Bioinformatics Jobs

Organization Overview Our Vertebrate Genome Laboratory conducts research and services for individual and large vertebrate genome projects such as the Vertebrate Genomes Project (VGP/G10K) that aims to sequence high-quality genomes for all 66,000 vertebrate species on the planet. https://vertebrategenomesproject.org/. Overview We seek a highly motivated individual with a strong background in Computer Science and Genomics to join the Bioinformatics team of the Vertebrate Genome Laboratory (www.vertebrategenomelab.org) at the Rockefeller University. This person will generate reference genomes of eukaryotic species as part of the Vertebrate Genomes Project (VGP, www.vertebrategenomesproject.org) and the Earth Biogenome Project (EBP, https://www.earthbiogenome.org/). In particular, the individual is expected to help achieve the following goals: • Work closely with the VGL data production and bioinformatics teams, and the broader international scientific community of the VGP, to actively generate draft high-quality genomes. • Help make the current pipeline, which is already heavily streamlined, fully automated, such that the sequencing data is automatically processed into draft assemblies along with QC, ready for manual curation. • Consistently improve the pipeline for genome assembly quality and efficiency, based on feedback from genome curators, incorporating novel data types, and adding or help in designing novel tools. Our current workflow involves: 1) in-house generation of a variety of long- (PacBio, Nanopore) and short- (Hi-C, Element, Illumina) read data; 2) in-house generation of reference-grade draft genome assemblies; 3) manual curation of the draft assemblies; 4) submission of the final, curated assemblies to the public archives. The individual will be integrated in step 2, and will be responsible to run, maintain, further develop, and improve the VGL genome assembly pipeline currently implemented in Galaxy (Lariviere et al. 2024 Nature Biotechnology DOI: 10.1038/s41587-023-02100-3). Responsibilities Responsibilities include: • Genome assembly • Genome assembly pipeline maintenance Qualifications The ideal candidate will have a sound knowledge of genomics, ideally with insights into genome assembly, genome curation and genome analysis. Required: • Master's degree required, Ph.D. preferred • Educational emphasis in computer science or computational biology • Strong programming skills, includin knowledge of computational data-analysis workflows (e.g. CWL) • Familiarity with Unix and HPC environments • The ability to work both independently and as part of a team Preferred: • Previous experience with Galaxy workflows is a plus • The ability to organize, prioritize and plan a diverse range of work to meet deadlines • An investigative and solution-orient mindset • Good communication skills • Skilled in working effectively within large national and international scientific consortia The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above. The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Compensation Range: Min USD $62,400.00/Yr. Compensation Range: Max USD $80,000.00/Yr.

Pay Range: $115,000 - $135,000 / year Salary offers are based on a wide range of factors including relevant skills, training, experience, education, and, where applicable, certifications obtained. Market and organizational factors are also considered. Successful candidates may be eligible to receive annual performance bonus compensation. Benefits Information: We are proud to offer best-in-class benefits and programs to support employees and their families in living healthy, happy lives. Our pay and benefit plans have been designed to promote employee health in all respects – physical, financial, and developmental. Depending on whether it is a part-time or full-time position, some of the benefits offered may include:  Medical/Prescription Drugs  Dental  Vision  Flexible Spending Accounts (FSAs)  Supplemental Health Plans  401(k) Plan – Company match dollar-for-dollar up to 5%  Employee Stock Purchase Plan (ESPP)  Supplemental Life Insurance  Dependent Life Insurance  Short- and Long-Term Disability buy-up  Blueprint for Wellness  Emotional Well-Being Resources  Educational Assistance  Paid time off / Health Time  Variable Compensation Plans  Sales Incentive Plans Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people. The Bioinformatics Engineer will maintain and support current systems in a regulated, clinical environment with patient care as our top priority. This professional will support our San Juan Capistrano, CA and Chantilly, VA labs. 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. QUALIFICATIONS Required Work Experience: 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. At least 1 year of experience working in a life sciences environment. Professional software development or technical engineering experience Preferred Work Experience: Bioinformatics tools such as BWA, SamTools, GATK, Dragen. Skills: Professional software development in a variet of languages including Python, Perl, R, SQL Education: Bachelor’s Degree(Required) Master’s Degree Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets

About the Research Investigating and onboarding novel organisms and engineering novel properties into chassis biosystems requires management and analysis of bioinformation. The successful candidate will work across a number of teams to provide bioinformatic support to genetic, proteomic, biochemical, pathway, and systems biology research projects. Purpose: Microbial bioinformatics to include data analysis, predictive and descriptive modeling of genomic, metagenomictranscriptomic, proteomic, and metabolic datasets, relationships and phenomena. • Experience/Skills:* • Advanced degree (PhD or Masters with equivalent experience) in biological or chemical sciences/engineering, with focus on combined theoretical/experimental approaches to understand and engineer microbial consortia. • Must have experience with analysis of multi-omics data driving toward development of whole-system models of microbial consortia. • Experience with microbial engineering, genome-scale metabolic modeling, and experimental design are preferred. • Must have expertise in R and/or Python as well as Linux. • Must be able to obtain a secret clearance. • Able, interested, and motivated to work in a multidisciplinary environment. • Able to work on multiple sub-projects simultaneously. • Excellent English skills in speech and writing. • Overarching Position Description:* The Biotechnology Branch of the US Army Research Laboratory seeks a contract Bioinformatician to join a multidisciplinary team of microbiologists, biological engineers, computational biologists, chemists, and materials scientists performing research on microbial consortia for materials conversion. The contract Bioinformatician will be responsible for processing and analyzing large-volume sequencing, transcriptomic and proteomic data, and will contribute to the design of the –omics experiments that generate these data. In addition, this team member will build, maintain, and refine genome-scale metabolic models describing individual organisms as well as multi-organism consortia, in order to help guide the team's efforts to understand key metabolic features and relationships of natural and designed material-converting microbial consortia. Interacting and developing technical collaborations with external leaders in the field and maintaining a keen awareness of the current literature and developments in the field are also important components of this position. • Specific Tasks and Duties:* Assist with the design of genomic and metagenomic sequencing experiments. • Design and implement novel state-of-the-art analysis pipelines and methods to distill large sequencing and –omics datasets into the most significant and actionable results aligned with the experimental objectives. • Construct and analyze results from single- and multi-organism genome-scale metabolic models to predict or constrain the space of expected products and metabolic relationships between organisms in consortia. • Communicate results in presentations, written reports, open journal publications, and patent applications. • Maintain current awareness of the relevant technical landscape by reading literature and participating in technical conferences or symposia. • Identify potential external collaborators. Develop strategic and mutually beneficial collaborative relationships to advance Army capabilities and accelerate accomplishment of project goals. ARL Advisor: Valerie E. Martindale ARL Advisor Email: valerie.e.martindale.civ@army.mil About HRED The Human Research and Engineering Directorate (HRED) is ARL’s principal center for research and development directed toward optimizing Soldier performance and human-autonomy teaming. Research within HRED focuses on how to improve Soldier performance in a dynamic and changing battlefield. As technology and autonomous systems become an increasingly integral part of Soldier teams, it is critical to determine how these systems can work with and be adapted to the Soldier and their capabilities. Autonomous systems must be able to be integrated into Soldier teams and move from tools to teammates. Critical to this is an understanding of how humans and human teams perform and change in dynamic environments and situations. HRED leverages human-robot interaction, human-informed machine learning, human cognition and adaptive teaming to improve human-autonomy teaming for future Army teams. About ARL-RAP The Army Research Laboratory Research Associateship Program (ARL-RAP) is designed to significantly increase the involvement of creative and highly trained scientists and engineers from academia and industry in scientific and technical areas of interest and relevance to the Army. Scientists and Engineers at the CCDC Army Research Laboratory (ARL) help shape and execute the Army's program for meeting the challenge of developing technologies that will support Army forces in meeting future operational needs by pursuing scientific research and technological developments in diverse fields such as: applied mathematics, atmospheric characterization, simulation and human modeling, digital/optical signal processing, nanotechnology, material science and technology, multifunctional technology, combustion processes, propulsion and flight physics, communication and networking, and computational and information sciences. A complete application includes: • Curriculum Vitae or Resume • Three References Forms • An email with a link to the reference form will be available in Zintellect to the applicant upon completion of the on-line application. Please send this email to persons you have selected to complete a reference. • References should be from persons familiar with your educational and professional qualifications (include your thesis or dissertation advisor, if applicable) • Transcripts • Transcript verifying receipt of degree must be submitted with the application. Student/unofficial copy is acceptable If selected by an advisor the participant will also be required to write a research proposal to submit to the ARL-RAP review panel for : • Research topic should relate to a specific opportunity at ARL (see Research Areas) • The objective of the research topic should be clear and have a defined outcome • Explain the direction you plan to pursue • Include expected period for completing the study • Include a brief background such as preparation and motivation for the research • References of published efforts may be used to improve the proposal A link to upload the proposal will be provided to the applicant once the advisor has made their selection. Questions about this opportunity? Please email ARLFellowship@orau.org.

Payroll Title: BIOINFORMATICS PROGR 1 Department: MEDICINE/ Endocrinology & Meta Hiring Pay Scale $33.29 - $35.22 / Hour Worksite: Campus Appointment Type: Limited Appointment Appointment Percent: 100% Union: Uncovered Total Openings: 1 Work Schedule: Days, 12 Hour Shifts, Monday-Friday #133146 Bioinformatics Programmer Filing Deadline: Mon 12/2/2024 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply. This position is a limited position with the possibility of extension/career conversion. UCSD Layoff from Career Appointment: Apply by 11/18/24. for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/2/24. Eligible Special Selection clients should contact their Disability Counselor for assistance. Depending on experience of the selected candidate, this position will be hired at the BIOINFORMATICS PROGR 1 or BIOINFORMATICS PROGR 2 level. This position will work a hybrid schedule which includes a combination of working both onsite at La Jolla and remote. DESCRIPTION The Bioinformatics Programmer will work under the direct supervision of the PI with a multi-disciplinary group to assist in the design, develop, debug, and utilize new state-of-the-art artificial intelligence methods that address areas of clinical need. The lab’s primary bioinformatics focus is on the heterogeneity of patients with diabetes and supporting clinician decision-making. Assists with generating well-documented code and clear project reports. Provides solutions that implement appropriate software security functionality. Under direct supervision, works with end-users to ensure that solutions meet requirements for algorithm usage and interpretation. Assists in managing code-hosting on online repositories and necessary material for end user utility. Collaborates with colleagues, managers, and department researchers to understand complex problems. Under direct supervision, applies professional bioinformatics concepts and computational procedures to complete small projects or portions of projects. Works on assignments of limited scope and complexity. Follows standard programming procedures to analyze situations and data from which answers can be readily obtained. MINIMUM QUALIFICATIONS • Four years of related experience, education/training, OR a Bachelor’s degree in related area. • Basic knowledge of bioinformatics methods and data structures. Experience developing and debugging machine learning algorithms. • Basic knowledge of applications programming and web development. Ability to write and curate code for analyses of patient data. • Basic knowledge of databases. • Basic project management skills. • Basic knowledge of modern biology and applicable field of research. Theoretical knowledge of Biology, Molecular Biology, Structural Biology, and Biochemistry or other related field generally acquired through a Bachelor’s Degree; or an equivalent combination of education and experience. • Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization. Good interpersonal communication skills including tact, diplomacy, and flexibility with students, staff, faculty, and visitors of various cultures and backgrounds. • Ability to communicate technical information in a clear and concise manner. Ability to follow verbal and written instructions and procedures. • Self motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills. Ability to maintain confidentiality of matters related to work. • Basic knowledge of application and data security concepts. • Experience in Python coding and management of Github repositories. • Enthusiasm for learning and a genuine interest in scientific research. Willingness and ability to learn new skills, research methods, and scientific principles. • Ability to record scientific data in a well-organized laboratory notebook. Good organizational skills including ability to keep clear and accurate records. • Knowledge of hazard communication and injury and illness Prevention Program. Knowledge of laboratory safety precautions including appropriate clothing and shoes, safe handling of chemical, use of protective items such as gloves and goggles, etc. • Willingness and demonstrated ability to embrace and consistently uphold the principles of community for a collaborative work environment. SPECIAL CONDITIONS • Employment is subject to a criminal background check. Pay Transparency Act Annual Full Pay Range: $69,500 - $123,500 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $33.29 - $59.15 Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable). Apply Now If employed by the University of California, you will be required to comply with our Policy on Vaccination Programs, which may be amended or revised from time to time. Federal, state, or local public health directives may impose additional requirements. If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable. UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community. UC San Diego is an Equal Opportunity/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, age or protected veteran status. For the University of California’s Affirmative Action Policy please visit: https://policy.ucop.edu/doc/4010393/PPSM-20 For the University of California’s Anti-Discrimination Policy, please visit: https://policy.ucop.edu/doc/1001004/Anti-Discrimination UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information. UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening. Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts a conditional offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; received notice of any allegations or are currently the subject of any administrative or disciplinary proceedings involving misconduct; have left a position after receiving notice of allegations or while under investigation in an administrative or disciplinary proceeding involving misconduct; or have filed an appeal of a finding of misconduct with a previous employer. a. "Misconduct" means any violation of the policies or laws governing conduct at the applicant's previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, discrimination, dishonesty, or unethical conduct, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct: • UC Sexual Violence and Sexual Harassment Policy • UC Anti-Discrimination Policy • Abusive Conduct in the Workplace

SHIFT: Day (United States of America) Seeking Breakthrough Makers Children’s Hospital of Philadelphia (CHOP) offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation. At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care—and your career. CHOP’s Commitment to Diversity, Equity, and Inclusion CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children. We strongly encourage all candidates of diverse backgrounds and lived experiences to apply. A Brief Overview The Genomic Diagnostic Laboratory (GDL) of the Children’s Hospital of Philadelphia is seeking a highly motivated Supervisory Bioinformatics Scientist to manage our Bioinformatics team consisting of Bioinformatics Scientists, Bioinformatics Engineers, and RIA Programmers. This is an exciting opportunity to join our laboratory where we use a wide variety of molecular and cytogenetic test methodologies to provide accurate, timely diagnostic testing that has a direct impact on patient care. The team also supports cutting edge R&D efforts including new clinical test development and clinical research. The Supervisory Bioinformatics Scientist is a key member of the leadership team in the GDL, collaborating with other lab leaders including the Director of Bioinformatics, clinical directors, managers, and supervisors). The successful candidate will have a strong human genetics, bioinformatics, and management background that will be applied to training, clinical work, R&D, and troubleshooting. Good documentation practices as well as strong organizational and communication skills are essential. Job responsibilities include scheduling work duties, providing semi-annual performance reviews, assuring that all accreditation requirements are in full compliance, and participating in quality improvement initiatives. We seek a leader who has an interest in strategic planning to develop and improve our bioinformatics pipelines and other tools to support our expanding test menu. This position can be worked fully on-site at our campus in Philadelphia, PA, or as a hybrid role with an expectation of on-site presence at least once a week, and additional on-site presence possible based on the needs of the lab. In addition to many of the subject matter expert responsibilities of the Principal Bioinformatics Scientist, the Supervisory Bioinformatics Scientist will also: • Build and supervise a team responsible for the architecture, development, testing and production rollout of integrated biomedical data resources and applications. • Balance competing priorities and resource allocation across a portfolio of matrixed projects and collaborations. • Promote common standards and best-practice use of multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research. • Serves as the data integration team lead on larger complex projects that include informatics, clinical and translational researchers. • Propose staffing plans for multi-year strategic data resource initiatives. • Train, mentor, and hold junior staff accountable to the results of modern technology development methodologies such as code test coverage, continuous integration, monitoring. • Educate staff, students, and trainees (fellows, post-docs) on appropriate staffing and expertise levels for application of data integration methods in the clinical and translational research environment. What you will do • A Supervisory Bioinformatics Scientist functions as both subject matter expert and team manager. The responsibilities echo those of a Principal Bioinformatics Scientist, but include direct supervision of team members and projects. A Supervisory Bioinformatics Scientist will: • Directly lead and mentor junior staff in a direct supervisory capacity. • Guide and develop the skills and expertise of junior staff • Build project budgets by estimating time and effort costs • Hold data integration and technical teams accountable to high-level project goals and timelines, mapping detailed project plans into these timelines. • Recruit, hire, and retain a focused team of any of Bioinformatics Scientists, Bioinformatics Engineers, and Bioinformatics Programmers. • Provide bioinformatics academic and thought leadership for joint collaborations with CHOP PIs. Education Qualifications • Master's Degree Required • Doctorate Bioinformatics, Computational Biology, Computer Science, Information Science, Informatics, Biomedical Engineering, Biological Science or a related discipline Preferred Experience Qualifications • At least seven (7) years Experience in bioinformatics analysis, bioinformatics database development, bioinformatics database administration, bioinformatics data management, or related discipline, with progressively more complex projects in a biomedical science or healthcare environment. Required • At least one (1) year Small team supervisory experience. Required Skills and Abilities • Experience in bioinformatics and statistical data analysis on highly dimensional data types such as derived from genomics and observational clinical or human subjects research data. • Expert knowledge of relational database management systems such as PostgreSQL, MySQL, Oracle required. • Expert knowledge of bioinformatics applications and algorithms. • Expert knowledge of one or more of the following required: Python/Django, R, Perl, Scala, Ruby or other scripting languages. • Expert biological domain knowledge. • Must exhibit excellent oral, presentation, and written communication skills. • Experience with source code management, application development, and project lifecycle management. • Project management experience of complex matrix projects required. • Proficiency in the areas of bioinformatics analysis, statistical modeling, data integration, and bioinformatics thought leadership in the larger biomedical community. To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine. Learn more. Employees may request exemptions for valid religious and medical reasons. Start dates may be delayed until candidates are immunized or exemption requests are reviewed. EEO / VEVRAA Federal Contractor | Tobacco Statement

Research Computing at Boston Children’s supports basic, translational, and clinical research by providing researchers with access to digital tools and technologies. Our computing environment consists of high-performance computing clusters, virtual machines, PetaByte-scale high-performance storage and cloud platforms. We work with BCH scientists to develop solutions in support of cutting-edge research ranging from genomics to epigenetics and transcriptomics, proteomics and metabolomics. The Senior Bioinformatics Data Scientist will work with PhD-level bioinformatics scientists and researchers who have single-cell RNA-seq, single-cell ATAC-seq, spatial transcriptomics, bulk RNA-seq and ChIP-seq data to investigate mouse and human diseases as well as with other pediatric scientists at BCH. The primary responsibilities will be building pipelines for the analysis, integration and sharing of these data. You will analyze, integrate different types of next-generation sequencing data and interpret the results and will have the opportunity to publish high-profile papers with prominent authorship depending on the intellectual contribution. The ideal candidate should have enthusiasm for developing collaborative relationships and a desire to foster the use of bioinformatics data in research studies. Responsibilities include: • Providing computational support services to Boston Children's Hospital scientists and clinicians by applying a wide range of bioinformatics tools, methods and technologies. • With minimal supervision and direction, completing highly complex assignments in the required timeframe; consistently adhering to and Promoting standard operating procedures and best practices; maintaining and upgrading a wide range of Research Computing tools, methods, and technologies, migrating data, documenting changes, and adjusting internal processes; resolving highly complex problems associated with assignments and seeking supervisor assistance when needed. • Routinely leading, co-leading, or participating in complex bioinformatics projects with other members from the BCH research community; setting goals and objectives for projects and demonstrating achievement of those goals and objectives; • Training staff and researchers; effectively tailoring presentations; developing, implementing and maintaining knowledge management systems. To qualify you must have: • Minimum of 4-year Bachelor's degree in STEM. A minimum of one year of position-specific experience, which might potentially include experience acquired through MSc or Ph.D. studies. Preference for candidates with a Ph.D. in Bioinformatics, Computational Biology or related. • Extensive knowledge of the use of bioinformatics computations in high-performance computing environments, including open-source bioinformatics software and pipelines to support diverse bioinformatics analyses such as single-cell RNA-seq, bulk RNA-seq, ChIP-seq, methylation, etc. • Extensive knowledge of technologies used in support of biomedical research, such as programming languages (R and Python), databases (SQL), version control (Git), scientific workflow tools and high-performance computing clusters. • Ability to resolve a wide range of complex Research Computing assignments in support of biomedical research. Ability to routinely lead complex projects and coordinate project teams; readiness to seek advice and guidance when needed and to operate effectively in collaboration with scientists and clinicians; ability to follow, improve and create technical documentation and standard operating procedures. • Strong publication record. Ability to effectively convey messages through written communication that are tailored to target audience; meeting discussions and one-on-one verbal communications are clear and effective; ability to conduct effective meetings, to present in departmental and hospital forums, and to develop training instructions and manuals. #LI-Remote

About Ancestry: When you join Ancestry, you join a human-centered company where every person’s story is important. Ancestry®, the global leader in family history, empowers journeys of personal discovery to enrich lives. With our unparalleled collection of more than 40 billion records, over 3 million subscribers and over 23 million people in our growing DNA network, customers can discover their family story and gain a new level of understanding about their lives. Over the past 40 years, we’ve built trusted relationships with millions of people who have chosen us as the platform for discovering, preserving and sharing the most important information about themselves and their families. We are committed to our location flexible work approach, allowing you to choose to work in the nearest office, from your home, or a hybrid of both (subject to location restrictions and roles that are required to be in the office- see the full list of eligible US locations HERE). We will continue to hire and promote beyond the boundaries of our office locations, to enable broadened possibilities for employee diversity. Together, we work every day to foster a work environment that's inclusive as well as diverse, and where our people can be themselves. Every idea and perspective is valued so that our products and services reflect the global and diverse clients we serve. Ancestry encourages applications from minorities, women, the disabled, protected veterans and all other qualified applicants. Passionate about dedicating your work to enriching people’s lives? Join the curious. Introduction: We are seeking a highly motivated and experienced Senior Bioinformatics Engineer to join our team. Our ideal candidate will have significant experience in bioinformatics and a solid background in cloud computing. As a Senior Bioinformatics Engineer, you will be responsible for developing and maintaining bioinformatics pipelines, optimizing AWS infrastructure and automating workflows to support our scientific research projects. Responsibilities: • Collaborate with scientists to design, implement and maintain high quality bioinformatics workflows and tools for analyzing large datasets. • Automate existing science processes and collaborate with stakeholders to transition research and machine learning software into production environments. • Work closely with other Bioinformatics engineers to build and support a scalable cloud environment used by Ancestry’s DNA Science team. • ​​Manage and optimize AWS infrastructure to support scalable bioinformatics pipelines and advanced scientific computing workloads. • Champion coding and software best practices to improve software quality. • Drive the enhancement of legacy codebases to improve efficiency, performance and maintainability. Qualifications: • A Master’s degree in Bioinformatics, Computer Science, or related field with 3 years of relevant industry experience, or equivalent combination of education and experience • Significant expertise in developing and deploying bioinformatics pipelines for large datasets • Fluency in multiple programming languages: Python, Rust, C++, PySpark. • Strong experience with AWS infrastructure management, including AWS Batch and Parallel Cluster • Proven expertise in deploying pipelines in the cloud (e.g. AWS, GCP, Azure) • Significant experience with workflow orchestration tools like Nextflow, and Snakemake • Strong experience with Conda for managing packages and environments. • Solid experience with git and with developing and managing CI/CD pipelines. • Expertise working with infrastructure tools including Terraform, and AWS CloudFormation • Excellent communication and interpersonal skills • Ability to work independently and as part of a team Preferred Qualifications: • Comprehensive experience working with containerization technologies such as Docker and Kubernetes. • Deep expertise working with infrastructure tools like Terraform • Significant expertise with cloud computing and distributed computing architectures As a signatory of the ParityPledge in Support of Women and the ParityPledge in Support of People of Color, Ancestry values pay transparency and pay equity. We are pleased to share the base salary range for this position: $97,920 - $130,590 with eligibility for bonus, equity and comprehensive benefits including health, dental and vision. The actual salary will vary by geographic region and job experience. We will share detailed compensation data for a specific location during the recruiting process. Read more about our benefits HERE. Additional Information: Ancestry is an Equal Opportunity Employer that makes employment decisions without regard to race, color, religious creed, national origin, ancestry, sex, pregnancy, sexual orientation, gender, gender identity, gender expression, age, mental or physical disability, medical condition, military or veteran status, citizenship, marital status, genetic information, or any other characteristic protected by applicable law. In addition, Ancestry will provide reasonable accommodations for qualified individuals with disabilities. All job offers are contingent on a background check screen that complies with applicable law. For San Francisco office candidates, pursuant to the San Francisco Fair Chance Ordinance, Ancestry will consider for employment qualified applicants with arrest and conviction records. Ancestry is not accepting unsolicited assistance from search firms for this employment opportunity. All resumes submitted by search firms to any employee at Ancestry via-email, the Internet or in any form and/or method without a valid written search agreement in place for this position will be deemed the sole property of Ancestry. No fee will be paid in the event the candidate is hired by Ancestry as a result of the referral or through other means.

Organization Overview Our Vertebrate Genome Laboratory conducts research and services for individual and large vertebrate genome projects such as the Vertebrate Genomes Project (VGP/G10K) that aims to sequence high-quality genomes for all 66,000 vertebrate species on the planet. https://vertebrategenomesproject.org/. Overview We seek a highly motivated individual with a strong background in Computer Science and Genomics to join the Bioinformatics team of the Vertebrate Genome Laboratory (www.vertebrategenomelab.org) at the Rockefeller University. This person will generate reference genomes of eukaryotic species as part of the Vertebrate Genomes Project (VGP, www.vertebrategenomesproject.org) and the Earth Biogenome Project (EBP, https://www.earthbiogenome.org/). In particular, the individual is expected to help achieve the following goals: • Work closely with the VGL data production and bioinformatics teams, and the broader international scientific community of the VGP, to actively generate draft high-quality genomes. • Help make the current pipeline, which is already heavily streamlined, fully automated, such that the sequencing data is automatically processed into draft assemblies along with QC, ready for manual curation. • Consistently improve the pipeline for genome assembly quality and efficiency, based on feedback from genome curators, incorporating novel data types, and adding or help in designing novel tools. Our current workflow involves: 1) in-house generation of a variety of long- (PacBio, Nanopore) and short- (Hi-C, Element, Illumina) read data; 2) in-house generation of reference-grade draft genome assemblies; 3) manual curation of the draft assemblies; 4) submission of the final, curated assemblies to the public archives. The individual will be integrated in step 2, and will be responsible to run, maintain, further develop, and improve the VGL genome assembly pipeline currently implemented in Galaxy (Lariviere et al. 2024 Nature Biotechnology DOI: 10.1038/s41587-023-02100-3). Responsibilities Responsibilities include: • Genome assembly • Genome assembly pipeline maintenance Qualifications The ideal candidate will have a sound knowledge of genomics, ideally with insights into genome assembly, genome curation and genome analysis. Required: • Master's degree required, Ph.D. preferred • Educational emphasis in computer science or computational biology • Strong programming skills, includin knowledge of computational data-analysis workflows (e.g. CWL) • Familiarity with Unix and HPC environments • The ability to work both independently and as part of a team Preferred: • Previous experience with Galaxy workflows is a plus • The ability to organize, prioritize and plan a diverse range of work to meet deadlines • An investigative and solution-orient mindset • Good communication skills • Skilled in working effectively within large national and international scientific consortia The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above. The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Compensation Range: Min USD $62,400.00/Yr. Compensation Range: Max USD $80,000.00/Yr.

Job DescriptionJob Description Are you passionate about turning complex biological data into meaningful insights that drive breakthroughs in health, medicine, and biotechnology? Do you have the skills to analyze and interpret genomic data, build computational models, and develop algorithms that unravel the mysteries of life itself? If you're excited about using technology to transform the fields of genomics, drug discovery, and personalized medicine, our client has the perfect opportunity for you. We're looking for a Bioinformatics Specialist (aka The Data-Driven Biologist) to develop innovative computational tools and data-driven approaches that solve complex biological challenges. As a Bioinformatics Specialist at our client, you'll work closely with biologists, geneticists, and data scientists to analyze large-scale biological datasets, develop algorithms, and design software tools that aid in understanding molecular biology and genetics. Your work will drive research and development in areas like genomics, proteomics, and personalized medicine, pushing the boundaries of what's possible in biotechnology. Key Responsibilities: • Analyze and Interpret Biological Data: • Analyze large-scale genomic, proteomic, and transcriptomic datasets using bioinformatics tools and software. You'll extract meaningful insights from complex data to support research in genetics, drug development, and molecular biology. Develop Computational Models and Algorithms: • Design and implement algorithms that process and interpret biological data, including sequence analysis, gene expression profiling, and protein structure prediction. You'll create models that help predict biological functions and interactions. Collaborate with Cross-Disciplinary Teams: • Work closely with molecular biologists, geneticists, and data scientists to integrate bioinformatics tools into research projects. You'll translate biological questions into computational problems and provide solutions that drive scientific discoveries. Build and Maintain Bioinformatics Pipelines: • Develop automated data analysis pipelines that handle high-throughput sequencing data, including next-generation sequencing (NGS), RNA-seq, and CRISPR screens. You'll ensure that pipelines are scalable, efficient, and user-friendly. Stay Up-to-Date with Advances in Bioinformatics: • Keep abreast of the latest developments in bioinformatics, computational biology, and data science. You'll experiment with new tools, databases, and software to continuously improve your analytical techniques and methodologies. Visualize and Present Data Insights: • Create visual representations of biological data to communicate findings to researchers, stakeholders, and non-technical audiences. You'll use data visualization tools to illustrate complex results clearly and effectively. Ensure Data Quality and Reproducibility: • Focus on ensuring the accuracy, quality, and reproducibility of bioinformatics analyses. You'll develop validation methods and maintain data integrity to ensure that results can be trusted in scientific and clinical applications. Requirements Required Skills: • Bioinformatics and Computational Biology Expertise: Strong experience in analyzing biological datasets, including genomics, proteomics, and transcriptomics. You're proficient in using bioinformatics tools and software like BLAST, Bioconductor, and Python or R for data analysis. • Algorithm Development and Data Analysis: Expertise in developing algorithms and computational models for sequence analysis, gene expression profiling, and protein structure prediction. You have a deep understanding of data structures and machine learning techniques relevant to bioinformatics. • Programming and Scripting Languages: Proficiency in programming languages like Python, R, Perl, or Java. You're skilled in using these languages for data manipulation, statistical analysis, and developing custom bioinformatics tools. • Data Visualization: Experience with data visualization tools and libraries like Matplotlib, Seaborn, or ggplot2. You know how to create intuitive visualizations that make complex biological data easy to understand. • Collaboration and Communication: Strong communication skills with the ability to explain computational results to biologists, researchers, and non-technical stakeholders. You can work effectively in multidisciplinary teams, driving projects from data analysis to biological interpretation. Educational Requirements: • Bachelor's or Master's degree in Bioinformatics, Computational Biology, Genomics, or a related field. Equivalent experience in bioinformatics and computational data analysis is highly valued. • A Ph.D. in Bioinformatics, Computational Biology, or related fields is a plus but not mandatory. • Certifications in data analysis, machine learning, or specialized bioinformatics courses are a bonus. Experience Requirements: • 3+ years of experience in bioinformatics, with a proven track record of analyzing biological datasets and developing computational tools. • Hands-on experience with high-throughput sequencing technologies like NGS, RNA-seq, and CRISPR. • Experience in genomics research, drug discovery, or precision medicine is highly desirable. Benefits • Health and Wellness: Comprehensive medical, dental, and vision insurance plans with low co-pays and premiums. • Paid Time Off: Competitive vacation, sick leave, and 20 paid holidays per year. • Work-Life Balance: Flexible work schedules and telecommuting options. • Professional Development: Opportunities for training, certification reimbursement, and career advancement programs. • Wellness Programs: Access to wellness programs, including gym memberships, health screenings, and mental health resources. • Life and Disability Insurance: Life insurance and short-term/long-term disability coverage. • Employee Assistance Program (EAP): Confidential counseling and support services for personal and professional challenges. • Tuition Reimbursement: Financial assistance for continuing education and professional development. • Community Engagement: Opportunities to participate in community service and volunteer activities. • Recognition Programs: Employee recognition programs to celebrate achievements and milestones.

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). 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.