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    BACKGROUND

    The Center for Computational Biology (CCB) of the Simons Foundation's Flatiron Institute invites applications for multiple post-doctoral Flatiron Research Fellows (FRF) positions. Applications will be reviewed beginning in Fall 2022, and considered on a rolling basis until the positions are filled. For full consideration, submission of a complete application by November 15, 2022 is strongly recommended.

    The goal at CCB is to advance the understanding of fundamental and historically challenging biological processes by developing theory, innovative modeling tools for large-scale biophysical simulations, and computational frameworks for analyzing increasingly large and complex experimental datasets. Living systems are built hierarchically; as such, CCB's research activities span several scales of biological organization, bridging the gap between microscopic detail and large-scale behaviors, and providing natural continuity between our groups' efforts. CCB currently comprises more than 45 research and data scientists at career stages from recent Ph.D. graduates through senior scientists, as well as visiting scientists, guest researchers, graduate students, interns, and administrative support staff. For a full description of CCB research areas and scientific staff, please see our website.

    RESPONSIBILITIES

    Responsibilities include but are not limited to:
    • Performing theoretical and computational research
    • Developing, implementing and maintaining scientific software
    • Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars, workshops and meetings
    • Participating in the preparation of manuscripts for publication and of presentations at scientific conferences
    • Assisting in student mentorship
    • Sharing expertise and providing training and guidance to CCB staff and visitors as needed.
    FRF positions are generally two-year appointments that can be renewed for a third year, contingent on performance. Fellows will be based, and have a principal office or workspace, at the Simons Foundation's offices in New York City. Fellows may also be eligible for subsidized housing within walking distance of the Flatiron Institute.

    REQUIREMENTS

    Related skills & other requirements:
    • Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis
    • Ability to do original and outstanding research in computational biology, and expertise in computational methods, data analysis, software and algorithm development, modeling machine learning, and scientific simulation
    • Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
    • Strong oral and written communication, data documentation, and presentation skills

    PREFERENCES

    CCB welcomes applicants interested and capable in the following areas of research:
    • Biological Transport Networks: Areas of interest include modeling of vascular networks at multiple scales, including their function, development and remodeling, using machine learning and methods from topological data analysis to quantify large datasets of the microvasculature, understanding and incorporating the effects of fluid structure interactions (e.g. valves) into large scale networks of vessels. Applicants with interests in fluid dynamics and applied mathematics, networks or machine learning are particularly encouraged to apply.
    • Biophysical Modeling: Areas of interest include the dynamics of complex and active materials, and collective behavior and self-assembly in both natural systems (e.g., inside the cell) and synthetic ones. Approaches are based on mathematical modeling and analysis, the development and application of software tools for large-scale biophysical simulation, and close collaboration with experimentalists. Applicants with backgrounds in computational and applied mathematics, and theoretical biophysics are especially encouraged.
    • Developmental Dynamics: Areas of interest include small cell clusters, graph dynamics in rearranging cell networks, and the effects of activating mutations in signaling enzymes. Our theoretical and computational work is designed to integrate and abstract rapidly accumulating heterogeneous datasets, to propose critical tests of multiscale regulatory mechanisms, and to guide our own genetic and imaging experiments.
    • Genomics: Areas of interest include developing deep learning approaches for genome interpretation; development of methods for multi-omic data analysis and integration with phenotypic and clinical data; and machine learning approaches for network modeling and regulatory module detection. These and other methods are developed in tight collaboration with experimental biologists, biomedical scientists, and clinicians and are applied to specific biological problems, both fundamental (e.g. understanding transcriptional and posttranscriptional regulation and cell type definition) and biomedical (e.g. regulatory variant impact in mental health disorders or cancer). Applicants with backgrounds in machine learning/computer science, biomedical informatics, statistics, applied mathematics, and quantitative biology are especially encouraged.
    • Structural and Molecular Biophysics: Areas of interest include developing and using mathematical approaches and computational algorithms to understand the molecular mechanisms involved in key biological processes using cryo-electron microscopy experiments.
    • Structural Biology: Areas of interest include in particular membrane protein structural biology, protein modeling with flexibility, structure prediction, protein-protein interactions, high-resolution refinement, protein design, modeling the effect of mutations, and the integration of experimental data. We are further interested in analyzing sequence-structure-function relationships of large-scale microbiome databases and integrating structural methods with machine learning algorithms.
    FRFs in CCB are individuals at the postdoctoral level with backgrounds in one or more of the following areas: applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines. Reporting to Research Scientists, Data Scientists or the Center Director, as appropriate, Fellows are expected to carry out an active research program that can be independently directed and/or involve substantial collaboration with other members of CCB or the Flatiron Institute. In addition to their research, Fellows help build the rich scientific community at CCB and the Flatiron Institute by participating in seminars, colloquia, and group meetings; developing their software, mathematical and computational expertise through internal education opportunities; and sharing their knowledge through scientific publications, presentations, and/or software releases, with the financial support of the Institute. Fellows have access to the Flatiron Institute's powerful scientific computing resources.

    TERMS

    Full-Time

    LOCATION

    New York, New York 10001, United States

    HOW TO APPLY

    Required application materials:
    • Cover Letter, which should include a summary of applicants' most significant contributions in graduate school
    • Curriculum vitae with publications list and, if relevant, links to software
    • Research statement of no more than three (3) pages describing the applicant's past important results, current and future research interests which may include both scientific topics and algorithm and software development, and potential synergies with activities at CCB
    • Two (2) letters of recommendation submitted confidentially by the recommenders directly to ccbjobs[at]flatironinstitute.org.
    Apply Here: https://www.click2apply.net/1wmMQEUAOY2besgOzIlLaA

    DEADLINE

    Applications for available positions that begin in 2023 will generally be reviewed beginning mid-November 2022, and will be considered on a rolling basis until the positions are filled. For full consideration, candidates are strongly encouraged to submit their complete application by November 11, 2022.

    More information about career opportunities at the Simons Foundation's Flatiron Institute is also available at https://www.simonsfoundation.org/careers.

    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.

    PI193528303

    BACKGROUND

    The UF Health Cancer Center is currently seeking a Doctoral level or senior Master's level staff bioinformatician to join our Division of Quantitative Sciences and Biostatistics & Quantitative Sciences Shared Resource. Our Center stands alone in the state in our unique ability to blend comprehensive patient care and innovative research in a collaborative, multi-disciplinary environment. The UFHCC has been serving Floridians for over 20 years and invite you to join our talented team!

    RESPONSIBILITIES

    As part of our Division of Quantitative Sciences and the Biostatistics & Quantitative Sciences Shared Resource, you will be responsible for leading the bioinformatics unit and for mining and analyzing large, complex, and unstructured biological datasets for our membership as they conduct critical oncology research across the University of Florida.

    This is a highly visible, essential position critical to the mission and vision of the UFHCC as well as to the successful progression and development of cancer research at the University of Florida. In your role, you must present a professional demeanor and attitude, maintain a high level of confidentiality, and exercise independent judgment when completing assigned tasks and responsibilities.

    In your new role you will be responsible for the following:
    • Leading the bioinformatics team, ensuring project quality, assessing workloads, and managing problem resolution under the direction of the Director of the BQS-SR.
    • Developing, modifying, and applying software, algorithms, or pipelines to genomic or other biological data sets with the goal of understanding biological processes, diseases, or disorders in support of cancer researchers.
    • Developing databases to compile vast amounts of information from research activities conducted by UFHCC members and their labs.
    • Creating data algorithms and specialized computer software to identify and classify components of cancer biology and related areas to analyze data sets.
    • Designing and analyzing experiments or data sets. Developing mathematical models for integrating disparate data sources for deeper analysis.
    • Assisting in the analysis and interpretation of research results and contributing to publications and/or presentations.
    • Enhancing knowledge base and practices through continuing education activities, such as computational biology and/or statistical meetings, webinars, and seminars.
    These responsibilities require an extensive skillset in bioinformatics, data management, and statistical analyses (at the advanced graduate level) as you will be called upon to independently program, conduct statistical analyses, select and apply appropriate statistical methods, take steps to ensure that your work meets a high standard of quality, and work efficiently and diligently to meet your project deadlines.

    A complete job description will be provided to candidates selected for interview.

    REQUIREMENTS

    A master's degree in appropriate area of specialization and two years of experience or a bachelor's degree and four years of experience.

    PREFERENCES

    As an ideal candidate you will have/be:
    • A Ph.D. in bioinformatics, biostatistics, or related field and relevant research training and experience, or a M.S. with a minimum of 3 years of relevant experience required.
    • Diverse expertise in data management and statistical methods (SAS, R, etc.) are essential to perform the essential functions of this position, programming skills (Stata, SQL, SPSS, C++, Python, Excel, etc.).
    • Strong interpersonal skills, as well as the ability to work with a broad range of people including investigators, industry sponsors, partners at other institutions, UFHCC staff, and others.
    • Highly resourceful team-player, with the ability to also be extremely effective independently, interact professionally, and utilize effective writing and organizational skills.
    • Demonstrated understanding and effective use of Emotional Intelligence strategies and skills.
    • Proven ability to handle confidential information with discretion, be adaptable to various competing demands, and demonstrate the highest level of customer/client service and response.
    • Demonstrated ability to achieve high performance goals and meet deadlines in a fast-paced environment.
    • Forward-thinking mentality, actively seeking opportunities and proposing creative solutions with strong decision-making capability.
    • Demonstrated ability to establish and maintain effective working relationships with stakeholders and critical staff, both internally and externally, through a variety of communication mediums and venues.
    • Demonstrated data analysis skills with ability to synthesize aggregate data into meaningful operational metric and benchmarking reports and to communicate that data in meaningful ways to stakeholders.
    • Ability to collaborate with internal and external stakeholders across functions to optimize performance and drive projects to completion.
    • Excellent meeting management, group facilitation, and consultation skills.
    • Proficiency with Microsoft Office suite, particularly Excel, Word.

    TERMS

    Full-Time Staff

    COMPENSATION

    $80,000 - $90,000; Commensurate with Education and Experience.

    LOCATION

    Gainesville, FL, USA

    HOW TO APPLY

    Submit your application including cover letter, Curriculum Vitae or resume, and a list of three professional references to https://explore.jobs.ufl.edu/cw/en-us/job/523970/lead-bioinformatician-uf-health-cancer-center

    DEADLINE

    Application must be submitted by 11:55 p.m. (ET) of the posting end date. Current closing date is October 16, 2022. Deadline may be extended to allow for additional applications.

    BACKGROUND

    The UConn Institute for Systems Genomics is seeking a Research Technician to support the work of its Computational Biology Core. The Core supports the research mission of the University of Connecticut through a mix of paid research projects, project support and consultation, training workshops and the management of a high performance computing (HPC) facility along with providing support for the HPC user base.

    DUTIES & RESPONSIBILITIES

    • Support of the HPC facility
    • Support users through installing open-source scientific software and trouble-shooting user code
    • Manage and update shared databases
    • Support online workshops
    • Triage requests received via e-mail, Slack, and our help desk

    REQUIREMENTS

    Minimum qualifications:
    • B.A./B.S. or higher in computational or biological sciences
    • Experience with analyzing high-throughput sequence data
    • Proficiency with Linux
    • Comfort interacting with an HPC system
    • Strong presentation and communication skills
    • Positive attitude and ability to work as part of a team (multi-tasking extraordinaire)
    Preferred qualifications:
    • Comfort with R and/or Python programming
    • Proficiency with open-source software installation

    COMPENSATION

    This temporary special payroll position requires 40 hours per week, with an hourly rate of $28.00. This short-term role (6 months – 1 year) may transition to a permanent role for the right candidate (staff scientist).

    LOCATION

    The position can be on-site, remote or hybrid (must be able to attend meetings and support all users during Eastern Standard Time working hours). This position does not offer sponsorship benefits.

    HOW TO APPLY

    To apply, please email a resume and cover letter detailing your qualifications to jill.wegrzyn[at]uconn.edu, with the subject line "Research Technician Application." Screening will begin immediately.

    DEADLINE

    ASAP

    BACKGROUND

    About Us:
    Benaroya Research Institute at Virginia Mason (BRI) is an internationally recognized medical research institute committed to finding a cure for autoimmune and immune-mediated diseases, through a combination of basic and translational research programs. This means you can contribute to scientific advances that have a direct impact on people afflicted with these diseases, including type 1 diabetes, rheumatoid arthritis, multiple sclerosis, allergies and asthma.

    BRI research leadership has identified Bioinformatics as a key enabling technology, so there is broad and strong support for the analysis, and visualization of research data.

    Overview:
    GENOMIC ANALYSIS OF IMMUNE CELLS IN RESPONSE TO THERAPY IN CANCER AND AUTOIMMUNE DISEASE. Come join our team and help fight immune diseases!

    The Linsley Lab is broadly engaged in basic and applied studies using complex systems theory, high throughput techniques as well as mathematical and computational tools to understand the functioning of the immune system in health and disease. The group works closely with informaticians and immunologists in many groups at BRI, resulting in a rich environment for quantitative, computational, and laboratory collaborations in immune disease research. Funding is available for two years, contingent upon periodic reviews, with an expectation of extension and expansion. Opportunities for training, conference attendance and publication are available.

    RESPONSIBILITIES

    We need an individual to apply cutting edge big data approaches to study of the human immune system. We believe that understanding how the immune system is broken in diseases like cancer and autoimmunity will lead to better patient care. We are looking for a highly motivated and creative individual who enjoys working in a multidisciplinary team-oriented environment to use Systems Biology approaches to help discover new mechanisms, biomarkers and therapies for immune diseases.

    The Linsley Lab at BRI is seeking a Postdoctoral Research Associate. This individual will drive projects involving RNA-seq profiling (single cell and bulk), and/or cytometry (flow and mass) to elucidate the role of immune cells in response to therapy of autoimmune disease and cancer.

    REQUIREMENTS

    Qualifications:
    • Strong academic record and history of productivity
    • Knowledge of modern experimental biological science
    • Fundamental understanding of the application of statistics to scientific data
    • Experience with statistical tools (R, SAS, Matlab) and/or scripting or higher-level programming languages (Shell, Python, Perl, Java)
    • Strong interpersonal, verbal, and written communication skills
    Education:
    A successful candidate for this position will have a Ph.D. degree in bioinformatics, biostatistics, or life science, with a strong understanding of the principals of biology and bioinformatics.

    HOW TO APPLY

    Visit https://careers-benaroyaresearch.icims.com/jobs/1806/bioinformatics-postdoctoral-research-associate/job to apply for this position.

    POLICY

    All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, citizenship, disability or protected veteran status.

    BACKGROUND

    The Royal Botanic Gardens, Kew is establishing a new benchmark in plant biology by completing the plant tree of life, mining Kew's collections with novel genomic methods and generating DNA data unprecedented in scale and diversity. Over the past six years, we have assembled genomic data for over half of the 13,600 genera of flowering plants, making them publicly available on-line and using them in an extensive scientific research programme. We have recently secured major new funding and are now building a team to finish the job. We're looking for a highly motivated, collaborative expert to play a central role in delivering the bioinformatic requirements of the project.

    RESPONSIBILITIES

    The successful candidate will join an established, vibrant, multi-disciplinary team of scientists. In collaboration with existing project informaticians, you will be responsible for analysing and managing project data, as well as developing software to enable the construction of a complete tree of life for plants.

    REQUIREMENTS

    You will be an excellent bioinformatician or software engineer with appropriate professional experience and a proven background in genomic data manipulation and management, ideally in a research environment. You will have a track record of helping to design and build robust bioinformatics pipelines, with experience of high-performance computing, relevant programming languages (such as Python) and relational databases. Expertise in phylogenomics is desirable but not essential. You will be a proven team player, with the ability and appetite to deliver project outputs, outreach, and to train and support researchers and students as required.

    COMPENSATION

    £32,000 - £37,000 per annum.

    Our fantastic benefits package includes opportunities for continuous learning, a generous annual leave entitlement, flexible working to help you maintain a healthy work-life balance, an Employee Assistance Programme and other wellbeing support such as cycle to work scheme and discounted gym membership. We also offer a competitive pension, an employee discount scheme and free entry into a wide range of national museums and galleries, as well as access to our own beautiful gardens at Kew and Wakehurst.

    LOCATION

    This role is based at the Royal Botanic Gardens, Kew (UK) with the option of regular home working, subject to operational requirements.

    HOW TO APPLY

    Complete the online form, applicants must also upload 1) a letter of motivation and 2) a full CV, including details of publications and software.

    https://careers.kew.org/vacancy/bioinformatician-completing-the-plant-tree-of-life-project-500729.html

    DEADLINE

    11 October 2022

    Submitter

    BACKGROUND

    St. Jude Children's Research Hospital is seeking highly motivated individuals to join our Cancer Genomics team at the forefront of the application of NGS technologies to the clinical management of cancer patients and wants to make a difference in the lives of children with catastrophic illnesses. New team members will analyze and classify somatic and germline genetic alterations in pediatric cancer patients ascertained from whole genome, whole exome, and transcriptome sequencing and present findings to pathologists, oncologists, and genetic counselors. They will work closely with our bioinformatics pipeline and visualization teams to help develop or refine novel analytical approaches that aid molecular classification of cancer and clinical reporting in pediatric cancer patients. Successful candidates may also contribute to bioinformatic research projects concerning the pediatric cancer genome. Ideal candidates will have a deep understanding of cancer biology and expertise in genomic and transcriptomic variant analysis through NGS. We are interested in individuals with expertise in the classification of germline variation in the context ACMG guidelines for clinical variant interpretation, as well as somatic variation. Prior experience within a CAPCLIA clinical environment and experience in clinical test development and validation is desirable. Recognized as a world leader in deciphering the genetic landscape of pediatric cancer, St Jude Children's Research Hospital has developed state-of-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise applied comprehensively to all of its cancer patients.

    Bioinformatic Research Scientist:
    The Bioinformatics Research Scientist will work as part of a team of genomic analysts who evaluate and interpret comprehensive NGS data from whole genomes, whole exomes, and transcriptomes of pediatric cancer patients to assist clinicians in deriving diagnoses and treatment plans. Expertise in the recognition and interpretation of somatic and germline variation is essential, and knowledge of cancer biology is preferred. The incumbent performs data analysis and data visualization using existing analytical pipelines for NGS data processing to characterize pediatric cancer patient's tumor and germline genomes and reports results to a team of Molecular Pathologists. Pathogenic genomic variants are deposited in the patient's medical records for use by Oncologists in the clinical management of the patient. The successful candidate must also participate in software testing of routine pipeline improvements and the development of novel analytical approaches to tumor genome characterization. This individual will also provide bespoke bioinformatic analyses as required to decipher unusual tumor genomes and communicates analytical results to clinicians. Occasionally the incumbent will participate in preparing and submitting manuscripts for publication. The successful candidate must contribute ideas to automate or improve existing analytical methods and innovative algorithm development. The Bioinformatics Research Scientists assist with establishing and documenting protocols and standard operating procedures to ensure that clinical genomics testing meets CAPCLIA requirements for accreditation and reporting.

    Sr. Bioinformatics Analyst:
    The successful candidate will be part of a team composed of genomics scientists and bioinformaticists responsible for maintaining and extending computational genomics pipelines to analyze and characterize tumor and germline genomes of cancer patients at St. Jude Children's Hospital. The incumbent must have the facility of reading extant programs written in a variety of languages for troubleshooting or refactoring legacy code, as well as developing new pipelines to take advantage of cutting-edge cancer genomics research. The incumbent is responsible for advanced analysis of biomedical data produced from next-generation sequencing platforms including WGS, whole exome and deep sequencing capture array, and whole transcriptomes. The successful applicant will develop, improve, modify, and operate data analysis pipelines with minimal supervision. The bioinformatics analyst will develop bioinformatics pipelines or use extant software to conduct data analysis of biomedical datasets. Works closely with genomics analysts, scientists, and clinicians to provide technical consultation, generate/provide analysis results and reports, project reports and perform requested custom analyses. Perform statistical analysis of results and interprets results under supervision. Ability to evaluate and recommends software tools to meet the growing needs of St Jude Children's Research Hospital SJCRH) is critical. Excellent written and oral communication skills are required.

    RESPONSIBILITIES

    Bioinformatic Research Scientist:
    • Provides clinical support and delivers high-quality results.
    • Formulates an efficient analytical approach with NGS data.
    • Helps document the analytical processes.
    • May participate in manuscript preparation concerning interesting patient's who are consented for research.
    • Participates in establishing and documenting protocols or best practices for standard clinical tasks.
    • Formulates analytical plans using the best approach to address data analysis questions in challenging patients.
    • Participates in the evaluation and testing of new methods and technologies.
    • Contributes ideas to automate or improve existing analytical methods.
    • Implements the improvement or works with programmers and computational biologists to do so.
    • May develop reusable code and pipeline components.
    • Upon occasion participates in the department's independent research and interdepartmental team projects.
    • Performs other duties as assigned to meet the goals and objectives of the department and institution.
    Sr. Bioinformatics Analyst:
    • Analyzes genomic data produced from next-generation sequencing systems.
    • Performs advanced statistical analysis, algorithm implementation, and bioinformatics programming.
    • Evaluates data for quality assurance, and mine bioinformatics databases.
    • Is proficient with national and international genomics data repositories such as the UCSC Genome Browser, the Genomic Data Commons, the ICGC Data Portal, dbGaP, the National Center of Biotechnology Information, PubMed, and others.
    • Proven experience in developing analytical pipelines with both local compute clusters and cloud computing.
    • Is proficient in one or more scripting languages for manipulation of large data sets such as R, Python, Java, Ruby.
    • Performs analysis and develops software support requirements.
    • Assists senior analysts and scientists in the courses and training in biological computing, data mining, and analysis.
    • Establishes protocols or best practices for common research tasks.
    • Documents standard operating procedures (SOPs) on wiki pages.
    • Makes these protocols available to other group members and to interdepartmental investigators.
    • Assists with the preparation of graphs, charts, and figures for documentation of software validation and presentations.

    REQUIREMENTS

    Bioinformatics Research Scientist:
    • Seven (7) years of relevant post-degree work experience is required.
    • Five (5) years of relevant post-degree work experience is required with a Master's degree.
    • Two (2) years of relevant post-degree work experience is required with a PhD.
    Sr. Bioinformatics Analyst:
    • Four (4) years of relevant experience is required.
    • One (1) year of relevant experience may be acceptable with a Master's degree.

    LOCATION

    Memphis, TN

    HOW TO APPLY

    Apply online: https://careers-stjude.icims.com/jobs/10363/bioinformatics-research-scientist/job?mode=view&mobile=true&width=300&height=500&bga=true&needsRedirect=false&jan1offset=-360&jun1offset=-300

    POLICY

    St. Jude is an Equal Opportunity Employer

    No Search Firms:
    St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.

    COVID-19 vaccine:
    St. Jude Children's Research Hospital has mandated the COVID-19 vaccine for all employees, excluding those with an approved medical or religious accommodation, as a condition of employment.

    BACKGROUND

    The Department of Epidemiology and Biostatistics in the Arnold School of Public Health (ASPH) at the University of South Carolina (UofSC) invites applications for two nine-month tenure-track faculty positions in Biostatistics at the rank of Assistant Professor. All areas of biostatistics expertise will be considered but candidates with research expertise in bioinformatics, computational biology, high-dimensional data analysis, classification, risk prediction, precision medicine, and causal inference with applications to public health and/or medicine are particularly encouraged to apply.

    REQUIREMENTS

    Requirements include an earned doctoral degree by the start date of employment in biostatistics, statistics, bioinformatics, or a related field with demonstrated evidence of high-quality scholarly research in the development of statistical methods. The candidate should demonstrate potential to successfully compete for external research funding, teach graduate-level courses, and collaborate with public health and/or biomedical researchers. The successful applicant will contribute to the department's mission of research and training by maintaining an active methodological research program, collaborating with multidisciplinary research teams, mentoring graduate students, and teaching graduate level biostatistics courses to biostatistics and public health students.

    LOCATION

    Located in Columbia, South Carolina.

    HOW TO APPLY

    Applications require: 1) letter of application; 2) curriculum vitae; 3) research statement; 4) teaching statement; 5) diversity statement that describes how your approach to research, teaching, and service activities contribute to enhancing diversity, equity, and inclusion, and 6) contact information for three references. Submit your application at the following link: https://uscjobs.sc.edu/postings/128427. Posting Number FAC00184PO22. All applications received by November 1st will receive full considerations, but the search will continue until the positions are filled. The anticipated start date is August 2023. For additional information please contact Emily Writer at EPIDSCH[at]mailbox.sc.edu, or (803)-777-7353.

    POLICY

    UofSC is an affirmative action, equal opportunity employer. UofSC and ASPH condemn racism and injustice in all its forms and actions. UofSC does not discriminate in educational or employment opportunities or decisions for qualified persons on the basis of race, color, religion, sex, national origin, age, disability, sexual orientation, protected veteran status, or genetics. UofSC offers a robust benefits package described at: http://www.sc.edu/about/offices_and_divisions/human_resources/benefits/index.php

    BACKGROUND

    The South Australian Genomics Centre (SAGC) is a multi-institutional, national genomics and bioinformatics facility that is supported by Bioplatforms Australia (BPA) through the Australian Government's National Collaborative Research Infrastructure Strategy (NCRIS). The SAGC has consolidated genomics and bioinformatics expertise in the state, with a group of ~10 genomics and bioinformatics staff working side-by-side to deliver innovative genomics and bioinformatics solutions across all areas of genomics research, including agriculture, healthcare and ecology. An exciting opportunity now exists for a post-doctoral researcher or experienced MSc-level bioinformatician to join the SAGC bioinformatics team. To flourish in this role, you will need to be able to work across multiple different projects and to possess excellent organisational and time-management skills. This role is primarily responsible for supporting SAGC users to appropriately design genomics-related projects and to analyse and interpret their data. Working collaboratively with researchers across different disciplines, you will have a varied and interesting workload across projects in different areas of genomics, leading bioinformatics analyses with varying levels of complexity. There are significant opportunities for professional growth and development through exposure to data sets from different genomics technologies including single cell and spatial transcriptomics. Staff are expected to enable research by leading the development of reproducible, standardised pipelines for genomics data analysis and, where necessary, develop new methods and pipelines. Your career development will be supported and you will be encouraged to publish your research and to collaborate on major funding applications to national and international funding bodies. You will also be supported to develop your bioinformatics capabilities; ensuring that the SAGC can remain at the forefront of genomics. It is expected that you will have interest in and develop your capabilities in at least one specialist area of bioinformatics.

    RESPONSIBILITIES

    • Support researchers to design innovative but rigorous genomics projects and collaboratively support the bioinformatics aspects of these projects.
    • Develop and maintain reproducible bioinformatics pipelines and analyses approaches for routine analyses.
    • Where needed develop and implement new bioinformatics approaches, methods or data visualisation approaches.
    • Contribute to/or lead the drafting of reports and publications.
    • Contribute to/or lead the drafting of applications to major funding bodies.

    REQUIREMENTS

    • MSc, PhD, or equivalent experience, in either bioinformatics, computer science, physics, statistics or other relevant discipline
    • Have a broad understanding of at least two of the following areas and a significant interest in developing a deep understanding in at least one:
      • Transcriptomics: bulk RNAseq, scRNAseq, spatial transcriptomics,
      • Genomics: variant, haplotype and diversity analysis, genome assembly, metagenomics, epigenetics
      • DevOps: version control: test driven development and continuous integration, containerisation using Docker/Singularity
      • Systems biology: multi-omics data integration, network analysis
      • Statistics: linear models, ANOVA, hypothesis testing
      • Visualisation: data visualisation and User Interface/Experience design
      • Workflow systems: Snakemake and/or Nextflow
      • Other Omic's technology: metabolomics, proteomics
    • Prior experience with at least one of the following scripting languages: bash, R, Python and Perl

    TERMS

    Full-time, 2 year contract.

    LOCATION

    The SAGC is headquartered in the iconic South Australian Health and Medical Research Institute (SAHMRI) in the Adelaide CBD, Australia.

    HOW TO APPLY

    For more information or to apply please visit: https://sahmri.org.au/careers-and-study/working-at-sahmri/vacancies/bioinformatics-officer-2

    DEADLINE

    10 October 2022

    RESPONSIBILITIES

    GDIT is seeking a Cytogenetics Bioinformatic Scientist to support National Cancer Institute's (NCI's) Cancer Gateway in the Cloud (CGC) Cloud Resource – ISB-CGC. In this role you will work on various tools and datasets for cancer researchers using cytogenetics. You will also describe how these tools and data can be easily and effectively used in the Google cloud to perform groundbreaking, impactful cancer research.

    In this role, a typical day will include:
    • Collaborating with NCI clients and cancer researchers worldwide to develop further understanding of cancer mechanisms, develop cancer diagnostics, therapies, and treatments
    • Developing Jupyter/R -omics workbooks with an emphasis on cytogenetics incorporating rapidly developing laboratory and computational technologies to allow ISB-CGC end users to optimize the use of NCI cytogenetics data
    • Directly demonstrating to end users how to best use cytogenetics data and tools with other bioinformatics tools/pipelines on the Google Cloud.
    • Presenting the system to cancer researchers worldwide to increase use of the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer hosted on ISB-CGC
    • Working with the open-source cytogenetic to genome mapping software "CytoConverter" written in R programming language, as well as leading the debugging of the ISB-CGC branch of the CytoConverter code in collaboration with the original developer and enhancing the functionality over time.
    • Participating in the Extract, Transformation and Loading of new releases of the datasets to be made available to the cancer research community
    • Helping to expand available cytogenetic and other public datasets and assisting with the improvement of querying and analysis capabilities across multiple datasets
    • Aiding researchers with customizing their own analysis to answer specific research questions
    • Keeping up-to-date with the GA4GH and other worldwide -omics and personalized medicine initiatives

    REQUIREMENTS

    What you'll need:
    • BS degree (or equivalent) in bioinformatics, computational biology, computer science, or related field and five years related experience
    • Experience working with cytogenetics data
    • Experience implementing bioinformatics pipelines/workflows, Jupyter notebooks and R scripts in a research environment
    • Experience in Linux/Unix work environment
    • Proficiency in SQL, R, and Python programming
    • Prior experience interacting with bioinformaticians and computational biologists through creating documentation and presenting tutorials
    • Must have or be able to obtain a public trust level of security
    Desired Qualifications:
    • Experience with cloud development ecosystems – Google and / or AWS
    • Experience using the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer
    • Experience with tools and methods for cytogenetics and -omics data analysis (e.g. CytoConverter, bwa, GATK, Picard, samtools, vcftools, RVTESTS, beagle, GenomicRanges, tools for RNAseq analysis)
    • Prior cancer research experience

    HOW TO APPLY

    To apply, please go to: https://www.gdit.com/careers/job/bfa667f32/cytogenetics-bioinformatics-scientist/

    OVERVIEW

    Competitive salaries and full benefits including, medical, dental, and vision insurance, retirement program, vacation and sick leave, onsite cafe and much more!

    The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) located in Oklahoma City. OMRF investigators have internationally recognized expertise in Autoimmunity, Immunology, Genetics, Aging, Cardiovascular Disease, and Cancer. Investigators at OMRF enjoy close scientific interactions with OUHSC faculty and participate in OUHSC graduate programs. Additional information about OMRF can be found at the Oklahoma Medical Research Foundation web site: http://www.omrf.org.

    OMRF's excellence can only be fully realized by individuals who share our commitment to diversity, equity and inclusion. Successful candidates will demonstrate commitment to these values. OMRF is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to gender, sexual orientation, gender identity, race, color, national origin, age, religion, disability, veteran status or any other legally protected characteristic.

    RESPONSIBILITIES

    The https://omrf.org/research-faculty/research-centers/center-for-biomedical-data-sciences-about/ is seeking a bioinformatician/data analyst to support biomedical research projects and training across the institute. The hire will implement and optimize pipelines for genomic data analysis and facilitate training of individuals in the use of a variety of software, including R and Python packages, for the analysis of datasets from a variety of genomic methods, including RNAseq, ChIPseq, and scRNA-seq. The hire will also work with senior scientists and staff to organize and implement access to training materials and software.

    REQUIREMENTS

    Bachelor's degree in Bioinformatics, Mathematics, Statistics, Biostatistics, Computer Science, MIS, or a relevant field and 3 years relevant experience/training in a biomedical research setting or combination of experience/education. Candidates must have prior hands-on experience in genomic data analysis using R and/or Python packages. Preference will be given to candidates who have demonstrated strong skills in project management, contribution to multiple projects, customer service, verbal and written communication, time management, organization, and experience with education/training.

    HOW TO APPLY

    To apply, visit https://apptrkr.com/3434114

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    https://www.jobelephant.com

    BACKGROUND

    The Ji Lab at the University of Texas at Tyler (UTT) focuses on regenerative niches for the remodeling of injured lungs. UTT North Campus is widely recognized for its exceptional, innovative, and collaborative research environment, and is investing significant resources in expanding interdisciplinary research in the computational, genomic, cellular, and molecular bases of pulmonary diseases. The Ji Lab is dedicated to applying state-of-the-art computational strategies to identify new molecular endotypes, biomarkers, and microbiota of acute lung injury/acute respiratory distress syndrome (ARDS). The lab is located in the UTT North Campus, a heavily shaded campus by southern pine trees, and on I-20 in east Texas.

    RESPONSIBILITIES

    This position is available immediately at the Ji Lab. The individual will identify and implement computational solutions to research problems related to ARDS and sarcoidosis. They will be responsible for taking on highly interdisciplinary projects and key functions in this endeavor, including applying state-of-the-art open-source software for basic and advanced analysis of next-generation sequencing data (scRNAseq) and proteomics data. They will also analyze epigenetics and transcriptomic datasets.
    • Analyze omics data using online available R or Python packages for omic data processing
    • Process omics data for clustering and function annotations to identify new endotypes
    • Identify biomarkers from human and microbial proteins using R or Python
    • Correlate identified molecular endotypes with phenotypes
    • Collaborate with wet lab scientists to prepare cell/tissue samples for LC-MS and scRNAseq
    • Prepare reports, charts, and graphs for presentations and publications
    • Maintain detailed records of computational code and processes
    • Manage omics and metadata
    • Search and evaluate scientific literature in support of research projects
    • Prepare manuscripts, progress reports, and grant applications

    REQUIREMENTS

    The ideal candidate will be highly motivated, well organized, manage time effectively, and can work independently as well as part of a team. They will have a background in bioinformatics, computational biology, and/or biostatistics and have essential skills of biological lab.
    • Programming Languages: Python, R, and others
    • Analytical: critical thinking, data modeling, problem-solving, troubleshooting
    • Demonstrated ability working with open-source bioinformatics software
    • Experience in bioinformatics analysis of RNA-Seq and proteomics data
    • A record of taking initiative to solve problems and working to high-quality standards
    • Attention to detail and accurate record keeping
    • Ability to multitask, work and learn independently, and be self-motivated
    • Publication record: demonstration of productivity in omics data analysis
    • Masters' or Ph.D. in Bioinformatics, Biostatistics, Computational Biology, Computer Science, Genetics, Biology or a related field. Multi-disciplinary trainee, with a working experience of 3+ years, is preferred.

    TERMS

    This is a full-time position supported by a new NIH R01 award. The position is renewable. UTT is a public state university.

    COMPENSATION

    In addition to a full fringe benefit, including insurance, paid holidays, and a retirement plan for both employee and family, the salary will match the NIH guide based on the experience.

    LOCATION

    Tyler, Texas. The North Campus of University of Texas at Tyler.

    HOW TO APPLY

    Please email a cover letter explaining relevant work experience, a CV, and the names and contact information for three references to james.ji[at]uthct.edu. A short list of candidates will be directly contacted by the PI.

    DEADLINE

    December 30, 2022

    POLICY

    As an Equal Opportunity Employer, the University will, in accordance with State and Federal law and regulations, provide equal opportunity in all employment related activities without regard to race, color, religion, national origin, gender, age, disability, sexual preference, or status as a disabled veteran or a veteran of the Vietnam Era. The University requires pre-employment drug & alcohol screening, proof of COVID-19 vaccination and/or medical or religious exemption, and health immunizations and criminal background check on all hires. Specific job requirements or physical location of some positions allocated to this classification, may render this position security sensitive, and thereby subject to the provisions of Section 51.215, Texas Education Code.

    DESCRIPTION

    The French CEA (Commissariat à l'Energie Atomique et aux Energies Alternatives) is looking for a talented computational biologist to join its laboratory of semantic analysis of texts and images.

    In this exciting project, you will integrate an interdisciplinary team aiming to move closer to the goal of predictive and generative artificial intelligence for biology by exploiting deep contextual language models of biological sequences, whose representations generalize to several applications like the prediction of mutational effects.

    Background:
    Exponential growth in sequencing throughput together with the sampling of natural (uncultured) populations are providing a deeper view of the diversity of proteins sequences across the tree of life. Proteins are molecular engines sustaining cellular life and the unobserved determinants of their structure and function are encoded in the distribution of observed natural sequences. Therefore, such vast amounts of (unlabelled) sequences provide evolutionary data that can form the ground for unsupervised learning of predictive and generative models of biological function.

    Our focus here will be to train high-capacity Transformer-based language models on sequence data, in a way analogous to what is done in natural language understanding, where the semantics of words is determined from the contexts in which they appear in sentences. Intrinsic organizing principles captured in the resulting representations can then be applied in transfer learning settings to different prediction sub-tasks using limited experimental data, like the effect of sequence variation on function. Following promising recent results, we plan to also explore zero-shot inference with no additional training and/or supervision from experimental data.

    This project will be an excellent opportunity for a candidate who is looking to contribute to cutting-edge research and to train with experts in the field. We are seeking a detail-oriented computer scientist and problem solver passionate in science.

    RESPONSIBILITIES

    • Tune and optimize existing unsupervised transformer-based language models for protein sequences.
    • Develop and optimize code and machine learning algorithms for predictive models.
    • Integrate and analyze large data volumes.
    • Interact continuously with scientists in an interdisciplinary team.

    REQUIREMENTS

    • Ph.D. or M.Sc. in a quantitative discipline, e.g. Applied Mathematics, Computer Science, Computational Biology, Physics or a closely related discipline.
    • Experience with Python, open-source software libraries for machine learning and Linux (file systems, shell, hardware/software monitoring, etc).
    • Strong mathematical background and analytical skills.
    • Effective organizational skills, e.g. the ability to prioritize work and contribute to the planning of a program of scientific research.
    • Demonstrated interpersonal skills including both the ability to work independently and perform collaborative research in an interdisciplinary team environment.
    • Good oral and written communication skills.

    PREFERENCES

    Previous experience with transformer-based techniques for NLP pre-training and unsupervised transformer language models.

    TERMS & COMPENSATION

    This 2 years position is open to a range of candidates from recent college graduates to more experienced scientists (e.g. post-docs) – the chosen candidate's salary will be commensurate with their level of education, skills, and experience.

    LOCATION

    We are based on the Paris-Saclay research campus in the south of Paris.

    HOW TO APPLY

    Interested candidates should submit a resume and short cover letter to deepgenseq « at » saxifrage.saclay.cea.fr

    ABOUT US

    About CEA LIST: https://list.cea.fr/en/
    About the LASTI lab: https://kalisteo.cea.fr/index.php/ai/ and https://kalisteo.cea.fr/index.php/textual-and-visual-semantic/
    About Genoscope: https://www.genoscope.cns.fr

    BACKGROUND

    The http://omrf.org/ghd at the https://omrf.org invites candidates to apply for an investigator position at the Assistant Member level (Assistant Professor equivalent). Current investigators in GHD study questions related to human disease through both model organism and human studies. Our expertise varies from stem cell biology, genome editing, genomics bioinformatics, and neuroepigenetics to human health-related problems including autoimmune diseases, aging, hearing loss, and regeneration. We seek to identify a candidate who will establish an independent research career as well as catalyze collaborative research in our highly interactive program.

    COMPENSATION

    All investigators at OMRF have access to state-of-the-art core facilities, including an Imaging Core, animal facilities, and modern, next generation sequencing technology and bioinformatics platforms. The successful candidate will receive a generous, multi-year, start-up package with significant salary, equipment, and research funding. OMRF also provides substantial ongoing salary support and research support after the start-up period has ended.

    HOW TO APPLY

    To apply, visit https://apptrkr.com/3402393

    ABOUT US

    OMRF is an independent, not-for-profit biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) in Oklahoma City. Oklahoma City offers a dynamic and burgeoning midtown area near the campus, and a very reasonable cost of living.

    We are committed to addressing additional needs of faculty, including dual career couples and single parents. We are particularly focused on overcoming barriers to gender equity in science. OMRF is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to gender, sexual orientation, gender identity, race, color, national origin, age, religion, disability, veteran status, or any other legally protected characteristic.

    POLICY

    OMRF's excellence can only be fully realized by individuals who share our commitment to diversity, equity and inclusion. Successful candidates will demonstrate commitment to these values. OMRF is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to gender, sexual orientation, gender identity, race, color, national origin, age, religion, disability, veteran status or any other legally protected characteristic.

    Copyright ©2022 Jobelephant.com Inc. All rights reserved.

    https://www.jobelephant.com

    BACKGROUND

    The Department of Biological Sciences at Virginia Tech is seeking to hire a tenure track assistant professor in the broad area of Computational Biology/Bioinformatics. We welcome applicants whose research addresses important biological questions at any scale, and applications involving all relevant research areas will be considered. Departmental research programs that may be attractive to applicants are listed here.

    RESPONSIBILITIES

    The successful applicant will be expected to establish a research program that generates peer-reviewed scholarship and is supported by extramural funding. They will be expected to provide effective instruction at the undergraduate and graduate levels, as well as mentoring and advising to a diverse population of undergraduate and graduate students. Other responsibilities include continued development of professional capabilities and scholarly activities, including advancing equity and inclusion, participation in national and international conferences, curriculum development, involvement in department, college, and university governance, and professional service.

    REQUIREMENTS

    Applicants must have a PhD or equivalent degree in a relevant discipline by the appointment start date. Additionally, applicants must be dedicated to education at the undergraduate and graduate levels and committed to teaching a student body that is diverse with respect to socio-economic status, interests, and abilities. Applicants need to demonstrate a clear understanding and willingness to address issues of diversity, equity, inclusion, and justice across their research, teaching, and service. Position may require occasional travel to attend conferences and meetings.

    COMPENSATION

    Commensurate with experience

    LOCATION

    Blacksburg, Virginia, United States

    HOW TO APPLY

    Virginia Tech is an equal opportunity and affirmative action employer. Women, minorities, individuals with disabilities, and protected veterans are strongly encouraged to apply. Applications must be submitted online at https://jobs.vt.edu and should include (1) a cover letter, (2) curriculum vitae, (3) a summary of research experience and future plans (max. three pages), (4) a statement of teaching and mentoring experience and philosophy (max. two pages), (5) a diversity statement (max. two pages; click here for details) and (6) contact information for three references. Review of applications will begin on September 26, 2022 and continue until the position is filled. Later in the hiring process, the successful applicant must provide an official transcript and pass a criminal background check. For questions, please contact search chair David Popham (dpopham[at]vt.edu).

    More information on this position can be found here: https://careers.pageuppeople.com/968/cw/en-us/job/521528/assistant-professor-of-computational-biologybioinformatics

    DEADLINE

    September 26, 2022

    BACKGROUND

    The University of Applied Sciences is looking back at 125 years of research and education and sees itself as a global and diverse university. We are currently educating around 2.700 students in engineering and natural sciences, offering approximately thirty different degree programs. Our recognized practice-oriented research and sound teaching performance distinguishes as the only STEM university in the region.

    The Department of Technology, Computer Science and Economics is looking for applicants for a full-time position (39 h/week) PhD Position in Artificial Intelligence based Protein Function at the next possible date. We are offering you a contract for the duration of 3 years.

    In collaboration with the newly founded institute for bioinformatics (IBG-4) within the institute for bio- and geosciences at the Forschungszentrum Jülich a PhD research project has been set up.

    In this PhD project we want to develop a new method of protein function prediction relying not on textual similarity but similarity of chemical and physical amino acid features. For the identification of significantly similar references sharing similar physico-chemical features we shall explore spectral analysis, fingerprinting, and artificial intelligence methodologies.

    RESPONSIBILITIES

    Your tasks:
    • Analysis and profiling of physico-chemical properties of well studied groups of reference proteins of known function
    • Exploration of methods to extract significant features to robustly distinguish these functional groups
    • Implementation of a fingerprinting method, possibly based on fuzzy hashing, to store these features in a machine readable, indexable format that also lends itself to identify closely related fingerprints
    • Exploration of machine learning artificial intelligence methods for the identification of significantly similar indexed fingerprints for query proteins of yet unknown function
    • Experimentation with spectral analysis decomposition methods for fingerprinting, possibly with discrete wavelet decomposition

    REQUIREMENTS

    Your profile:
    • A successfully achieved Master's Degree in computer science, machine learning or bioinformatics with a strong experience in artificial intelligence
    • Good experience in Scripting a scientific programming language, e.g. Python
    • Good experience in Shell-Scripting (Bash)
    • Intermediate in handling the Linux operating system
    • Experience in data visualization is desirable
    • Experience with a high level language like C/C++, Rust, Fortran, or Julia is desirable
    • Good organizational skills and the ability to work independently
    • Very good cooperation and communication skills and ability to work as part of a distributed team in an international and interdisciplinary environment
    • Excellent communication skills in English are mandatory

    COMPENSATION

    Our offer:
    • Salary in line with pay group 13 of the Collective Agreement for the Public Service (TV-L)
    • Possibility to join a pension scheme with the VBL
    • We are offering a family-friendly workplace and flexible working hours
    • Outstanding scientific and technical infrastructure
    • Possibility of mobile working
    • Further development of your personal strengths, e.g. via a comprehensive further training programme

    LOCATION

    The place of employment is mainly at Forschungszentrum Jülich.

    HOW TO APPLY

    Please submit your application via our application portal (https://www.th-bingen.de/karriere/stellenangebote/).

    For further Information please contact Prof. Dr. Asis Hallab (a.hallab[at]th-bingen.de).

    DEADLINE

    We look forward to receiving your application by 14. September 2022 at the latest.

    POLICY

    The University of Applied Sciences (Technische Hochschule Bingen) is committed to equal rights for women and men and therefore explicitly encourages women to apply. Equally qualified handicapped applicants will be given preference.
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