Bioinformatics Jobs

Description Join a dynamic team at the forefront of genomic research. The Technology Center for Genomics & Bioinformatics (TCGB) provides next-generation sequencing (NGS) services to over 200 investigators, processing 200–400 samples weekly. As our Administrative Assistant, you will play a pivotal role in ensuring the smooth, efficient operation of our research and educational programs. Primary duties include: • Serve as the primary liaison between clients and TCGB, managing communications with researchers and collaborators. • Coordinate specimen drop-offs, provide updates on turnaround times, and respond to client inquiries regarding genomic testing services. • Coordinate complex schedules, meetings, and event logistics. • Facilitate travel arrangements and process reimbursements. • Obtain quotes from vendors and assist with purchasing. • Input requested services to billing log. • Follow-up on SFSA and PO process. • Support the preparation of grant applications, justifications, budgets, and educational materials. • Assist with the planning and execution of educational seminars. • Maintain organized records, files, and inventory tracking systems. • Oversee shipping and receiving of samples and reagents. Salary Range: $30.36 - $43.49/hour

ay Range: $115,000.00 - $135,000.00 / 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: • Day 1 Medical, supplemental health, dental & vision for FT employees who work 30+ hours • Best-in-class well-being programs • Annual, no-cost health assessment program Blueprint for Wellness® • healthyMINDS mental health program • Vacation and Health/Flex Time • 6 Holidays plus 1 "MyDay" off • FinFit financial coaching and services • 401(k) pre-tax and/or Roth IRA with company match up to 5% after 12 months of service • Employee stock purchase plan • Life and disability insurance, plus buy-up option • Flexible Spending Accounts • Annual incentive plans • Matching gifts program • Education assistance through MyQuest for Education • Career advancement opportunities • and so much more! Complete oversight of BME operations for large, complex sites and/or multiple sites to ensure service program efficiency and to satisfy the equipment support needs of the company. The purpose of the BME Sr. Manager position is to develop, coordinate, and expand the BME program as necessary to ensure all aspects of service (internal and external) for all lab instrumentation and general lab equipment satisfy the quality and regulatory requirements and service needs for each lab, enabling operations to run efficiently, profitably, and with excellent quality. The Sr. Manager has more experience than As a Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing. This position is in our Bioinformatics Operations group, part of the Research and Development organization, in Advanced Diagnostics based in San Juan Capistrano, CA. This position is intended to be either on site or hybrid – working on site at least 2-3 days per week in our San Juan Capistrano, CA lab. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment, using short and long-read sequencing as the basis of evidence. The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics Operations group supports, hones, and executes the processes defined by our Engineering and Lab Operations groups with emphasis on compliance and continuous improvement. While coupled tightly to regulation through standards in validation, documentation, and data retention, the group is an integral part of the development cycle of our analysis workflows and visualization. This professional will work in a hybrid capacity with 3 days onsite at our San Juan Capistrano, CA facility. Additionally, our Marlborough, MA location is an option as well. Quest Diagnostics honors our service members and encourages veterans to apply. While we appreciate and value our staffing partners, we do not accept unsolicited resumes from agencies. Quest will not be responsible for paying agency fees for any individual as to whom an agency has sent an unsolicited resume. Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets or any other legally protected status. • Support production day-to-day operations, quickly pivoting focus to respond to incidents and requests • Monitor, execute, and improve sequence analysis workflows and automation • Track, troubleshoot and mitigate issues encountered in processing production samples to meet strict Turnaround Times (TAT) and business SLAs • Plan and develop solutions to recurring issues to be merged back into development branch maintained by the Engineering group • Generate, wrangle, merge and glean information from varied and complex data sets • Use of RESTful APIs linked to various systems including LIMS, AWS job runners and other systems necessary for data processing and execution • Design and perform validation, testing, and production deployment of systems and software to standardize processes across all Quest Diagnostics genetic testing labs • Design and perform analytical validation analysis for new genomic testing products • Write and maintain production documentation for compliance and supportability of all bioinformatics processes in production environment • Produce charts and visualization for dashboards, reporting, and in support of data driven hypothesis testing • Support interface, integration, and testing projects • Utilize a Software Development Life Cycle documentation procedure • Be an active team player and support the group • Accept input on solutions from other colleagues and teams • Availability for on-call support The ideal candidate will have a history of using bioinformatic technical skills to deliver accurate and timely results. Required: • 5 yr experience using formal programming and scripting languages • 5 yr experience working on a Linux command-line to process, parse, and merge varied data sets • 3 yr experience working with web services and utilizing API communications (REST, SOAP, etc) • 3 yr experience in a distributed cloud HPC environment • Knowledge and understanding of genomics, next-generation sequencing, and bioinformatics including parsing and working with typical file formats (FASTQ, BAM, VCF) • Experience supporting production grade software • Experience with source control in a development, testing, and production environment • Experience communicating technical results and data • Experience working with APIs to pull/query data Preferred: • Automated testing experience; CI/CD experience preferred • Knowledge of CAP documentation requirements or working in a regulated environment a plus • Microsoft UI: Access, VBA, Macros • Pipeline Workflow Manager: Nextflow • CI/CD in GitHub Education: • Required: B.S. in Computer Science, Software Engineering, Bioinformatics, or a related field. • Preferred: MSc/PhD degree in Computer Science, Software Engineering, Bioinformatics Preferred Technical Training: • Agile certification • Nextflow training • Cloud Computing • Data Science

The Regents of the University of California on behalf of their Los Angeles Campus Los Angeles, CA Department Summary The central mission of the Bioinformatics IDP is to train talented and highly motivated students to become next-generation leaders in the field of Bioinformatics. We offer rigorous and integrated training for students interested in undertaking research at the interface of computer science, mathematics, statistics, biology, and biomedicine to address the fundamental challenges of data-rich research in biosciences. Position Summary UCLA Bioinformatics IDP is seeking an experienced Sudent Services Advisor to guide students through the 5-year PhD program. Salary & Compensation • UCLA provides a full pay range. Actual salary offers consider factors, including budget, prior experience, skills, knowledge, abilities, education, licensure and certifications, and other business considerations. Salary offers at the top of the range are not common. Visit UC Benefit package to discover benefits that start on day one, and UC Total Compensation Estimator to calculate the total compensation value with benefits. Qualifications University Systems Experience with admissions and funding systems used by UC (Preferred) Office systems Experience using MS Office (Required) Website/online Experience with Wordpress, Google suite (Preferred) Student affairs Counseling and advising students in an academic environment (Preferred) Strong interpersonal skills sufficient to establish and maintain productive, cooperative and effective working relationships with colleagues (Required) Excellent written and verbal communication skills sufficient to interpret and convey complex information relating to the duties of the position. (Required) Ability to notice and respond to details (Required) Ability to organize and prioritize large amounts of information (Required) Education, Licenses, Certifications & Personal Affiliations Bachelor's Degree In related area and / or equivalent experience / training (Required) Special Conditions for Employment Background Check: Continued employment is contingent upon the completion of a satisfactory background investigation. Live Scan Background Check: A Live Scan background check must be completed prior to the start of employment. Age Requirement: Candidate(s) must be 18 years or older to be eligible to be hired. Schedule 8.00am - 5.00pm Union/Policy Covered 99-Policy Covered Complete Position Description https://universityofcalifornia.marketpayjobs.com/ShowJob.aspx?EntityID=38&jobcode=40060527University Systems Experience with admissions and funding systems used by UC (Preferred) Office systems Experience using MS Office (Required) Website/online Experience with Wordpress, Google suite (Preferred) Student affairs Counseling and advising students in an academic environment (Preferred) Strong interpersonal skills sufficient to establish and maintain productive, cooperative and effective working relationships with colleagues (Required) Excellent written and verbal communication skills sufficient to interpret and convey complex information relating to the duties of the position. (Required) Ability to notice and respond to details (Required) Ability to organize and prioritize large amounts of information (Required) UCLA Bioinformatics IDP is seeking an experienced Sudent Services Advisor to guide students through the 5-year PhD program. Job Information Job Category: Executive

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 As a Senior Bioinformatics Scientist II, you will collaborate in cross-functional teams to design, implement and continually improve advanced computational pipelines for high-throughput analysis of multiple types of NGS data. You will work independently in refining methodologies for data analysis, processing, visualization and storage. You will also be assigned leadership roles in projects with mentor responsibility to junior members of the team. You will strive to maximize efficiency, quality, reliability and customer usability and satisfaction. Key Job Elements Research and Development • Investigate and refine available algorithms, methods and data sources. • Work independently to define, prioritize and complete objectives to meet company goals. • Make recommendations for pipeline component improvements, or new pipelines. • Write SOPs for new or updated pipeline components, or new pipelines. • Write specifications for implementation by software developers. • Oversee pipeline development and integration. Production and Customer Support • Investigate and resolve analysis and pipeline production issues. • Review client projects for compatibility with current pipelines, make recommendations and implement customizations as needed. • Oversee sequencing service projects, ensuring timely processing, quality results and client satisfaction. • Support software and LIMS developers in automation efforts. • Perform specialized analyses as needed for specific projects. • Keep up-to-date with current best practices and emerging methods. • Treat data with a high level of integrity and ethics. Data Maintenance • Investigate available annotation and reference data sources. • Validate and deploy/update selected data sources. • Write reports detailing validation/update methodology and results. • Write SOPs for updating existing or new data sources. Validation • Develop appropriate procedures for testing and validation of new or updated pipelines or pipeline components. • Document and maintain data used for testing and validation. • Write validation reports detailing validation methodology and results. Knowledge/Experience • Ph.D. degree from an accredited institution in Bioinformatics, Biostatistics or related field. • 10+ years of experience in a related scientific discipline (Bioinformatics preferred). • Demonstrated mastery of Fulgent specific methods and processes. • Experience analyzing multiple types of next-generation sequencing (NGS) data • Expertise with statistics for big data analysis and multiomics data integration. • Expert level hands-on skills in bioinformatics databases and tools. • Expert level in relevant programming languages, preferably Scala, Java, Python, and Bash. • Must enjoy working in a multi-disciplinary and collaborative environment. • Ability to troubleshoot both individually and as part of a team. • Excellent oral and written skills with the ability to communicate in an open, transparent, timely and consistent manner. • Experience in team software development and integration projects is a plus. Technical Leadership: • Provide technical leadership to the team • Be the mentor for junior team members. SUPERVISOR RESPONSIBILITIES: • None REPORTS TO: • Director of Bioinformatics 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 Please note that Fulgent (and its affiliated companies, including Inform Diagnostics and CSI Laboratories) does not accept unsolicited information and/or resumes from search firms or agencies for our job postings. Search firms or agencies without an applicable contract and/or express approval to recruit for the role in question — that choose to submit a resume or client information to our career page or to any employee of Fulgent — will not be eligible for payment of any fee(s), and any associated shared data will become the property of Fulgent.

Work Schedule Standard (Mon-Fri) Environmental Conditions Office Job Description As the Senior Manager, Bioinformatics, you will manage and provide technical leadership to our genetic sciences bioinformatics team responsible for custom array designs for genetic analysis in research, human health, and agricultural genomics. Leading this team requires a good understanding of both population-scale studies as well as an understanding of the importance of a variety of individual markers that might be important in a given study. You will partner with R&D bioinformatics leaders to ensure we are applying the state-of-the-art array design capabilities in a consistent high throughput setting. This position reports directly to the Director, Microarray Laboratory and Bioinformatics Services. Key Responsibilities: Customer Centric • Work directly with customers and collaborators to collect project goals and analysis requirements to meet their scientific goals. • Effectively work with cross-functional teams such as Sales, Marketing, Finance, Support, Purchasing, and Research and Development. Ensure these teams are aligned to meet and/or exceed customer needs. • Ensure the protection and confidentiality of all customer data. People and Technical Leadership • Select, develop, and evaluate personnel for talent management, including leadership growth and key skill-set development for operational and strategic objectives. • Ability to mentor staff on good computational practices, including documentation and consistent analysis. • Influences and motivates staff to deliver. Operational Excellence • Develop policies and procedures, for consistent, high quality custom designs as associated analysis files. • Own the day-to-day operations of the array design team. • Coordinate creation and maintenance of SOP's and training. • Coordinate the resource planning and scheduling for the team. Results • High visibility & proactive leadership of team. Present and on-site, acting daily to build successful work environment for team. • Establish, monitor, and report key performance Indicators for the array designs and analysis files. Qualifications: • MS in Bioinformatics, Genetics, Computational Biology or related field, plus 5+ years work experience; PhD preferred • Strong communications, both written and oral • 4+ years-experience leading technical teams • Ability to code in a high level language such as python or R • Familiarity with relational databases • Familiarity with Microarray analysis and NextGen Sequencing • Experienced in life sciences, genetics • Demonstrates and drives the Thermo Fisher values – Integrity, Intensity, Involvement and Innovation At Thermo Fisher Scientific, each one of our 100,000 extraordinary minds have a unique story to tell. Join us and contribute to our singular mission—enabling our customers to make the world healthier, cleaner and safer. We offer competitive remuneration, annual incentive plan bonus scheme, healthcare, company pension, and a range of employee benefits! Thermo Fisher Scientific is an EEO/Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status. We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. Compensation and Benefits The salary range estimated for this position based in California is $163,100.00–$220,000.00. This position may also be eligible to receive a variable annual bonus based on company, team, and/or individual performance results in accordance with company policy. We offer a comprehensive Total Rewards package that our U.S. colleagues and their families can count on, which includes: • A choice of national medical and dental plans, and a national vision plan, including health incentive programs • Employee assistance and family support programs, including commuter benefits and tuition reimbursement • At least 120 hours paid time off (PTO), 10 paid holidays annually, paid parental leave (3 weeks for bonding and 8 weeks for caregiver leave), accident and life insurance, and short- and long-term disability in accordance with company policy • Retirement and savings programs, such as our competitive 401(k) U.S. retirement savings plan • Employees’ Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount For more information on our benefits, please visit: https://jobs.thermofisher.com/global/en/total-rewards

Note: The job is a remote job and is open to candidates in USA. Karius is a life science company focused on advancing diagnostic science through microbial insights. The Sr. Bioinformatics Scientist will be a key member of the Assay Development Analytics team, responsible for driving computational aspects of assay development and conducting innovative analyses to enhance diagnostic capabilities for infectious diseases. Responsibilities • Individual contributor to Assay Development Analytics (ADA), which drives the computational aspects of assay development, focusing on analysis and optimization of new chemistries and lab techniques. • Participate in experimental design, conduct computational analyses, understand rationale, set the analysis plan, and execute using the necessary tools and methodologies to deliver innovative assays. • Work closely with colleagues across the Molecular Biology and Laboratory Operations teams to understand the properties of the assays and ways to improve our technologies. • Continue to grow and learn in the necessary mathematical, technological, and software aspects of the field through internal knowledge acquisition and staying current with the latest relevant literature. • Open to exploring multiple approaches for problem-solving and modeling including borrowing across a wide range of quantitative disciplines. • Ensure high standards of data integrity, quality control, and validation, while maintaining rigorous quality documentation and dissemination of scientific findings. • Provide clear visibility into areas of ownership and communicate weekly progress and results to stakeholders. • Continue to grow and learn in the necessary biological/scientific domains and technological aspects of the field through novel knowledge acquisition but also staying current with the latest relevant literature. • Share a passion for ensuring the quality of our statistical analysis, via reliability, reproducibility, and rigor. Skills • Ph.D. in computer science, statistics, mathematics, physics, genetics, bioinformatics, metagenomics, or related fields (preferably with a focus on computational biology or machine learning) with 3+ years of postdoctoral and/or industry experience; OR Master’s degree with 5+ years of directly relevant industry experience. • Publications demonstrating innovative investigation and interpretation of biological data. • Proven proficiency, and understanding of, modern statistics and machine learning. • Proven proficiency with high-dimensional, large-scale datasets characterized by low signal-to-noise. • Demonstrated excellence in communication and collaboration within cross-functional, multidisciplinary teams. • Self-starter with the ability to independently drive results and influence project direction. • Evidence of innovation in connecting biological insights to complex mechanisms of microbiome and host–environment interactions. • Familiarity with a range of relevant laboratory techniques (either through hands-on work or from collaborations with laboratory-focused colleagues). • Familiarity and experience with bioinformatics tools, approaches, and workflows, particularly those related to next-generation sequencing data analysis. • Familiarity with design of experiments (DOE) approaches to optimize process settings. • Passionate, purpose-driven, and excited about Karius’ mission: to conquer infectious diseases through innovations around genomic sequencing and machine learning. • Excellence at communication and collaboration within a cross-functional team. • Detail oriented with exceptional organizational and time management skills. • Self-starting mentality and ability to drive results. • Comfortable working in an environment which combines both research aspects as well as development. • Ability to work effectively and efficiently in a fast-paced (startup) environment. Company Overview • Karius delivers genomic insights into infectious diseases, helping clinicians make critical, life-saving treatment decisions. It was founded in 2014, and is headquartered in Redwood City, California, USA, with a workforce of 51-200 employees. Its website is https://kariusdx.com. Company H1B Sponsorship • Karius has a track record of offering H1B sponsorships, with 1 in 2024, 4 in 2021. Please note that this does not guarantee sponsorship for this specific role.

Vacancies Bioinformatics Scientist Job Introduction Thanks for checking out our vacancy, we're delighted you want to learn more about Dechra! Dechra is a growing, global specialist within the world of veterinary pharmaceuticals. Our expertise is in the development, manufacture, marketing and sales of high quality products exclusively for veterinarians worldwide. Here at Dechra, our values are embedded within our culture and thrive within our family of almost 3000 colleagues globally. From manufacturing to marketing, (D)edication, (E)njoyment, (C)ourage, (H)onesty, (R)elationships and (A)mbition are at the heart of our everyday operations and the way we do business. The Opportunity Provide Bioinformatics expertise to advance antibody discovery efforts for companion animals (dogs, cats, horses). Role Responsibility So, what will you be doing? This role has a broad and varied scope and the successful candidate will have responsibility for duties including: • Provide new target analysis by accessing and analyzing genomic and RNA-Seq datasets in the public domain. • Oversee external efforts to verify sequences for cat, dog or horse genes not currently in the publicly available databases • Oversee development of user-friendly databases containing antibody repertoire sequences from dog, cat and horse. • Lead the design of streamlining the input of data into Benchling to continuously improve data entry and organisation. • Carry out sequence liability remediation, and other biophysical property improvement of antibodies utilizing rational in-silico design approaches and/or publicly available software. • Assist in overseeing external collaborations utilising machine learning approaches • Curation and integration of relevant dog, cat, and horse genomic and RNA-Seq datasets from the public domain. • Analyse large numbers of antibodies from discovery campaigns by using clustering methods (clonotyping, sequence-based...) The Ideal Candidate Here at Dechra we pride ourselves on being an inclusive employer and we embrace candidates from all walks of life. We're particularly excited to hear from those who have/are: • In-depth knowledge and experience working with therapeutic antibodies (human or dog/cat) is required. • Knowledge of machine learning approaches for protein design & biological data analysis. • Proficient in antibody engineering, including experience with antibody sequence liability remediation and biophysical property improvement. • Experience with next generation sequencing data analysis (DNA & RNA) Desirable • Experience with successful implementation of bioinformatics tools for scientific data management and analysis of large datasets such as machine learning or other state-of-the-art approaches (e.g. from next generation sequencing applications and antibody library sequencing) and harmonizing different types of data sets for analyses. • Familiarity with molecular modeling softwares such as Rosetta, Schrodinger, Molecular Operating Environment (MOE) • Experience with next generation sequencing data analysis (DNA & RNA) About the Company As a people first values-based culture, we provide free weekly wellness sessions focused on our employee's physical and mental wellbeing, and flexible work arrangements. We offer a generous employer 401k match and an other incentives for long-term financial wellness. Our full array of health, financial and voluntary benefit programs are what you would expect from a recognized Best Place to Work.

We are hiring a Bioinformatics Associate to join our R&D Diagnostics group and in this position, you will support the analysis of large datasets using computer science, statistics, and programming to help solve biological problems. Key responsibilities include assisting with the execution and optimization of a mutation monitoring pipeline, as well as developing scripts and tools for various data analysis applications. It primarily involves data mining, basic script development, and troubleshooting, with opportunities to contribute to database management and software evaluation. Additionally, you will collaborate with researchers to interpret results and contribute to ongoing projects.You may also involve supporting PCR assay design and using tools such as Primer3 for primer and probe development. Experience working in a Linux-based computing environment is a plus. This is a fully onsite position based in San Diego, CA. Core Responsibilities • Data Analysis: Assist in analyzing biological datasets for mutation monitoring and performing in silico analyses of inclusivity and exclusivity. • Software and Tool Development: Write and maintain custom scripts and simple software tools (using languages such as Python, Java, or R) to manage and analyze biological data. • Database Management: Help design, maintain, and organize scientific databases for storing biological information. • Research Collaboration: Work closely with assay developers, lab scientists, and other team members to support experimental design, interpret results, and contribute to product development. • Communication and Training: Provide basic training and consultation to researchers on data analysis tools and methods. Present findings at internal meetings and communicate effectively with team members. • PCR Assay Design: Support PCR assay development by using DNA Software or Primer3 for primer and probe design and evaluation. Key Skills And Qualifications • Completed Bachelors/Masters degree in Computer science, Computational Biology, Bioinformatics, or related fields. • Working knowledge of statistics, computer science, and programming languages such as Python, Java, or R in a Linux environment. Ability to document analyses and report scientific data. • Experience or familiarity with PCR assay development and primer/probe design tools such as DNA Software or Primer3. • Experience or familiarity with PCR assay development and primer/probe design tools such as DNA Software or Primer3. • Good communication and teamwork skills for collaborating with scientific teams. • Ability to apply computational methods to address biological questions. The annualized base salary range for this role is $57,400 to $86,100 and is bonus eligible. Final compensation packages will ultimately depend on factors including relevant experience, skillset, knowledge, geography, education, business needs, and market demand. Why Hologic? We are committed to making Hologic the company where top talent comes to grow. For you to succeed, we want to enable you with the tools and knowledge required and so we provide comprehensive training when you join as well as continued development and training throughout your career. If you have the right skills and experience, apply today! Agency and Third Party Recruiter Notice: Agencies that submit a resume to Hologic must have a current executed Hologic Agency Agreement executed by a member of the Human Resource Department. In addition Agencies may only submit candidates to positions for which they have been invited to do so by a Hologic Recruiter. All resumes must be sent to the Hologic Recruiter under these terms or they will not be considered. Hologic, Inc. is proud to be an Equal Opportunity Employer inclusive of disability and veterans.

The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer II 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. Ashley’s research focuses on applying genomics and other omics data to improve clinical care, with an emphasis on cardiovascular disease and personalized medicine. Dr. Wheeler’s research centers on integrating large-scale molecular and clinical data to understand the genetic basis of diseases and to develop novel therapeutic strategies. In this role, you will focus on genome, epigenome, and transcriptome (GET) analyses (specifically WGS, ATAC-seq, and RNA-seq) running the pipelines and tools that convert raw sequencing data into clean, analysis-ready results for the consortium. You will architect and operate scalable workflows that adhere to best practices, including WGS variant calling and joint genotyping, RNA-seq quantification and differential expression, and ATAC-seq peak calling and differential accessibility. You will adapt rigorous QC frameworks across modalities; produce integrated multi-omics analyses (e.g., linking genetic variation, chromatin accessibility, and gene expression through eQTL/caQTL/colocalization); and deliver clear visualizations, genome browser tracks, and interactive dashboards that enable collaborative interpretation across teams. Your work will span data engineering and software development: building reproducible pipelines with Nextflow and/or WDL/Cromwell, containerizing and testing them for reliable deployment on cloud and HPC environments; leveraging GCP services such as Cloud Storage and BigQuery; and designing robust schemas for omics metadata and results. You will apply software engineering best practices (version control, code review, automated testing, and documentation) while implementing data governance aligned with FAIR principles and secure handling of controlled-access human genomic data. As a key contributor to our public-facing portal (https://motrpac-data.org), you will help push the boundaries of biomedical data analytics to accelerate discovery and translation. You will collaborate closely with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust computational analyses and to communicate findings in reports, presentations, and publications. Working within 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. This is an 18-month fixed term position. This is a hybrid eligible 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: • Transcriptomics and Gene Expression Analysis: Comprehensive RNA-seq workflows including read alignment (STAR, HISAT2), quantification (Salmon, Kallisto), QC (FastQC, MultiQC, RSeQC, Picard), normalization and differential expression (DESeq2, edgeR, limma), and pathway enrichment. Isoform analysis (StringTie) and fusion detection (STAR-Fusion) are a plus. • Advanced Genomics Data Analysis Expertise: Extensive experience with WGS data from raw FASTQ through variant calling, joint genotyping, annotation, cohort-level QC, and interpretation. Proficiency with BWA-MEM/BWA, GATK Best Practices (BQSR, HaplotypeCaller, joint calling, VQSR), DeepVariant, bcftools, and scalable VCF/BCF/CRAM handling. • Structural and Copy Number Variation: Experience with SV/CNV calling and QC (e.g., Manta, Delly, LUMPY, CNVnator), sample-level QC (coverage, duplication, contamination via VerifyBamID/Peddy/Somalier), and cohort metrics (Ti/Tv, call rate, Hardy–Weinberg). • Epigenomics and Chromatin Accessibility Analysis: Expertise in ATAC-seq processing and analysis, including alignment (BWA/Bowtie2), Tn5 shifting, peak calling (MACS2), replicate concordance (IDR), QC metrics (FRiP, TSS enrichment, nucleosome signal), differential accessibility (DiffBind/DESeq2), footprinting (HINT-ATAC), motif enrichment (HOMER/MEME), and browser tracks (bigWig/bigBed for IGV/UCSC). Regulatory element annotation using ENCODE/Roadmap resources. • Multi-omics Data Integration: Experience integrating WGS, ATAC-seq, and RNA-seq to identify regulatory relationships (eQTL/aseQTL/caQTL, colocalization), linking chromatin accessibility to gene expression and variant effects. • Advanced Python and R for Genomics: Deep proficiency in Python and R/Bioconductor with strong statistical and reproducible analysis skills. • Genomics Workflow Development: Proven experience designing, testing, and deploying complex workflows using Nextflow and/or WDL/Cromwell (or Snakemake) in cloud or HPC environments, with containerization (Docker, Singularity) and CI/CD for reproducibility. • Specialized Cloud and Database Skills: Hands-on experience with GCP (Cloud Storage, BigQuery), and genomics platforms (Terra, AnVIL). SQL skills and experience designing schemas for omics metadata/results; familiarity with gnomAD, ClinVar, Ensembl/RefSeq, dbSNP, UCSC. • Genome Browser and Visualization Expertise: Proficiency creating custom track hubs and sessions for IGV/UCSC; ability to produce publication-quality visualizations and interactive dashboards for large-scale genomics data. • Software Engineering Best Practices: Version control (Git/GitHub), code review, issue tracking, semantic versioning, packaging (setuptools/Poetry), automated testing (pytest), and comprehensive documentation (Sphinx/MkDocs). • Data Governance and FAIR Principles: Demonstrated experience with data lineage, provenance, audit trails, and adherence to FAIR; secure handling of controlled-access human genomic data (HIPAA/IRB compliance, DUAs), and submissions to dbGaP/GEO/SRA. • Cross-functional Collaboration and Communication: Proven ability to work with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust, actionable computational analyses. 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 $108,002 to $128,138 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.

Bioinformatics Support Specialist Caltech Job Category: Fulltime Term Exempt Overtime Eligible: Overtime Eligible Benefits Eligible: Benefit Based Caltech is a world-renowned science and engineering institute that marshals some of the world's brightest minds and most innovative tools to address fundamental scientific questions. We thrive on finding and cultivating talented people who are passionate about what they do. Join us and be a part of the diverse Caltech community. Job Summary The Ismagilov Lab at Caltech is hiring a full-time Bioinformatics Support Specialist for a 2-year term position. Reporting to Professor Rustem Ismagilov, the successful candidate will contribute to the lab's key projects and collaborations in human health, which include: developing novel tools that improve biological AI models by orders of magnitude; developing closed-loop systems that combine robotics and AI for rapid autonomous experimentation; discovering in human tissues novel bacteria, fungi and viruses (and corresponding genes and pathways) responsible for heath and disease; developing novel diagnostic approaches; understanding microbial origins of human diseases. Additional details about the lab can be found at https://apptrkr.com/get_redirect.php?id=6647096&targetURL= http://ismagilovlab.caltech.edu/ Essential Job Duties • Assist graduate students, postdocs, and research staff with bioinformatics/computational components of all ongoing projects. • Contribute to manuscript preparation and grant proposals, data visualization, and scientific presentations. • A highly motivated and qualified candidate may additionally develop their own independent aspects of ongoing projects. Bioinformatic Analyses • Learn and apply state-of-the-art statistical and computational methods for analyzing datasets from shotgun metagenomics, amplicon sequencing, and RNA-sequencing experiments. • Assist in the design, implementation, and benchmarking of in-silico experiments. • Generate computational results and publication-quality figures for clear communication of results to lab members and external collaborators. Scripting and Automation • Collaborate with lab members and external colleagues to learn and implement best practice methods and packages for data analysis and processing in the lab. • Work with lab members to understand needed bioinformatic capabilities and develop tools to accomplish them. • Work with lab members and external collaborators to help them develop, execute, and maintain state-of-the-art data processing pipelines on Caltech high-performance computing (HPC) clusters. • Develop and maintain scripts for routine analysis tasks such as qPCR quantification. • Develop and maintain scripts for automated robotic platforms to perform laboratory procedures. • Help lab members test and integrate LLM-based AI tools to improve efficiency of research tasks such as experimental design and technical writing. Bioinformatic Maintenance • Maintain well-organized computational workspaces, including data storage, version-control systems, containerization, and documentation in a neat, detailed electronic lab notebook. • Maintain reference databases of microbial genomes, gene clusters, antimicrobial resistance markers, and metabolic pathways. • Maintain organized and version-controlled repositories and containerized computational environments (Docker/Conda), using Python and/or R. • Assist with data management on remote computing clusters and back-up servers, including organizing raw and processed data, maintaining version control, and ensuring data integrity and reproducibility. Basic Qualifications • Bachelor's degree in science with educational emphasis in computational sciences, bioinformatics, biology, microbiology, computer science, bioinformatics, computational biology, data science, or a related field required at time of application. • Experience with programming languages for scripting and data analysis: Python, R, and Bash required. • Familiarity with basic molecular biology topics. • Experience (including coursework or internships) in data analysis using at least one scripting or programming language (e.g., Python, MATLAB, R). • Experience working with next generation sequencing data and/or big data (e.g. genomics, RNA-seq, single-cell RNA-seq, epigenomics, proteomics, metabolomics, etc.). • Experience working in Linux/Unix environments. • Strong drive to learn and to make positive impacts on the lab and lab's mission. • Ability and desire to collaborate and support collaborative projects. • Highly detail-oriented; must have examples of well-documented code (e.g., Git repositories) involving complex technical tasks or data analyses available upon request. • Ability to rapidly learn technical skills, particularly in computational methods and bioinformatic workflows. • Strong organizational, time-management, and project-management skills; ability to professionally and continuously communicate priorities, workload, and current progress to all lab members. • Must be able to use sound judgment to handle multiple simultaneous tasks, prioritize effectively, and troubleshoot problems independently. • Must be able to work independently as well as part of a collaborative team in a dynamic, fast-paced environment. • Ability to write clean, well-documented, and reproducible code for data processing and analysis. • Ambition to develop research skills and advance scientific understanding through high-quality computational analyses and interpretation of biological data. Preferred Qualifications • Experience with cloud computing environments (e.g., AWS, Google Cloud, or institutional equivalents) and using High-Performance Computing (HPC) clusters with the Slurm workload manager. • Experience performing bioinformatic analyses involving shotgun metagenomics, RNA sequencing, or 16S rRNA gene sequencing. • Experience with workflow management systems for pipeline automation (e.g., Snakemake, Nextflow). • Proficiency with Git for collaborative coding, project tracking, and version control. • Experience performing statistical analyses or modeling of complex biological datasets. • Experience with containerization (Docker, Conda, Singularity). • Experience creating visualizations or interactive notebooks (e.g., Jupyter, R Markdown, Dash). • Experience fine-tuning LLMs for analysis or writing tasks. • Co-authorship on a scientific publication. • Solid understanding of statistical analysis methods (NHST, probability distributions, etc.) • Ambition to pursue advanced training or career in computational biology, bioinformatics, ambition to enter a top medical or graduate school or a similar high-performance, high-impact environment in industry or academia. Required Documents • Resume (describe relevant experiences and accomplishments). • Cover letter with specific examples demonstrating a) candidate's alignment with lab's mission, b) candidate's level of ambition, motivation, and drive; c) candidate's attention to detail and ability to produce data others can trust; d) the level of technical mastery of the top three most relevant experimental skills described in the resume. • GitHub (preferred) or code examples. To be considered for this position please visit our web site and apply on line at the following link: https://hr.caltech.edu/work/job_openings We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, or any other characteristic protected by law. Copyright 2025 Jobelephant.com Inc. All rights reserved. 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