease etiology and to provide a foundation for the development of new drugs and more targeted treatments.

    RESPONSIBILITIES

    The candidate(s) will work on projects developing innovative computational approaches to design and systematically analyze bulk and single-cell CRISPR perturbation experiments and integrate transcriptome, epigenome, proteome, and genome structural datasets to investigate how genetic variants and regulatory elements control gene expression and phenotypes at an unprecedented scale.

    One major activity will be to contribute to the recently NIH funded Impact of Genomic Variation on Function (IGVF) consortium: www.genome.gov/Fund[...]rtium. Our group recently joined this consortium, and it is funded for 5 years to work with other investigators to understand how genomic variation alters human genome function, and how such variation influences human health and disease.

    Read more about our research, recent publications, and software here: pinellolab.org

    REQUIREMENTS

    • The ideal candidate(s) should have received (or expect to receive soon) a Ph.D. in Computer Science, Statistics, Genetics, Bioinformatics, Computational Biology, Mathematics, Physics, or related fields
    • First (or co-first) author in one or more peer-reviewed scientific publication
    • Excellent communication and writing skills
    • Able to work both independently and in teams
    Preferred Skills (not required):
    • Proficiency in Python and/or R
    • Strong statistical background and preferably statistical genetics background
    • Experience with commonly used bioinformatics tools and databases
    • Experience working with different types of NGS data such as ChIP-seq, RNA-seq, ATAC-seq
    • Knowledge of commonly-used machine learning methods
    • Experience in the analysis of single cell data and genome editing data
    • Experience in developing computational pipelines with Snakemake or Nextflow
    • Web development

    HOW TO APPLY

    If you are interested, please send your CV and a cover letter describing your current and future research interests, and the contact of 3 references to Luca: lpinello[at]mgh.harvard.edu.

    POLICY

    Our lab is committed to diversity and equality; therefore, we encourage applications from underrepresented minorities.

    Lawrence Berkeley National Lab's (LBNL, www.lbl.gov) Molecular Biophysics & Integrated Bioimaging Division (biosciences.lbl.gov/mbib/) has an opening for a National Lab and Synchrotron Postdoc for Biology to join the team.

    RESPONSIBILITIES

    In this exciting role, you will integrate into a multi-disciplinary team of scientists to tackle national priorities in pandemic response and climate change through structural biology. The Postdoc will manipulate samples (typically macromolecular complexes or cells) provided by an extensive network of collaborators both external and internal to LBNL and prepare them for synchrotron-based techniques (small angle X-ray scattering, crystallography, X-ray Tomography, and others). The Postdoc will help collect data from samples and connect results to biologically relevant phenomenon. The Postdoc will be involved in planning experiments, sometimes as early as the proposal stages. The Postdoc may interface with viral proteins, antibodies and their derivatives, engineered proteins, metalloproteins, and microbial metabolism regulation proteins and pathways. While centered at the Advanced Light Source (ALS) synchrotron, the Postdoc will develop ties to other LBNL organizations like the Joint BioEnergy Institute (JBEI), Joint Genome Institute (JGI), Molecular Foundry, and National Energy Research Scientific Computing Center (NERSC).

    What You Will Do:
    • Participate with other members of the scientific team in the application of unique LBNL infrastructure to address pandemics and climate change through structural biology.
    • Plan and execute the collection of crystallographic, SAXS and X-ray Tomography on core mission samples.
    • Publish scientific papers in peer-reviewed journals and present findings at seminars and conferences.
    • Participate in development of grant proposals for new research directions and preparation of competing renewals of current research grants.
    • Maintain an accurate and detailed online laboratory notebook of all experiments performed and provide sufficient details to ensure methods and results can be duplicated by others.
    • Collaborate with program projects that utilize synchrotron beamlines for research and develop new collaborations as appropriate to further the scientific goals of the programs (sibyls.als.lbl.gov).
    • Cooperate with other members of the SIBYLS beamline and the Advanced Light Source division.
    Additional Responsibilities as needed:
    • Participate in professional scientific activities (e.g., review of papers, research proposals, etc.).
    • Support and contribute to the development of research project ideas and proposals.
    • Participate in relevant professional societies with relevance to the program and group activities.

    REQUIREMENTS

    What is Required:
    • PhD in Biology, Chemistry, or Physics
    • Experience in expression, purification, and handling of biological macromolecules
    • Computational programming skills in any major programming language (C, Python, etc.)
    • A passion to solve national priorities in climate and human health
    • Excellent communication skills and a commitment to team science
    • Ability to work as a member of a small team where each member fills in gaps in effort and expertise
    • In-depth understanding of protein, DNA, and RNA structure
    Desired Qualifications:
    • Computational tools in protein engineering
    • Experience working with antibodies
    • Experience working with metalloproteins
    • Experience working on DNA or RNA binding proteins
    • Start to finish protein production to X-ray crystal structure

    TERMS & COMPENSATION

    • This is a full-time, 2 year, postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 2 years of paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.
    • This position is represented by a union for collective bargaining purposes.
    • Salary will be predetermined based on postdoctoral step rates.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

    LOCATION

    Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]09144 and follow the on-line instructions to complete the application process.

    Organization: MB-Molecular Biophys & Integ Bio

    ABOUT US

    Molecular Biophysics and Integrated Bioimaging:
    Mission: To generate a mechanistic and predictive understanding of biological processes, by developing and applying molecular- and meso-scale visualization and advanced spectroscopies, enabling the control, manipulation and generation of biological function.

    Vision: To generate fundamental knowledge that inspires a mechanistic understanding of biological processes, with the ultimate goal of manipulating, controlling, and creating biological functions in order to solve national challenges in energy, environment, health and biomanufacturing.

    POLICY

    Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, diversity.lbl.gov/ideaberkeleylab/) and strives to continue building community with these shared values and commitments

    Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

    Know your rights, click here (www.dol.gov/ofcc[...]t.htm) for the supplement: "Equal Employment Opportunity is the Law" and the Pay Transparency Nondiscrimination Provision (www.dol.gov/site[...]c.pdf) under 41 CFR 60-1.4.
    Opportunity: Staff Associate III @ Columbia University -- New York, NY (US)
    Submitted by VPS HR; posted on Thursday, September 30, 2021

    BACKGROUND

    The Staff Associate III will be a part of the Wang Lab wanglab.c2b2.columbia.edu at Columbia University Medical Center, and will work under the supervision of the principal investigator (PI) and in collaboration with others in the laboratory in the area of systems and synthetic biology and microbiome research. The goal of the research is to develop methods to engineer the mammalian gut microflora to improve health and fight disease. The Staff Associate III should possess at least four years of prior laboratory experience and a solid knowledge of molecular biology, bacterial culturing techniques (anaerobic and aerobic), and recombinant DNA protocols (PCR, transformation, cloning).

    RESPONSIBILITIES

    The Staff Associate III will assist in ongoing research projects in the lab and help perform laboratory experiments as needed. These research activities may include molecular, cellular, and animal experiments. In addition, they will coordinate research efforts, organize intra-lab group meetings, project planning and budgeting, assist in grant writing, and help oversee timely completion of research activities by other lab members. They will meet with the PI on a regular basis to coordinate these activities and update the PI on status of various projects and discuss any potential issues that may arise.

    The Staff Associate III will work independently on routine work and receive instruction on new assignments. The position requires technical proficiency necessary for achieving precise and consistent results. Ability to accurately record data and keep a very neat, well organized and up-to-date notebook is essential.

    The Staff Associate III will carry out responsibilities to manage general laboratory resources and equipment, maintain laboratory organization, (i.e., databases, reagent inventory, protocols, laboratory space), ordering and acquisition of laboratory reagents and equipment to support research needs, and participate in organizational and budgetary planning meetings, as appropriate. Excellent interpersonal and organizational skills and both written and oral communication skills are required.

    REQUIREMENTS

    • Bachelor's degree in biology, biochemistry or related field
    • At least four (4) years professional experience
    • Must have prior research experience in working with mice.

    PREFERENCES

    • Master's or higher degree in biology, biochemistry or related field

    TERMS

    Continuing Appointment Type

    LOCALE

    New York, NY USA

    COMPENSATION

    Commensurate with experience.

    HOW TO APPLY

    All interested applicants must apply on the Columbia's Careers website at apply.interfolio.com/94340.

    DEADLINE

    Open until filled.

    POLICY

    Columbia University is an Equal Opportunity Employer / Disability / Veteran
    Opportunity: Postdoc in bioinformatics @ UCSF -- San Francisco, CA (US)
    Submitted by Aaron Diaz; posted on Thursday, September 30, 2021

    DESCRIPTION

    A Postdoc position is available in the Diaz lab at UCSF (diazlab.ucsf.edu), funded by grants from the NIH, DoD and private foundations. As a member of the UCSF Brain Tumor Center (braintumorcenter.ucsf.edu) our mission is the development of therapeutics for brain cancers. Our core competencies include bioinformatics and systems biology.

    We have ongoing research efforts that study emerging immunotherapies, profiling clinical specimens using single-cell technologies. Our ongoing efforts have generated hundreds of thousands single-cell mRNA and ATAC libraries from hundreds of human adult and pediatric longitudinal brain-tumor specimens, and counting. We are actively developing spatial profiling, single-cell Cut&Tag and other cutting-edge genomics assays. These novel modalities require sophisticated bioinformatics approaches.

    The duties of bioinformatics postdocs include bioinformatics analyses of single-cell and bulk 'omics data, data interpretation and participation in experimental design. The minimum requirements for the position are: 1) a PhD in the biomedical sciences, bioinformatics or a related discipline; 2) experience with 'omics data analysis and strong programming skills in a relevant language (e.g. R, Python); 3) first-author papers in respectable journals; 4) fluency in English, and the interpersonal skills to negotiate professional interactions in a diverse environment; and 5) the willingness to work hard in the pursuit of shared goals.

    HOW TO APPLY

    Interested candidates should send an email to aaron.diaz[at]ucsf.edu, with the following:
    • CV
    • Cover letter, please indicate your preferred start date
    • Names and contacts of three references

    BACKGROUND

    Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, proteomics, multi-electrode recording, and multiple high-resolution imaging modalities. The mission of the Center for Computational Biology is to create new computational frameworks that will enable scientists to analyze the large and complex data sets that are being generated by these new experimental technologies. Principle areas of research include biophysical modeling, development dynamics, genomics, molecular biophysics, and systems biology.

    The Flatiron Institute is dedicated to advancing scientific research through computational methods, including data analysis, theory, modeling and simulation. It currently houses five science centers, focused on computational astrophysics (CCA), computational biology (CCB), computational mathematics (CCM), computational neuroscience (CCN) and computational quantum physics (CCQ), as well as a scientific computing core.

    CCB and CCM have created a joint research group in Structural and Molecular Biophysics. The goals of this new group include the creation of new computational methods that will enable scientists to analyze the large, complex data sets that are being generated by new experimental technologies, as well as new simulation techniques for molecular and structural modeling.

    RESPONSIBILITIES

    Applications are invited for a post-doctoral Flatiron Research Fellow (FRF) position with Structural and Molecular Biophysics at the Center for Computational Biology (CCB).

    In addition to conducting independent research, Flatiron Research Fellows in Structural and Molecular Biophysics will apply and develop methods in molecular dynamics (MD) simulation to better understand mechanisms of biological importance, such as ion channel function. In addition, they will work closely with experimental data and experimentalists to better combine single molecule and/or cryo-EM data with MD to improve our understanding of protein dynamics.

    More generally, Flatiron Research Fellows will disseminate their results through scientific publication or software release, collaborate with other members of the Center for Computational Biology and/or other Flatiron Institute research centers, and participate in the life of the Center for Computational Biology, and Mathematics, the Flatiron Institute by attending seminars, colloquia, group meetings and other opportunities for scientific exchange.

    REQUIREMENTS

    Education:
    • Applicants are required to have a Ph.D. in biochemistry, biophysics, physics, applied mathematics, computational biology, computer science, or related disciplines or, if selected, will receive their PhD before the start of the FRF appointment.
    Related skills and other requirements:
    • Exceptional abilities in molecular simulation and analysis, statistical mechanics, and/or relevant methods in computational biology.
    • Ability to do original and outstanding research in computational biology
    • Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
    • Strong oral and written communication, data documentation, and presentation skills
    • Excellent collaborative and interpersonal skills required.

    TERMS

    FRF positions are generally two-year appointments and can be renewed for a third year, contingent on performance.

    LOCATION

    These positions will be based in our New York City offices.

    COMPENSATION

    FRFs receive a research budget and have access to the Flatiron Institute's powerful scientific computing resources. FRFs may be eligible for subsidized housing within walking distance of the Flatiron Institute.

    HOW TO APPLY

    Apply Here: www.click2apply.net/da55[...]sL8XJ

    Required application materials:
    • Cover letter (optional)
    • Curriculum vitae with bibliography
    • Research statement of no more than three (3) pages describing the applicant's past work and potential synergies with activities at Structural and Molecular Biophysics and the Flatiron Institute as a whole.
    • Two (2) letters of recommendation submitted confidentially by the recommenders directly to ccbjobs[at]flatironinstitute.org.

    DEADLINE

    Please submit all application materials by December 3, 2021. Interviews with selected candidates will take place during the last two weeks of January 2022.

    POLICY

    The Simons Foundation's diversity commitment:
    Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law.

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