Bioinformatics Jobs

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.

Job Description Are you a passionate and dedicated research professional? The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group established in 2016, with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. The Hitchins Laboratory undertakes translational cancer research with a focus on genetic and epigenetic alterations associated with cancer, in particular cancer-specific changes in DNA methylation. Researchers in the Hitchins Lab undertake studies on genetic and epigenetic alterations that predispose to cancer onset, as well as the discovery and development of epigenetic alterations to serve as tumor biomarkers for applications to cancer diagnosis, prognosis or prediction of treatment outcomes. To learn more, please visit: Hitchins Lab | Cedars-Sinai. The Clinical Research Associate I works under the direction of a Clinical Research Coordinator, Research Program Administrator, Research Nurse, or other supervising staff to assist in tasks supporting the coordination/implementation of noncomplex research studies. Supports objectives of research studies through noncomplex tasks such as data collection, prescreening of potential and scheduling of current research participants, assisting in IRB submission activities, budget and billing, and ensuring overall compliance with all federal and local guidelines. Primary Duties and Responsibilities: • Works under the direction of a Clinical Research Coordinator, Research Program Administrator, Research Nurse, or other supervising staff to assist in tasks supporting the coordination/implementation of noncomplex research studies. • Collects, evaluates and/or abstracts clinical research data. May assist in designing forms for data collection/abstraction. Enters and processes clinical research data into Electronic Data Systems (EDCs) that are provided by the sponsors. • Completes Case Report Forms (CRFs). • Assists with prescreening of potential research participants for various clinical trials. Schedules research participants for research visits and research procedures. Provides supervised patient contact or independent patient contact for long term follow-up patients only. • Assists supervising staff with regulatory submissions to the Institutional Review Board (IRB) including submission of Adverse Events, Serious Adverse Events, and Safety Letters in accordance with local and federal guidelines. • Assists with clinical trial budgets and patient research billing. • Responsible for sample preparation and shipping and maintenance of study supplies and kits. • Ensures compliance with protocol and overall clinical research objectives. Ensures compliance with all federal and local agencies including the Food and Drug Administration (FDA) and local Institutional Review Board. Maintains research practices using Good Clinical Practice (GCP) guidelines. Maintains strict patient confidentiality according to HIPAA regulations and applicable law. • May serve as one point of contact for external sponsors for select trials. May respond to sponsor inquiries and attend meetings regarding study activity under the direction of supervising staff. Department-Specific Responsibilities: • Assists with data searches and related administrative tasks. • Verifies specimen identification and quality of specimen by recognizing factors that affect procedures and results; takes appropriate action when corrections are indicated. • Identifies patients and patient samples by strict adherence to established procedures; Labels samples accurately and completely. • Reports test results to appropriate individuals and exercise professional discretion with patient information. • Safe transportation of patient samples from clinic to laboratory. • Assists with lab-based sample processing, freezing, and inventory. • Data entry into a relational research database. • Attends research meetings. • Maintains organized paper and electronic research files. Qualifications Education: • High School Diploma/GED, is required. Bachelor's degree preferred. Experience and Skills: • One (1) year of clinical research related experience is preferred. • Ability to interpret and apply knowledge of State, Federal and Agency standards to comply with regulations. • Ability to convey and/or receive written/verbal information to/from various audiences in different formats. • Computer skills, including Word and Excel, and ability to use standard office equipment is required. About Us Cedars-Sinai is a leader in providing high-quality healthcare encompassing primary care, specialized medicine and research. Since 1902, Cedars-Sinai has evolved to meet the needs of one of the most diverse regions in the nation, setting standards in quality and innovative patient care, research, teaching and community service. Today, Cedars- Sinai is known for its national leadership in transforming healthcare for the benefit of patients. Cedars-Sinai impacts the future of healthcare by developing new approaches to treatment and educating tomorrow's health professionals. Additionally, Cedars-Sinai demonstrates a commitment to the community through programs that improve the health of its most vulnerable residents. About the Team Cedars-Sinai is one of the largest nonprofit academic medical centers in the U.S., with 886 licensed beds, 2,100 physicians, 2,800 nurses and thousands of other healthcare professionals and staff. Choose this if you want to work in a fast-paced environment that offers the highest level of care to people in the Los Angeles that need our care the most. Req ID : 5221 Working Title : Clinical Research Associate I - Hitchins Lab - Center for Bioinformatics and Functional Genomics Department : Research - BMS - Bioinfo and Func Genomics Business Entity : Cedars-Sinai Medical Center Job Category : Academic / Research Job Specialty : Research Studies/ Clin Trial Overtime Status : NONEXEMPT Primary Shift : Day Shift Duration : 8 hour Base Pay : $19.50 - $32.86

About Probably Genetic Probably Genetic is changing the lives of patients living with severe, complex diseases. Our technology discovers undiagnosed patients online, analyzes their disease state using machine learning and at-home testing, and connects patients to relevant resources. In doing so, we help patients access diagnoses, clinical trials, and treatments as early as possible. Our data platform is used by drug developers and patient advocacy groups to develop and launch treatments for these patients. We are a tight-knit group of hard-working, ambitious problem solvers united by a mission greater than ourselves. We do well by doing right by patients. We’re growing quickly and our roadmap is packed with innovations in bioinformatics, machine learning, and patient-focused efforts. We are building an all-star team to help us bring our vision to life, and we want you to be a part of it. Probably Genetic has raised multiple rounds of funding from Silicon Valley’s best investors, including Threshold, Khosla, and Y Combinator, giving us the ability to pay competitive salaries, offer great benefits, and provide meaningful equity. We’re dedicated to ensuring your journey with us is unforgettable, with incredible team retreats to places like Barbados, the Alps, Mexico, Costa Rica, and Portugal, just to name a few. About the role We are looking for a Bioinformatician to lead the development and implementation of our bioinformatics strategy, helping us build an innovative patient intelligence platform. In this role, you'll collaborate closely with our teams in engineering, AI, data science, product, and program execution to tackle meaningful challenges in rare diseases. This is a hands-on opportunity for someone excited to work deeply with NGS data analysis and interpretation, bioinformatics pipeline development, and data analysis for drug development. What you will do • Design, implement, and optimize bioinformatics pipelines to analyze rare disease patient genomes • Collaborate with our AI team to automatically train our system with your results • Collaborate with software engineers to turn your bioinformatics work into scalable processes in our data platform • Work closely with our external sequencing, bioinformatics, and telehealth vendors to ensure high quality results • Partner with our Growth & Patient experience team to develop a new paradigm to cut test costs by 10x and increase our data volume by 10x Who you are We are looking for a few specific things that will help you succeed in this role: • PhD in Bioinformatics, Genomics, Computational Biology, or a related field. • 3-5 years of post-PhD experience working in genomics, ideally in a startup or dynamic research environment • Strong hands-on experience with rare disease next generation sequencing (NGS) data analysis using command line as well as point-and-click bioinformatics tools • Proficiency in programming languages such as Python, R, or similar • Knowledge of cloud-based platforms and high-performance computing for bioinformatics • Self-motivated, independent, and eager to collaborate with cross-functional teams Some things that are not required, but you will learn on the job: • Experience with genomic analysis methods commonly used for drug development (GWAS, PheWAS, Mendelian Randomization, and others) • Experience with traditional machine learning approaches As with all new hires at Probably Genetic, you will also need to be: • A good person. We work with some of the most marginalized populations on the planet and empathy is key • Patient-focused and motivated to have a lasting, positive impact on humanity • Comfortable in a fast-paced, often ambiguous environment with rapid change • Action-oriented and excited to build a company from the ground up The salary range for this role is $122,000-$183,000 annually. Actual compensation offered will depend on several factors including but not limited to: work experience, education, skill level, and/or other business and organizational needs. What We Offer at Probably Genetic: • An engaging and supportive team • Generous Flexible Time Off policy • Hybrid, flexible work • Pet-friendly office space in Downtown San Francisco • A “work from anywhere” policy, up to 4 weeks a year • Competitive equity grants • All-expenses paid quarterly team retreats • Benefits including medical and dental • Parental Leave Benefits (12 weeks for both birthing and non-birthing parents!) Probably Genetic is committed to fostering a welcoming and inclusive work environment for people of all genders, sexuality, ethnicity, socioeconomic background and life experiences. We urge candidates of all backgrounds to apply. If you require specific accommodations as you interview or consider working with us, please let us know.

About Us Founded in 2011, Fulgent has evolved into a premier, full-service genomic testing company built around a foundational technology platform. Through our diverse testing menu, Fulgent is focused on transforming patient care in oncology, anatomic pathology, infectious and rare diseases, and reproductive health. We believe that by providing a wide range of effective, flexible testing options in conjunction with best-in-class service and support, we can redefine the way medicine is managed for patients and clinicians alike. Since integrating with our therapeutic development business, Fulgent is also developing drug candidates for treating a broad range of cancers using a novel nanoencapsulation and targeted therapy platform. By merging our fields of expertise, we aim to become a fully integrated precision medicine company. Summary Of Position The Director of Bioinformatics leads a team of experts in bioinformatics and biostatistics in the planning, designing, and implementing bioinformatics infrastructure to address clinical diagnostics production, R&D, and client needs. The Director formulates strategic plans for bioinformatics solutions, working closely with other team leads and executive leadership. The Director serves as the expert and champion of bioinformatics, strongly emphasizing innovation and development of best-in-class bioinformatics solutions. Key Job Elements • Direct the planning, designing, development, implementation, and maintenance of the bioinformatics infrastructure, including data, hardware and software components, and system integration. • Oversee bioinformatics production, R&D, and client service efforts. • Provide the organization with short-term and long-term bioinformatics strategic plans to meet business objectives. • Direct a team of bioinformatics scientists in developing bioinformatics infrastructure, R&D, and client service. • Develop and deploy novel bioinformatics analyses and tools. • Monitor, review, and utilize emerging technologies. • Serve as bioinformatics subject matter expert to cross-functional teams. • Direct resolution of bioinformatics production issues. • Review and provide feedback on design, validation, testing methodology, documentation, and reports • Provide advice, guidance, and mentoring to bioinformatics staff. • Build and manage a staff of bioinformatics professionals. Knowledge/Experience • Master’s or Ph.D. in Bioinformatics, Computer Science, or related field. • 7-10 years of experience in related Bioinformatics. • Extensive hands-on and in-depth experience with next-generation sequencing (NGS) analysis, NGS databases and tools, and NGS pipeline development. • Extensive experience analyzing multiple types of NGS data and facility with statistics for big data analysis and multi-omics data integration. • Extensive experience in designing, developing, implementing, and managing NGS analysis pipelines and workflows. • Experience leading bioinformatics development teams. • Strong hands-on skills in relevant programming languages. • Must enjoy working in a multi-disciplinary and collaborative environment and leading and mentoring a bioinformatics team. • Excellent oral and written skills, including the ability to communicate openly, transparently, in a timely, and consistent manner. Supervisory Responsibilities • Yes Reports To • TBD Environment Fulgent Therapeutics LLC is an Equal Employment Opportunity Employer. The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job. Reasonable accommodations may be made to enable qualified individuals with disabilities to perform the essential functions. The term “qualified individual with a disability” means an individual with a disability who, with or without reasonable accommodation, can perform the essential functions of the position. For California residents, please see the link below to access our CCPA Privacy Notice. CCPA Privacy Notice for California Residents https://tinyurl.com/FulgentCCPA

Payroll Title: BIOINFORMATICS PROGR 3 Department: SURGERY Hiring Pay Scale $40,000 - $60,000 / Year Worksite: Remote Appointment Type: Career Appointment Percent: 50% Union: Uncovered Total Openings: 1 Work Schedule: Days, 4 hour shifts, Monday - Friday #132991 Bioinformatics Programmer 3- Remote Filing Deadline: Wed 11/13/2024 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. Please note that this position is a part-time appointment UCSD Layoff from Career Appointment: Apply by 10/31/2024 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 11/13/2024. Eligible Special Selection clients should contact their Disability Counselor for assistance. Candidates hired into this position may have the ability to work remotely. DESCRIPTION The Department of Surgery at UC San Diego is a leader in research and patient care, with a mission to provide expert treatment, conduct cutting-edge research, and train the next generation of surgeons and scientists. The department has over 102 full-time faculty members and a global research portfolio exceeding $19M. The Alsaigh Lab at UCSD is seeking a highly skilled Senior Bioinformatics Scientist to lead and contribute to translational data science projects focused on cardiovascular medicine, genomics, and precision health. This position offers the opportunity to work closely with clinicians and leverage advanced bioinformatics and data science techniques to improve patient outcomes. Uses skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms; identifies and resolves a wide range of issues / software bugs. Demonstrates good judgment in selecting methods and techniques for obtaining solutions. Operates independently. MINIMUM QUALIFICATIONS • Seven (7) years of related experience, education/training, OR a Bachelor's degree in related area plus three (3) years of related experience/training. • Thorough knowledge of bioinformatics methods, applications programming, web development and data structures. • Thorough knowledge of bioinformatics programming design, modification and implementation. • Understanding of relational databases, web interfaces, and operating systems. • Strong project management skills. • Thorough knowledge of modern biology and applicable field of research. • Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization. • Ability to communicate technical information in a clear and concise manner. • Ability to interface with management on a regular basis. • Self motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills. • Thorough knowledge of web, application and data security concepts and methods. PREFERRED QUALIFICATIONS • Advanced degree (Master’s or Ph.D.). • Seven (7) years of experience in bioinformatics, with demonstrated expertise in genomics, molecular biology, and data science. • Experience in cardiovascular disease research and metabolic disease studies. • Familiarity with high-throughput sequencing technologies and single-cell RNA sequencing. • Proven track record of leading complex bioinformatics projects and publishing high-impact research. SPECIAL CONDITIONS • Employment is subject to a criminal background check. Pay Transparency Act Annual Full Pay Range: $94,400 - $176,800 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $45.21 - $84.67 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.

Job Description When the work you do every single day has a crucial impact on the lives of others, every effort, every detail, and every second matters. This shared culture of happiness, passion, and dedication pulses through Cedars-Sinai, and it’s just one of the many reasons we rank as one of the top hospitals in the nation by U.S. News & World Report. From working with a team of committed healthcare professionals to using state-of-the-art facilities, you’ll have everything necessary do something incredible—for yourself and for others! Are you ready to be a part of breakthrough research? The Knott laboratory is searching for computational scientists to develop and apply machine learning tools to study next-generation single-cell datasets. The Knott lab is located in the Center for Bioinformatics and Functional Genomics at Cedars-Sinai Medical Center, in Los Angeles, California. The lab focuses on understanding the molecular mechanisms of disease using a combination of genomics, computational biology, and functional studies in animal models. To learn more, please visit Knott Research Lab | Cedars-Sinai. The Research Bioinformatician I performs general bioinformatics analysis and software support for projects involving in omics. The RBI manages omic data including loading and querying data from database system(s) and public repositories, and transforms and merges multilevel omic data into user-friendly formats. The RBI assists in the development, testing, and maintenance of modular software pipelines, and provides daily bioinformatics data analysis, preliminary interpretation of the data, and reports of the results for possible publications. Primary Job Duties & Responsibilities: • Provides general bioinformatics analysis support for omic projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers. • Summarizes data analyses results in the form suitable as the basis for the first draft of written reports, and makes preliminary interpretations of the data. • Assists in development, testing, and maintenance of modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences. • Manages data including loading and querying data from database systems, downloading omic data from public repositories, and transforming data to the necessary formats. • Helps to identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology. Qualifications Education: • Bachelor’s Degree in Computer Science, Electric Engineering, Computational Biology, or Bioinformatics, or relevant fields (e.g. Biology with strong quantitative training, biostatistics with a concentration in bioinformatics). Master's degree is preferred. Experience and Skills: • No experience is required. • Background and work knowledge in algorithms, scientific computing, and machine learning or statistics, Familiar with C/C++, Java, Perl, python, and the Unix (Linux) environment, Experiences in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets, both in exploratory and pipelined fashions, will be a plus. • Experiences in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets, both in exploratory and pipelined fashions, will be a plus. About Us Cedars-Sinai is a leader in providing high-quality healthcare encompassing primary care, specialized medicine and research. Since 1902, Cedars-Sinai has evolved to meet the needs of one of the most diverse regions in the nation, setting standards in quality and innovative patient care, research, teaching and community service. Today, Cedars- Sinai is known for its national leadership in transforming healthcare for the benefit of patients. Cedars-Sinai impacts the future of healthcare by developing new approaches to treatment and educating tomorrow's health professionals. Additionally, Cedars-Sinai demonstrates a commitment to the community through programs that improve the health of its most vulnerable residents. About the Team Cedars-Sinai is one of the largest nonprofit academic medical centers in the U.S., with 886 licensed beds, 2,100 physicians, 2,800 nurses and thousands of other healthcare professionals and staff. Choose this if you want to work in a fast-paced environment that offers the highest level of care to people in the Los Angeles that need our care the most. Req ID : 5224 Working Title : Research Bioinformatician I - Knott Lab - Center for Bioinformatics and Functional Genomics Department : Research - BMS - Bioinfo and Func Genomics Business Entity : Cedars-Sinai Medical Center Job Category : Academic / Research Job Specialty : Bioinformatics Overtime Status : EXEMPT Primary Shift : Day Shift Duration : 8 hour Base Pay : $71,219.20 - $121,076.80

Description Serves as a technical leader in applying computational theory to practice, with an in-depth understanding of diverse IT-related research application areas. The Bioinformatics Programmer manages assigned programs by utilizing principles of computational research, computer science, data science, and CI software development, along with relevant scientific knowledge and professional programming concepts for research projects. They have extensive experience analyzing neurological, physiological, and behavioral data. The Bioinformatics Programmer develops and optimizes a variety of computational, data science, and CI research tools and components. You will build and deploy custom AI models for supervised and unsupervised extraction of behavioral, neurological, and physical health patterns, including models not covered by standard platforms or repositories. You will perform highly complex analyses and tests of software and hardware, applying advanced programming principles and conduct research on current and future HPC, CI technologies, and edge computing, both hardware and data. The Bioinformatics Programmer engages in algorithm development, optimization, programming, and computer science research. You will collaborate with cross-functional teams and managers, and train data science teams to integrate and optimize research technologies ensuring compliance with relevant regulations and ethical standards. Salary Range: $112900 - $256900/Annually

The department of Computational Biology is seeking an experienced lead or principal-level bioinformatics research scientist to provide direction and lead the development of pipelines for use in our clinical genomics program. The clinical genomics program at St. Jude Children’s Research Hospital started in 2013 as a pioneer in the use of whole genome sequencing for clinical testing. This position in the department of Computational Biology will play a key role in continuing our innovation in this space. The ideal candidate brings knowledge of cancer biology and stays abreast of current methods and trends in published literature. By leveraging this knowledge, working in productive collaboration with stakeholders, this role can proactively identify viable opportunities and effective solutions, thereby serving as a catalyst to innovation within the clinical genomics program. This role involves directing the efforts of the multidisciplinary team that performs end-to-end development of bioinformatics pipelines, including evaluation of existing methods, development of annotation and filtering strategies, and validation in accordance with CAP/CLIA requirements. This requires bioinformatics rigor applied in a clinical context where turnaround time limits, workflow considerations, and unique analytical performance criteria apply. Candidates must possess strong communication and interpersonal skills, as the position will engage regularly with pathologists, analysts, bioinformaticians, and engineers within the departments of Pathology and Computational Biology, as well as clinicians and scientists from various departments in the institution. Job Responsibilities: • Design and lead advanced analyses and deliver high-quality results in a timely manner by identifying new technologies and methodologies and recommend for adoption when appropriate. • Coordinate development of novel software tools and infrastructure as scientific and technical advisor, by contributing code and providing scientific guidance to developers. • Conceptualize, initiate, and lead manuscript preparation and submission of benchmarking results, new pipelines, databases, and scientific discoveries where appropriate. • Establish best practices and new protocols for analysis matching skills and expertise, and share protocols with St. Jude investigators through open documentation and hands-on training. • Assist in acquiring funding to support methods evaluation, development, and infrastructure. • Lead and coordinate the development of curriculum to educate the St. Jude community. • Is an independent project leader for large-scale projects and mentors junior staff. • 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 13+ 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 11+ years of relevant post-degree experience (OR) PhD with 8+ years of relevant post-degree experience. • Substantial 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 $138,320 - $262,080 per year for the role of Lead/Principal Bioinformatics Research Scientist, Clinical Genomics. Explore our exceptional benefits! Diversity, Equity and Inclusion St. Jude Children’s Research Hospital has a diverse, global patient population and workforce, built on the principles of diversity, equity and inclusion. Our founder Danny Thomas envisioned a hospital that would treat children of the world—regardless of race, religion or a family’s ability to pay. Learn more about our history and commitment. Today, we continue the mission to advance cures and means of prevention for pediatric catastrophic diseases through research and treatment. As we accelerate this progress globally, we believe our legacy of diversity, equity and inclusion is foundational to success. With the commitment of leaders at all levels of the organization, we strive to ensure the St. Jude culture, leadership approaches and talent processes are equitable and culturally responsive. View our Diversity, Equity and Inclusion Report to learn about the hospital’s roots in diversity, equity and inclusion, where we are today and our aspirations for an even better future. 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.

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. Additional Information • Schedule: Full-time • Job Code: 4752 • Employee Status: Regular • Grade: I • Requisition ID: 104983 • Work Arrangement : Hybrid Eligible

SHIFT: Day (United States of America) Bioinformatics Engineer I – Children’s Hospital of Philadelphia (Philadelphia, PA): Support computational environments focused on the management, transfer, formatting, and general processing of complex data types associated with genomics and proteomics. Duties include: develop large-scale bioinformatics pipelines with NGS data such as Whole Genome Re-sequencing, Whole Exome Sequencing, and Small RNA analysis; facilitate the efficient transfer of bioinformatics data from data sources to data users, with benchmarking and data quality checks, and troubleshoot data quality issues or discrepancies; implement bioinformatics processing, storage, and the manipulation of bioinformatics data in a cloud environment; evolve processes for effectively using large-scale, cloud-based, bioinformatics storage frameworks; identify and test application/pipeline defects and fixes; work with the technical team to establish and maintain appropriate levels of availability, response time, and bioinformatics software and systems performance; and execute development testing for commonly used applications such as data processing pipelines. Requires a Bachelor’s degree in a natural science or computational discipline and 1 year of experience with computational skills including deep learning, ensemble learning, machine learning, distributed computing, and automation pipeline development, as well as experience with programs including SQL, Sklearn, TensorFlow, PyTorch, and Docker. Apply online at www.chop.edu/careers.