Bioinformatics Jobs

Why Mayo Clinic Mayo Clinic is top-ranked in more specialties than any other care provider according to U.S. News & World Report. As we work together to put the needs of the patient first, we are also dedicated to our employees, investing in competitive compensation and comprehensive benefit plans – to take care of you and your family, now and in the future. And with continuing education and advancement opportunities at every turn, you can build a long, successful career with Mayo Clinic. You’ll thrive in an environment that supports innovation, is committed to ending racism and supporting diversity, equity and inclusion, and provides the resources you need to succeed. Benefits Highlights • Medical: Multiple plan options. • Dental: Delta Dental or reimbursement account for flexible coverage. • Vision: Affordable plan with national network. • Pre-Tax Savings: HSA and FSAs for eligible expenses. • Retirement: Competitive retirement package to secure your future. Responsibilities A Research Fellow opportunity is available under the mentorship of Dr. Arjun Athreya in the Department of Molecular Pharmacology and Experimental Therapeutics. The successful candidate will work in bioinformatics research in a multi-omic integration program. Applicants who apply should have a strong background in bioinformatics skills, as well as excellent verbal and written skills. A Research Fellow in Bioinformatics/Biostatistics (BST) will have a primary focus in developing software and research techniques and/or tools to analyze and then aid in understanding biological data. Responsibilities and skills required involve computer programming, calculating statistics related to biological information, and mathematics. A Research Fellow at Mayo Clinic is a temporary position intended to provide training and education in research. Individuals will train in the research program of a Mayo Clinic principal investigator. Qualified individuals will demonstrate the potential for research as evidenced by their training and peer-reviewed publications and should become competitive for national research grants. Proof of English proficiency is required for J-1 Short-Term Scholars, Research Scholars, Professors, Specialists, and Student Interns sponsored by Mayo Clinic. To learn more about the exciting research being done on Mayo Clinic’s campuses, please visit Research at Mayo Clinic - Mayo Clinic Research. Applicants may search for research postdoc opportunities here: jobs.mayoclinic.org/post-doctoral-jobs. Qualifications Must have a Ph.D., M.D., or equivalent doctoral degree in a field deemed relevant by the program. Research Fellow is appropriate for individuals who have completed no more than one prior postdoctoral fellowship, at Mayo Clinic or elsewhere. Exemption Status Exempt Compensation Detail $68,564 - $80,210 / year; Education, experience and tenure may be considered along with internal equity when job offers are extended. Benefits Eligible Yes Schedule Full Time Hours/Pay Period 80 International Assignment No Site Description Just as our reputation has spread beyond our Minnesota roots, so have our locations. Today, our employees are located at our three major campuses in Phoenix/Scottsdale, Arizona, Jacksonville, Florida, Rochester, Minnesota, and at Mayo Clinic Health System campuses throughout Midwestern communities, and at our international locations. Each Mayo Clinic location is a special place where our employees thrive in both their work and personal lives. Learn more about what each unique Mayo Clinic campus has to offer, and where your best fit is. Affirmative Action and Equal Opportunity Employer As an Affirmative Action and Equal Opportunity Employer Mayo Clinic is committed to creating an inclusive environment that values the diversity of its employees and does not discriminate against any employee or candidate. Women, minorities, veterans, people from the LGBTQ communities and people with disabilities are strongly encouraged to apply to join our teams. Reasonable accommodations to access job openings or to apply for a job are available. Recruiter Kara Schott

The Bioinformatics Research Scientist performs data analysis, data visualization, statistical analysis, experimental design, database development, mathematical modeling, and novel method development. Provides bioinformatics analysis for investigators and communicates analytical process and results. The Center for Applied Bioinformatics (CAB) at St. Jude Children's Research Hospital is seeking a highly motivated Senior Bioinformatics Research Scientist to join the Transcriptomics Group. CAB is an institutional shared resource dedicated to providing state-of-the-art bioinformatics services to St. Jude investigators. Our Center collaborates with lab scientists and physician-scientists at multiple stages of their research, from study design, data analysis to preparation for presentations, grant proposals, and co-authoring manuscripts. We uphold the highest level of scientific rigor by carefully vetting and documenting all bioinformatics methods and pipelines. The successful candidate will develop and apply innovative analytical approaches to analyze & interpret new and existing multi-omic datasets obtained from both clinical and basic research lab, including bulk tumor/normal, single-cell/nucleus, and spatial-omic profiles. These analyses will contribute to understanding the underlying mechanisms driving pediatric cancers and other human diseases. The candidate will work closely with other bioinformatics personnel within CAB, playing an integral role in exciting research partnerships both within St. Jude and with external collaborators. He/she will contribute to establish the pipelines and best practice to characterize bulk or single cell RNA isoforms and noncoding RNA transcripts with long read sequencing technologies. He/she follows and adheres to best practices in structured transparent project management by tracking progress, identifying roadblocks, and proposing solutions, developing specific milestones for each research goal, and providing informative progress reports and summaries to principal investigators. The Center provides a highly interactive environment with collaborative opportunities across basic and clinical departments. You'll have access to high performance computing clusters, cloud computing environments, innovative visualization tools, highly automated analytical pipelines, and mentorship from experienced scientists. Members of this Center have the opportunities to publish high profile papers with prominent authorship depending on their intellectual contributions. The ideal candidate should have: · A PhD and extensive post-PhD experience in bioinformatics, computational biology, and data science. · A strong CV that includes high-profile publications in the field of computational biology, cancer genomics, and/or single-cell genomics. · Experience analyzing some/all the following platforms: whole-genome/exome sequencing, RNA-seq. ATAC-seq, ChIP-seq/CUT&RUN, single-cell/nucleus RNA-seq, CITE-seq, single cell multiome (ATAC+GEX), spatial transcriptomics, and long-read sequencing (e.g., PacBio and Oxford Nanopore) · Proficiency in relevant programming languages such as R and Python, preferably in a High-Performance Computing (HPC) environment. · Proficiency in tools for ensuring reproducibility of pipelines, such as workflow management systems (e.g., nextflow), and version control (e.g., git). · Proficiency in tool development, including examples documented in public repositories. · Extensive expertise in data integration and harmonization. · Proven problem-solving skills and collaborative nature in fast-paced environment. · Excellent communication and presentation skills. Job Responsibilities: • Provide research support and deliver high-quality results by formulating an efficient analytical approach with the available data. • Deliver data files, and document the analytical process. May participate in manuscript preparation at project's conclusion. • Assist with establishing and documenting protocols or best practices for common research tasks, and in the formulation of analytical plans that use the best approach to address challenging data analysis questions. • Assist in the evaluation and testing of new methods and technologies. • Contribute ideas to automate or improve existing analysis methods. Implement the improvement or work with others to do so. • Participate in the department's developmental projects and interdepartmental team projects. • Perform other duties as assigned to meet the goals and objectives of the department and institution. • Maintains regular and predictable attendance. Minimum Education and/or Training: • Bachelor's degree in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry) or related field. • Master's degree or PhD preferred. Minimum Experience: • Minimum Requirement: Bachelor's degree with 7+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry). • Experience Exception: Master's degree with 5+ years of relevant post-degree experience (OR) PhD with 2+ years of relevant post-degree experience. • Significant experience in at least one programming or scripting language and at least one statistical package, with R preferred. Compensation In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $86,320 - $154,960 per year for the role of Bioinformatics Research Scientist. Explore our exceptional benefits! 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.

Full-Time, 40 Hours/Week Day Shift Onsite, hybrid Summary: The Bioinformatics Analyst is responsible for the development, maintenance, and validation of bioinformatics pipelines and workflows to support clinical and research activities within the Molecular Diagnostics department. This includes tasks such as alignment, variant calling, variant annotation, copy number analysis, gene fusion detection, and the integration of data resources to streamline clinical data review and reporting. The role requires compliance with clinical accreditation standards (e.g., CAP), providing technical expertise for the clinical NGS workflow, collaborating with institutional IT and computing personnel, and contributing to research and educational initiatives at Akron Children’s Hospital. The Bioinformatics Analyst will play a critical role in both clinical operations and research, offering technical support and bioinformatics expertise to clinical genomics scientists, designing and maintaining analysis pipelines, and contributing to large-scale data analysis projects. The position also involves staying current with advancements in the field, applying AI and deep learning techniques, and conducting training sessions for researchers. Responsibilities: Duties and Responsibilities 1. Analyze and interpret complex clinical and research data across various -omics data types, including genomics, transcriptomics, and epigenetics. 2. Apply strong conceptual and practical knowledge in analyzing WES, WGS, targeted NGS panels, and OGM datasets. 3. Collaborate with clinical genomics scientists to design informatics experiments and interpret complex biological data. 4. Develop, document, and maintain tailored algorithms and analysis methods for NGS data. 5. Contribute to the scale-out of bioinformatics infrastructure and participate in external scientific discussions on technology evaluation. 6. Stay updated with advancements in bioinformatics by attending conferences, workshops, and engaging with the scientific community. 7. Design, develop, and maintain bioinformatics pipelines, ensuring public documentation and example workflows are up-to-date. 8. Apply rigorous statistical analysis and predictive analytics to extract insights from datasets, including those curated from public domains. 9. Innovate through the implementation of AI and deep learning algorithms to generate new insights from large datasets. 10. Conduct training sessions and create comprehensive tutorials to educate researchers on bioinformatics techniques, tools, and best practices. 11. Perform other duties as required. Other information: Technical Expertise 1. Strong understanding of statistical methods and data visualization techniques. 2. Proficiency in programming languages such as Python, R, and Perl. 3. Experience in Linux environments, cloud computing systems, and the development of statistical methods and algorithms. 4. Expertise in building and maintaining large-scale bioinformatics analysis pipelines for NGS data. 5. Hands-on experience with bioinformatics analysis, including variant filtering/calling, quality control monitoring, and variant annotation. 6. Experience with remote data storage and management, such as Amazon Web Services. 7. Familiarity with genomics databases and resources like ClinGen, HGMD, ClinVar, COSMIC, and OncoKB. 8. Excellent communication skills for effective collaboration and training. 9. Ability to work independently and as part of a team in a dynamic clinical laboratory environment. 10. Proficiency in MS Office (Outlook, Excel, Word) or similar software is required. 11. Experience with SAS, SPSS, and R software is preferred. Education and Experience 1. Education: Master’s degree in Bioinformatics, Computational Biology, or a closely related field is required; PhD is preferred. 2. Years of relevant experience: 2 years is required. 3. Years of experience supervising: None. Full Time FTE: 1.000000 Status: Fixed Hybrid

Department: Medicine | School Biomed Sci - Biomedical Informatics Tenure faculty (regardless of rank) - persons with the titles of professor, associate professor, assistant professor and instructor who serve on appointments totaling 50% or more service to the university and who are eligible for tenure or who have obtained tenure. Duties and responsibilities are assigned in accordance with the workload guidelines laid out in the pattern of administration of each faculty member’s tenure initiation unit (TIU) and, as appropriate, regional campus; obligations will include research, service and/or teaching or clinical practice. These faculty will have earned doctorate or other terminal degree in the relevant field of study or possession of equivalent experience. Division of Bioinformatics and Computational Biology (DBCB, https://medicine.osu.edu/departments/biomedical-informatics/divisions/division-of-bioinformatics-and-computational-biology-division-bcbs) in the Department of Biomedical Informatics (BMI, http://bmi.osu.edu) at The Ohio State University (OSU) is currently seeking applicants for a tenure-track faculty at the Assistant, Associate, and Full Professor levels with research interests in bioinformatics and computational biology. Position Overview Recruited faculty will join a highly collaborative community of more than thirty investigators working in a wide variety of BMI sub-domains including bioinformatics, biostatistics, artificial intelligence/machine learning (AI/ML) in digital health, clinical informatics, and implementation science, among others. Successful candidates will maintain an active research program in bioinformatics, collaborate with investigators across the health sciences campus, teach courses within our graduate programs, and mentor students. While open to all bioinformatics research areas, we are particularly interested in one or more of the following areas: AI and deep learning methods for multi-omics data modeling and integration Microbiome research with metagenomics and/or metaproteomics experience Immuno-informatics equipped with single-cell transcriptome, metabolomics, and imaging data. Comparative/population genomics Cloud computing and cyberinfrastructure construction Duties and Responsibilities Successful candidates will work as part of a collaborative team with investigators across the health sciences campus to develop grant proposals and design studies for clinical trials, basic science, and high-throughput omics at The Ohio State University. Opportunities to develop methodologies, teach courses within our graduate programs, and mentor graduate students are available and encouraged. Requirements Successful applicants will have a Ph.D. in bioinformatics, mathematics, computer science, or related fields. Department/Division Overview As part of the College of Medicine at the Ohio State Wexner Medical Center (OSUWMC, http://medicalcenter.osu.edu), the Department of Biomedical Informatics (BMI, https://bmi.osu.edu) provides an academic home for informatics and biostatistics research, development and training at Ohio State. The Department of Biomedical Informatics has the most comprehensive academic programs in the nation, including bioinformatics and computational biology, clinical informatics, AI in digital health, implementation science, and biostatistics. Division of Bioinformatics and Computational Biology of BMI stands at the crossroads of computer science, engineering, mathematics, biology, and medicine. Through advanced computational and analytical approaches, we deduce innovative biological hypotheses and conclusions. We champion the development and application of data-mining algorithms, computational methods, and systems-biology approaches, addressing vital challenges in biomedicine. BMI has a strong diversity, equity, and inclusive culture for faculty who develop careers in innovative and collaborative research. The BMI department dedicates significant effort to assisting grant writing and stimulating collaboration. The department has a robust training curriculum for PhD, Master, and Certificate programs. The department has also established a significant amount of resources in clinical data and high-performance computing and data storage. How to Apply To be considered, please submit your application electronically via Workday. Applicants should plan to upload a cover letter, a curriculum vitae, a statement of research plans (up to 3 pages), and a teaching statement. In the teaching statement, please outline your approach to teaching and learning and your goals and vision as an educator. Any questions can be directed to the chair of the search committee, Dr. Qin Ma (qin.ma@osumc.edu). Evaluation of applications is underway and will continue until positions are filled. Faculty Defined Tenure-Track faculty (regardless of rank) - Persons with the titles of assistant professor, associate professor, or professor who are eligible for tenure or who have obtained tenure. These faculty will have earned a doctorate (PhD), Doctor of Medicine (MD) or other terminal degree in the relevant field of study. Their primary career focus centers on research, service, and teaching. Tenure-track faculty with MD or MD/PhD degrees may also be involved in clinical care.​ The Ohio State University College of Medicine The Ohio State University College of Medicine, with more than 5,000 learners, is the only academic medical center in central Ohio. Ranked as the 28th Best Medical School – Research, 40th Best Medical School – Primary Care, and 13th Most Diverse Medical School by U.S. News & World Report, it is known nationwide for curricular innovation, pioneering research, and outstanding patient care at The Ohio State University Wexner Medical Center. With more than 2,600 faculty members, the college comprises 20 clinical departments, eight basic science departments and a School of Health and Rehabilitation Sciences. Additional Information: The Wexner Medical Center The Ohio State University Wexner Medical Center consists of The Ohio State University Health System, the College of Medicine, the Health Sciences Library and the Faculty Group Practice. The Ohio State Wexner Medical Center is committed to providing world-class care. At the Ohio State Wexner Medical Center, we're proud to be celebrating our 31st consecutive year ranked in the U.S. News & World Report Best Hospitals list. This year, the Ohio State Wexner Medical Center has 10 nationally ranked specialties out of 15 and two selected as high performing. U.S. News & World Report consistently ranks the Ohio State Wexner Medical Center as the top hospital in Columbus. The Wexner Medical Center is rated as high performing in 14 out of 20 common procedures and conditions, including abdominal aortic aneurysm repair, aortic valve surgery, heart attack, heart bypass surgery and heart failure. The University Ohio State is a top-20 public university, and its Ohio State Wexner Medical Center is one of America’s leading academic health centers and recently ranked No. 4 on Forbes’ list of best U.S. employers for diversity. Eligible Ohio State employees receive comprehensive benefits packages, including medical, dental and vision insurance, tuition assistance for employees and their dependents, and state or alternative retirement options with competitive employer contributions. The Ohio State University’s Shared Values include Excellence and Impact, Diversity and Innovation, Inclusion and Equity, Care and Compassion, and Integrity and Respect. Our university community welcomes differences, encourages open-minded exploration and courageous thinking, and upholds freedom of expression. Ohio State is a dynamic community where opportunity thrives, and individuals transform themselves and their world. Positions are available in countless fields and specialties. Become a Buckeye and contribute to an incredible legacy that serves to guide our future and shape a better tomorrow. The Ohio State University is committed to enhancing academic excellence. Recruiting, supporting, and retaining faculty of the highest caliber is a core component of this commitment. The Office of Academic Affairs (OAA) has established Dual Careers and Faculty Relocation (DCFR) to focus on supporting new and prospective faculty and their loved ones. Service offerings include dual careers partner consultations, identifying potential employers and/or employment opportunities, consultation and resources related to relocation, as well as identifying opportunities to engage on campus and in the surrounding community. While employment opportunities are not guaranteed, resources and consultation are provided to support the partners of new and prospective faculty as they are considering or transitioning to The Ohio State University. In addition to being responsive to dual-career opportunities, we strongly promote work-life balance to support our community members through a suite of institutionalized policies. Ohio State is an NSF ADVANCE institution and a member of the Ohio/Western Pennsylvania/West Virginia Higher Education Recruitment Consortium (HERC). Columbus, Ohio Located in Ohio’s capital city, Ohio State’s Columbus campus is near the center of a rapidly growing and diverse metropolitan area with a population of over 1.5 million. The area offers a wide range of affordable housing, many cultural and recreational opportunities, excellent schools, and a strong economy based on government as well as service, transportation, and technology industries. Additional information about the Columbus area is available here. In addition to its Columbus campus, Ohio State has four regional campuses including Ohio State Lima, Ohio State Mansfield, Ohio State Marion, and Ohio State Newark, in addition to Ohio State ATI in Wooster. All qualified applicants will receive consideration for employment without regard to age, ancestry, color, disability, ethnicity, gender, gender identity or expression, genetic information, HIV/AIDS status, military status, national origin, pregnancy, race, religion, sex, sexual orientation, or veteran status. Final candidates are subject to successful completion of a background check.

Bioinformatics Analyst I, Research Institute at Nationwide Children’s Hospital, Columbus, OH. Assist in all aspects of laboratory specific next-generation sequencing analysis including data generation, analysis, interpretation, and publication. Maintain, run, and troubleshoot genomic pipelines for next generation sequencing assays in clinical, translational, and research settings. Analyze a variety of research and clinical genomic data. Analysis and management of sequence data and submission of data to NCBI databases. Preparation of graphs and figures for presentations and publications. Development, validation, and deployment of in-house bioinformatics tools. Evaluation and integration of community-developed bioinformatics tools. Application development and maintenance of laboratory samples and animal databases. Ensuring compliance with data security and privacy regulations. Min. requirements include: Bachelor’s degree in Computer Information Science, Bioinformatics, Electronics Engineering, Electrical Engineering, or Software Engineering plus 2 years of experience including 2 years of experience with genomics and bioinformatics software development and data analysis along with Wet Lab experience; 2 years of experience with Linux/ R Script/Python/Web application programming languages; and 2 years of experience in next-generation sequencing methods and advanced bioinformatics analysis. Send resume to allison.holbrook@nationwidechildrens.org.

Look for more than answers. As a Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing. This position is in our Bioinformatics Solutions Engineering group, part of the Research and Development organization, in Molecular Genomics & Oncology unit. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment primarily using short and long-read sequencing as the basis of evidence. The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics Solutions Engineering group is a cross-functional unit focusing on end-to-end design, develop, document, validation and launching of new high quality diagnostic tests and services for the benefit our patients. This person can work 100% remote and must be located in the US. • Develop, validate, and implement new software applications, databases, processes, and interfaces relating to next-generation sequencing (NGS) data analysis, advanced diagnostic testing development and validation, data quality review, and clinical reporting. • Serve as SME on specific systems/workflows supporting advanced development and high-tier production support. • Participate in resolution of support requests. Regularly report progress and prepare data analyses for internal review • Prepare reports and other communications of technical activities related to business objectives such as product/process development and improvement. • Activities may be focused individual projects or, more usually, assignments as a member of a project team, often working closely with other Software Developers, R&D bench scientists, Genetic Counselors, Operations Scientists, and other technical business partners. 3+ years of experience with a Bachelor's degree or 1+ year with a Master's degree and experience in an industrial or academic setting working with clinical and biological data or equivalent and underlying technologies including bioinformatic methods, database development, query/scripting/programming languages, cloud development, agile methodology, DevOps and other data analysis tools. Preferred Work Experience / Skills: • Bioinformatics tools such as Dragen, bwa, VEP, FastQC, MultiQC, samtools, bedtools • Experience with sequencing data analysis, bioinformatics, variant data analysis • Pipeline workflow management languages: Nextflow (preferred), Cromwell, CWL, etc. • Database: SQL (e.g., postgress, MySQL), understanding of NoSQL databases • Cloud Computing: AWS • Infrastructure management: Terraform, AWS CDK • Programming Languages: Advanced level with interpreted/scripting languages such as Python, javascript/typescript, R, etc. • Containerizing: Docker • Experience with designing and working with application programming interfaces (e.g. JSON based RESTful APIs) • Web Frameworks: Python Flask, React Native, Bootstrap • Reporting: Familiarity with R Markdown, Jupyter Notebook • Visualization: Experience with any of ggplot2/tidyverse, Plotly, matplot lib, Tableau, d3.js • Source Control: Git • CI/CD: Gitlab CI/CD, Github CI/CD • Understanding of environment management • Experience of working in clinical diagnostics setting (regulations, controlled processes, environment management) is a plus. Education: Bachelor’s Degree(Required) Master’s Degree Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets

Our client is revolutionizing forensic investigations by integrating advanced lab science, innovative software, and optimized processes. Their proprietary technology helps law enforcement agencies worldwide solve complex DNA cases, with more successful forensic genetic genealogy outcomes than any other method. As a Software Engineer (Bioinformatics), you will develop and optimize software for this leading forensic DNA analysis platform. Combining web development, system programming, and algorithm design, you’ll create high-performance tools that streamline DNA workflows and enhance forensic capabilities, collaborating with scientists, developers, and law enforcement to ensure accuracy and scalability. Responsibilities: • Develop Web Applications: Build user-friendly interfaces and secure back-end systems using Java, Python, and modern web technologies. • Automate and Integrate Workflows: Develop tools for evidence data management and automate DNA analysis workflows. • Optimize Scalability and Performance: Design scalable cloud-based systems and optimize applications for large data processing. • Build Algorithms: Develop algorithms to analyze DNA data and enhance forensic capabilities. • Collaborate: Work with scientists and law enforcement to integrate tools and improve systems. • Innovate and Improve: Continuously enhance data processing pipelines and optimize performance. Requirements: • Strong foundation in C++ or other low-level languages. • Experience with bioinformatics workflows, particularly metagenomic sequencing. • Ability to work at the intersection of biology and technology. • Self-starter with problem-solving and innovation skills. • Experience with scalable systems and automation frameworks. Preferred Qualifications: • Experience designing and delivering large-scale projects. • Proficiency in C++, Python, or Java, with performance optimization experience. • Experience working with cross-functional teams in dynamic environments. • Proficiency with bioinformatics tools like SAMtools and Next-Generation Sequencing (NGS).

The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As part of this groundbreaking national research consortium, you will help unravel the molecular mechanisms underlying the benefits of physical activity. Under the supervision of co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler, you will play a crucial role in shaping the future of personalized exercise science and public health. Dr. Euan Ashley's research interests focus on the application of genomics and other omics data to improve clinical care, with an emphasis on cardiovascular disease and personalized medicine. Dr. Matthew Wheeler's research centers on the integration of large-scale molecular and clinical data to understand the genetic basis of cardiovascular diseases and to develop novel therapeutic strategies. By joining our team, your proficiency in applying advanced statistical methodologies, such as multivariate analysis, machine learning, and Bayesian approaches, will be essential for uncovering novel insights and driving innovation in our research efforts. Your strong statistical background and expertise in analyzing large biological datasets. experience in handling diverse omics data will contribute significantly to our understanding of complex biological systems and the development of personalized medicine. You will also contribute to the analysis, execution, and development of pipelines and bioinformatic tools for various omics data generated within MoTrPAC. This innovative project integrates large volumes of clinical and densely time-sampled molecular data, pushing the boundaries of biomedical data analytics. Our portal (https://motrpac-data.org) will push the boundaries of biomedical data analytics to provide insight into the basic and translational science of exercise. Working alongside our multidisciplinary team, you will be at the forefront of understanding how physical activity preserves and improves health, ultimately making a lasting impact on human well-being. To find out more about our studies, you can check our recent publication in Nature and other journals about the endurance exercise training in rats (visit https://motrpac-data.org/publications). To be considered, please submit a resume and a cover letter that describes your interest in this position, and what skills you would bring to this role. Responsibilities: As a Bioinformatics Engineer II, you will contribute to the analysis, execution, and development of pipelines and bioinformatic tools for various omics data generated within the MoTrPAC project. Your primary responsibilities will include: • Collaborate with a multidisciplinary team of scientists and engineers to analyze and interpret large-scale multi-omics data. • Develop and implement innovative bioinformatics tools and methods to further our understanding of molecular mechanisms underlying the effects of physical activity. • Prepare reports and presentations to communicate findings with the team and the larger scientific community. Qualifications: To be successful in this role, you should possess an advanced degree (Ph.D. or M.S.) in a field such as statistics, biomedical informatics, engineering, or computer science along with a minimum of two years of relevant professional experience. They should have expertise in the analysis, execution, and development of pipelines and bioinformatic tools for various omics data and be proficient in programming languages like R and/or Python, as well as Linux bash scripting. Familiarity with pipeline languages, container systems, code management platforms, and systems biology approaches for data integration is also essential. Candidates should demonstrate experience in large-scale data analysis (with emphasis on genomics, transcriptomics, epigenomics datasets), biological domain knowledge, bioinformatics, and software development team-based projects. Additionally, they should be willing to work in a highly collaborative environment, be able to adapt quickly, possess strong communication skills, and have the capacity to work independently. Due to extensive teamwork needed, this is a mostly on-site position. Why Join Us? • Work on a highly exciting and innovative multi-omics project with the potential to revolutionize our understanding of physical activity and health. • Be part of a world-class research team at Stanford University, led by Dr. Euan Ashley, a pioneer in personalized medicine. • Contribute to groundbreaking research with a significant impact on public health and the prevention of diseases. • Enjoy a collaborative and stimulating work environment at one of the top universities in the world. If you are a passionate and dedicated professional with the required qualifications and a strong interest in advancing scientific research, we encourage you to apply for this exciting opportunity. Join us in unraveling the mysteries of physical activity and making a lasting impact on human health. A complete application will include a cover letter. Duties include: • Prioritize and extract data from a variety of sources such as notes, survey results, medical reports, and laboratory data, and maintain its accuracy and completeness. • Determine additional data collection and reporting requirements. • Design and customize reports based upon data in the database. Oversee and monitor regulatory compliance for utilization of the data. • Use system reports and analyses to identify potentially problematic data, make corrections, and eliminate root cause for data problems or justify solutions to be implemented by others. • Create complex charts and databases, perform statistical analyses, and develop graphs and tables for publication and presentation. • Serve as a resource for non-routine inquiries such as requests for statistics or surveys. • Test prototype software and participate in approval and release process for new software. • Provide documentation based on audit and reporting criteria to investigators and research staff. DESIRED QUALIFICATIONS: • Graduate degree (MS, PhD) emphasizing statistics, biomedical informatics, engineering, and computer science are preferred. • Domain expertise in analysis and running pipelines and bioinformatic tools for at least one of the following ‘omes: genomics, transcriptomics, epigenomics (ATAC-seq, RRBS). Knowledge of metabolomics and proteomics analysis is a plus. • Experience in systems biology approaches for data integration. • Proficiency in Python and/or R and Linux bash scripting. • Experience and knowledge of code management such as GitHub. • Experience with pipeline languages such as WDL, snakemake, and/or nextflow. • Proven track record of working with data and infrastructure in an HPC (High-Performance Computing) cluster or cloud computing environments like Google Cloud Platform, AWS, or Azure. • Experience with container systems such as setting up virtual machines and docker instances. • Experience in developing tools and statistical methods for large-scale data analysis is a plus. • Biological domain knowledge (exercise science is a plus). EDUCATION & EXPERIENCE (REQUIRED): • Bachelor's degree and three years of relevant experience or combination of education and relevant experience. • Experience in a quantitative discipline such as economics, finance, statistics or engineering. KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED): • Substantial experience with MS Office and analytical programs. • Excellent writing and analytical skills. • Ability to prioritize workload. CERTIFICATIONS & LICENSES: • None PHYSICAL REQUIREMENTS*: • Sitting in place at computer for long periods of time with extensive keyboarding/dexterity. • Occasionally use a telephone. • Rarely writing by hand. WORKING CONDITIONS: • Some work may be performed in a laboratory or field setting. WORKING STANDARDS: • Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations. • Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned. • Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University’s Administrative Guide, http://adminguide.stanford.edu/. The expected pay range for this position is $104,358 to $128,038 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location and external market pay for comparable jobs. At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website (https://cardinalatwork.stanford.edu/benefits-rewards) provides detailed information on Stanford’s extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process. Why Stanford is for You Imagine a world without search engines or social platforms. Consider lives saved through first-ever organ transplants and research to cure illnesses. Stanford University has revolutionized the way we live and enrich the world. Supporting this mission is our diverse and dedicated 17,000 staff. We seek talent driven to impact the future of our legacy. Our culture and unique perks empower you with: • Freedom to grow. We offer career development programs, tuition reimbursement, or audit a course. Join a TedTalk, film screening, or listen to a renowned author or global leader speak. • A caring culture. We provide superb retirement plans, generous time-off, and family care resources. • A healthier you. Climb our rock wall or choose from hundreds of health or fitness classes at our world-class exercise facilities. We also provide excellent health care benefits. • Discovery and fun. Stroll through historic sculptures, trails, and museums. • Enviable resources. Enjoy free commuter programs, ridesharing incentives, discounts and more. Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources by submitting a contact form. Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

Look for more than answers. As a Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing. This position is in our Bioinformatics Solutions Engineering group, part of the Research and Development organization, in Molecular Genomics & Oncology unit. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment primarily using short and long-read sequencing as the basis of evidence. The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics Solutions Engineering group is a cross-functional unit focusing on end-to-end design, develop, document, validation and launching of new high quality diagnostic tests and services for the benefit our patients. This person can work 100% remote and must be located in the US. • Develop, validate, and implement new software applications, databases, processes, and interfaces relating to next-generation sequencing (NGS) data analysis, advanced diagnostic testing development and validation, data quality review, and clinical reporting. • Serve as SME on specific systems/workflows supporting advanced development and high-tier production support. • Participate in resolution of support requests. Regularly report progress and prepare data analyses for internal review • Prepare reports and other communications of technical activities related to business objectives such as product/process development and improvement. • Activities may be focused individual projects or, more usually, assignments as a member of a project team, often working closely with other Software Developers, R&D bench scientists, Genetic Counselors, Operations Scientists, and other technical business partners. 3+ years of experience with a Bachelor's degree or 1+ year with a Master's degree and experience in an industrial or academic setting working with clinical and biological data or equivalent and underlying technologies including bioinformatic methods, database development, query/scripting/programming languages, cloud development, agile methodology, DevOps and other data analysis tools. Preferred Work Experience / Skills: • Bioinformatics tools such as Dragen, bwa, VEP, FastQC, MultiQC, samtools, bedtools • Experience with sequencing data analysis, bioinformatics, variant data analysis • Pipeline workflow management languages: Nextflow (preferred), Cromwell, CWL, etc. • Database: SQL (e.g., postgress, MySQL), understanding of NoSQL databases • Cloud Computing: AWS • Infrastructure management: Terraform, AWS CDK • Programming Languages: Advanced level with interpreted/scripting languages such as Python, javascript/typescript, R, etc. • Containerizing: Docker • Experience with designing and working with application programming interfaces (e.g. JSON based RESTful APIs) • Web Frameworks: Python Flask, React Native, Bootstrap • Reporting: Familiarity with R Markdown, Jupyter Notebook • Visualization: Experience with any of ggplot2/tidyverse, Plotly, matplot lib, Tableau, d3.js • Source Control: Git • CI/CD: Gitlab CI/CD, Github CI/CD • Understanding of environment management • Experience of working in clinical diagnostics setting (regulations, controlled processes, environment management) is a plus. Education: Bachelor’s Degree(Required) Master’s Degree Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets

1.0 FTE Full time Day - 08 Hour R2546716 Hybrid 107520006 Path Lab Molecular Path Hillview Allied Health PALO ALTO, 3375 Hillview Ave, California If you're ready to be part of our legacy of hope and innovation, we encourage you to take the first step and explore our current job openings. Your best is waiting to be discovered. Day - 08 Hour (United States of America) This is a Stanford Health Care job. A Brief Overview The Bioinformatic Staff Scientist will be responsible for developing and maintaining Next Generation Sequencing data analysis workflows for use in a molecular genetic testing setting. This includes algorithms development as well as pipeline design. They will participate in development and implementation of bioinformatics tools for test development and validation, joining a team that develops leading-edge genomic assays and analysis tools that directly impact patient care. Locations Stanford Health Care What you will do • Develop, document and deploy novel clinical sequencing analysis approaches meeting CLIA and CAP guidelines for clinical NGS analysis • Develop, document and deploy in-house web-applications and databases for clinical genomics data storage, analysis and visualization • Enhance, maintain, and support established sequencing pipelines and workflows meeting CLIA and CAP guidelines for clinical NGS analysis • Develop, implement and maintain tools and workflows for system administration and data management • Collaborate with technical and medical teams in specifying requirements for tools to enhance workflow efficiency, turnaround times and robustness • Summarize results in written or oral reports for computational biologists, molecular biologists, clinicians, and internal researchers • Contribute to publishing of relevant findings in scientific journals Education Qualifications • Graduate Degree (Ph.D./M.S,) in bioinformatics, genetics and genomics, computer science or other work-related field/discipline from an accredited college or university Experience Qualifications • Ph.D. with no experience, or M.S. plus 3 years of experience developing pipelines and algorithms for computational biology, genomics, and/or clinical diagnostics preferred Required Knowledge, Skills and Abilities • Knowledge of algorithmic techniques common to bioinformatics (e.g., dynamic programming and graph algorithms), machine learning and statistical analysis methods (e.g., Bayesian inference, Hidden Markov Models, Principal Component Analysis) • Proficient in Python, competent in C++, Java, SQL, and R • Demonstrated experience in software development for bioinformatics applications • Experience with SQL and relational database design • Comfortable with Bash scripting and working in UNIX/Linux environments • Ability to produce readable, maintainable and well documented code • Experience with version control and source code management systems (e.g. Git) • Detail oriented mindset for working on applications that directly impact patient care • Ability to collaborate and communicate with other bioinformaticians, researchers and medical staff • Excellent problem-solving skills for common problems in bioinformatics • Familiarity with system administration and IT operations • Strong team-oriented work ethic with open, honest, and considerate communication skills Preferred Knowledge, Skills and Abilities • Molecular Pathology • Expertise in cancer genomics and NGS technologies including somatic variant calling • Familiarity with standard genomics/bioinformatics tools (e.g. Samtools, BWA, IGV) • Good understanding of human molecular genetics • Experience analyzing genomic sequencing data from Illumina platforms • Experience developing web-applications with Python and Django • Clinical Genomics • Cloud-based computation environment • Familiarity with workflow language, such as WDL • Familiarity with NGS and best practices for germline sequencing data analysis • Expertise in bioinformatics tools for alignment, variation calling and annotation such as DRAGEN, BLAST, BWA, GATK, samtools, bedtools, vcftools, IGV, UCSC genome browser, etc • Experience in public annotation databases such as ClinGen, ClinVar, HGMD, HGNC, OMIM, gnomAD, CADD, UniProt, RefSeq, and DGV Licenses and Certifications • None . These principles apply to ALL employees: SHC Commitment to Providing an Exceptional Patient & Family Experience Stanford Health Care sets a high standard for delivering value and an exceptional experience for our patients and families. Candidates for employment and existing employees must adopt and execute C-I-CARE standards for all of patients, families and towards each other. C-I-CARE is the foundation of Stanford’s patient-experience and represents a framework for patient-centered interactions. Simply put, we do what it takes to enable and empower patients and families to focus on health, healing and recovery. You will do this by executing against our three experience pillars, from the patient and family’s perspective: • Know Me: Anticipate my needs and status to deliver effective care • Show Me the Way: Guide and prompt my actions to arrive at better outcomes and better health • Coordinate for Me: Own the complexity of my care through coordination Equal Opportunity Employer Stanford Health Care (SHC) strongly values diversity and is committed to equal opportunity and non-discrimination in all of its policies and practices, including the area of employment. Accordingly, SHC does not discriminate against any person on the basis of race, color, sex, sexual orientation or gender identity and/or expression, religion, age, national or ethnic origin, political beliefs, marital status, medical condition, genetic information, veteran status, or disability, or the perception of any of the above. People of all genders, members of all racial and ethnic groups, people with disabilities, and veterans are encouraged to apply. Qualified applicants with criminal convictions will be considered after an individualized assessment of the conviction and the job requirements. Base Pay Scale: Generally starting at $51.15 - $67.78 per hour The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to, internal equity, experience, education, specialty and training. This pay scale is not a promise of a particular wage.