Bioinformatics Jobs

At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people. Quest Diagnostics Specialty Genetics products provide specific answers that clinicians need to deliver the appropriate diagnostic and prognostic care to their patients. 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. Bioinformatics, US Operations – the role 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 Marlborough, MA. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment primarily using short and long-read sequencing as the basis of evidence. The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics 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 position is 100% remote and the professional must be located in the US. • Execute and improve sequence analysis workflows and automation • Track, troubleshoot and mitigate issues encountered in processing production samples • Assist in planning and development of solutions to recurring issues to be merged back into development branch maintained by the Engineering group • Develop web-based results display and dashboards for clinical geneticists, medical directors and operations lab personnel providing clarity in our process • Generate, wrangle, merge and glean information from varied and complex data sets Design and implementation 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 validation analysis for new genomic testing products. • Support production day-to-day operations • Write and maintain production documentation for compliance and supportability of all bioinformatics processes in production environment • Work directly with medical/quality/compliance to identify, track, resolve and report on any relevant quality-related issues • Produce charts and visualization for dashboards, reporting, and in support of data driven hypothesis testing • Perform LIS support duties (maintain database for user, tests, clients….) • 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 • * 5 years experience using formal programming and scripting languages • 5 years experience working on a Linux command-line to process, parse, and merge varied data sets • 2 years experience working with web services and implementing API communications (REST, SOAP, etc.) • 3 years experience in a distributed HPC environment (cluster, cloud) • Knowledge and understanding of genomics, next-generation sequencing, and bioinformatics • Experience developing and testing software • Experience with source control in a development, testing, and production environment • Automated testing experience; CI/CD experience preferred • Knowledge of CAP documentation requirements a plus • Experience communicating technical results and data is desirable Current tech stack experience is a plus Examples: • Programming Languages: Python, PERL, Groovy, javascript, terraform • Web Frameworks: Python Flask, React Native, Bootstrap • Environments: R Statistical Language, iPython, Jupyter • Visualization: Plotly, matplot lib, ggplot2/tidyverse, Tableau, d3.js • Database: SQL (e.g., postgress, MySQL), MongoDB • Cloud Computing: AWS • Infrastructure management: terraform • Pipeline Workflow Manager: Nextflow • Source Control: Git • CI/CD: Gitlab, AWS CDK • Containerizing: Docker • Microsoft UI: Access, VBA, Macros Education: Bachelor’s Degree - Required Master’s Degree or PhD - Preferred Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets or any other legally protected status.

Overview Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. With a track record of global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy and COVID-19 vaccines, Fred Hutch has earned a reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality. At Fred Hutch we value collaboration, compassion, determination, excellence, innovation, integrity and respect. Our mission is directly tied to the humanity, dignity and inherent value of each employee, patient, community member and supporter. Our commitment to learning across our differences and similarities make us stronger. We seek employees who bring different and innovative ways of seeing the world and solving problems. The laboratory of Dr. Xueqiu Lin in the Computational Biology Program of the Public Health Sciences and Human Biology Divisions has an open position for a Bioinformatics Analyst I/II. We are seeking a highly motivated individual who will bring their knowledge and computational skills to the study of cancer functional genomics. Candidates who are excited to be part of a team working on computational/statistical model development and large/complex ‘omics’ data analysis of cancer genomes to study cancer are encouraged to apply. Please visit the lab website for more information: https://research.fredhutch.org/lin/en.html. The position has a competitive salary with great benefits. The Lin Laboratory uses CRISPR screen technologies, computational genomics, and interpretable deep learning models to study cancer risk and to advance precision medicine. We are building on this strong computational program by implementing wet-lab operations in a fully renovated laboratory space in the Lake Union Steam Plant Building, the newest Fred Hutch facility. The Steam Plant building is home to 23 laboratories consisting of 275 experts in computational biology, data science, and immunotherapy who use cutting-edge technologies and tools to revolutionize cancer treatment. We work in an interdisciplinary team environment with many local and external experts. All our projects involve partnering with investigators and laboratories who have diverse expertise in computational, genomic, molecular, experimental, and cancer biology, and in clinical research. The study areas for this position center on genomic regulation, single cell sequencing, chromatin and epigenetic profiling, cancer GWAS studies, high-throughput CRISPR screening and translation of cancer biomarkers to improve treatment strategies and develop CRISPR targeted therapy. The Bioinformatics Analyst I/II will work under the direction of the senior computational scientist to develop deep learning models and algorithm for deciphering the logic of regulatory code, work on a variety of bioinformatics analysis projects including bioinformatics method and software development; executing, improving, and developing bioinformatics pipelines based on evaluation of computational tools and reference databases; and working with experimental researchers to conduct and report data analysis using principles of good statistical scientific practice and reproducible research. Candidates with strong interest and/or expertise in any of these research areas are highly encouraged to apply • Application of statistical modeling, algorithm design, deep learning, machine learning and explainable artificial intelligence to study cancer and genetics. • Gene regulation, gene regulatory elements, cancer genomics, epigenetics, CRISPR high-content screen, genotype-environment interaction. • Analysis of large, complex CRISPR screen, genome, epigenome or transcriptome data To apply, please submit your application with the following: • Cover letter describing your experience and/or research interests is required. • Curriculum vitae • Example of your code either as (1) an attachment or (2) link(s) to public repositories (e.g. GitHub) Responsibilities The research interests/projects and responsibilities for this Analyst position in the Lin lab include: Bioinformatics Analyst I • Support and assist the senior computational scientist to develop deep learning models and implement algorithms. • Assist in the development and refinement of data analysis and integration methodologies and pipelines. • Generate figures and tables summarizing data outputs. • Work with research team to document, process, manage and store large datasets. • Developing and testing bioinformatics software. Bioinformatics Analyst II: • Interpret complex biological information, conduct statistical and genomic analysis. • Implement and maintain best practices in large-scale data management and database development. • Write custom scripts to access databases, perform and evaluate quality control and analyze Next Generation Sequencing (NGS) data. • Analyze FFPE-CUTAC to identify non-coding genomic mutations and interpret their function in oncogenic regulatory networks for novel biomarker identification and risk model development. • Develop and implement computational approaches to assist the design and development of high-throughput CRISPR screening. • Integrate the high-throughput CRISPR screening data with multi-omics data. • Prepare figures and written sections to document methods and results for manuscripts, presentations, and grant applications. • Engage in bioinformatics literature to ensure the availability of robust methods, resources, and data sources. • Present work at group meetings as well as occasional larger scientific meetings and contribute to scientific publications. Qualifications MINIMUM QUALIFICATIONS: Bioinformatics Analyst I: • Bachelor’s degree in one of these disciplines: Computer science, mathematics, statistics, physics, biostatistics, data science, bioinformatics, computational biology, computer/electrical engineering, or other related fields with at some prior experience applying computation analysis of large sequence-based molecular data in an academic research lab or industry setting. • Up to 2 years of experience with analyzing genome sequencing data. • Strong programming skills in R and Python. Bioinformatics Analyst II: All minimum qualifications from Level I, plus: • 3 years relevant experience, or a master’s degree with at least 1 year of relevant experience outside of the degree requirements PREFERRED QUALIFICATIONS: • Previous experience working with deep learning or statistical modeling • A background in cancer genomics • Experience working in and developing workflows for cloud computing environments • Experience with high performance computing environments • Strong skills in implementation of analytical tools at scale • Works well in team environments; strong communication skills; detail-oriented • Experience with pipeline management tools (Snakemake, WDL, Nextflow) Bioinformatics Analyst I: The annual base salary range for this position is from $77,976 to $102,211, and pay offered will be based on experience and qualifications. Bioinformatics Analyst II: The annual base salary range for this position is from $78,894 to $118,310, and pay offered will be based on experience and qualifications. This position may be eligible for relocation assistance.Fred Hutchinson Cancer Center offers employees a comprehensive benefits package designed to enhance health, well-being, and financial security. Benefits include medical/vision, dental, flexible spending accounts, life, disability, retirement, family life support, employee assistance program, onsite health clinic, tuition reimbursement, paid vacation (12-22 days per year), paid sick leave (12-25 days per year), paid holidays (13 days per year), paid parental leave (up to 4 weeks), and partially paid sabbatical leave (up to 6 months). Additional Information We are proud to be an Equal Employment Opportunity (EEO) and Vietnam Era Veterans Readjustment Assistance Act (VEVRAA) Employer. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability (physical or mental), marital or veteran status, genetic information, sexual orientation, gender identity, political ideology, or membership in any other legally protected class. We desire priority referrals of protected veterans. If due to a disability you need assistance/and or a reasonable accommodation during the application or recruiting process, please send a request to Human Resources at hrops@fredhutch.org or by calling 206-667-4700.

Job Title: Bioinformatics Scientist - III Location: Cambridge, MA Duration: 24 Months 02 Openings: 1 focusing on Genomic data & 2nd is for (Multi-Omics data & Transcriptomics analysis) Department: Data and Genome Sciences Group: Precision Genetics The Precision Genetics group within the Data and Genome Sciences Department is seeking a skilled Contractor to join our Computational Precision Genetics team. We are looking for a data scientist with extensive experience in genetic data analysis to contribute to our innovative research efforts. Key Responsibilities: • Data Ingestion: Query external databases to acquire relevant genetic/genomic datasets (e.g., dbSNP, 1000 Genomes Project, gnomAD, GTEx, Ensembl, Open Targets, ClinVar). • Genetic/Genomic Data Analysis: Perform quality control (QC) and analysis of genetic/genomic data, including genotype imputation from array data, variant calling and annotation using state-of-the-art methods (e.g., IMPUTE, Minimac, Eagle, BEAGLE, GATK, bcftools, samtools, ANNOVAR). • QTL Analysis: Conduct QTL analysis to identify genetic loci associated with quantitative traits, utilizing tools such as PLINK, R/qtl, or TASSEL. • Population Genetics Analysis: Analyze genetic variation across populations, including allele frequency estimation, linkage disequilibrium, and population structure analysis. • Data Integration: Integrate genetic datasets with other omics data, including genomic, epigenomic, transcriptomic and proteomic data, to provide comprehensive insights into gene function and regulation. • Documentation: Prepare detailed documentation of analysis methods and results in a timely manner. Quals: Required Qualifications, skills and experience: • Minimum: Ph.D. in Genetics, Genomics, Computational Biology, or a related field. • A proven track record of over 5 years in genetic data analysis. • Fundamental understanding of statistical methods and genetic data analysis and integration (e.g., variant analysis, population genetics, genomic annotations). • Proficiency in R, Python, and Bash, with the ability to establish best practices for reproducible data analyses. • Experience with high-performance computing (HPC) systems and AWS Cloud Computing (e.g., IAM, S3 buckets). • A collaborative and self-motivated individual with a strong work ethic, capable of managing multiple objectives in a dynamic environment and adapting to changing priorities. • Excellent written and verbal communication skills. Preferred Qualifications: • Experience with real-world genetic data processing and analysis. • Proficient in genetic/genomic data analysis tools and techniques. • Understanding of statistical genetics principles and methods. • Expertise in AI/ML. Note: • Onsite role at Cambridge, MA. • Do not submit candidates who are looking for remote. • Do not submit candidates with just BS/MS. Key skills: • Proficient in genetic/genomic data analysis tools and techniques-e.g., variant analysis, population genetics, genomic annotations. • Proficiency in R, Python, and Bash. • High-performance computing (HPC) systems and AWS Cloud Computing (e.g., IAM, S3 buckets).

At GSK, we have bold ambitions for patients, aiming to positively impact the health of 2.5 billion people by the end of the decade. R&D is committed to discovering and delivering transformational vaccines and medicines to prevent and change the course of disease. We believe the Greater Boston area is an important hub for the biotech and pharma industry, which is why we've invested in growing our footprint and expanding our R&D space in Cambridge, with a primary focus on additional state-of-the-art lab space. Here, we will bring together talent and expertise, building upon GSK's long history of vaccine development, to create globally leading viral capabilities and cutting-edge vaccines technologies, as we add to our robust portfolio targeting infectious diseases at every stage of life. In the plan to create a new hub for mRNA-based vaccine discovery in Cambridge, we are building new laboratories that will be focused on the development of state-of-the-art methods that will be supporting deep product understanding, process and product development, as well as testing of pre-clinical and clinical samples for new mRNA-based vaccines. As a Principal Bioinformatics Scientist in the Molecular Analytics team, you will be expected to contribute toward our omics-based program supporting our mRNA-based vaccine discovery efforts. You will join our diverse preclinical research and development team working on cutting-edge technologies in addition to developing new assays suitable for candidate screening and mechanism of action studies. Key Responsibilities: • Design, develop, optimize, and implement next-generation sequencing (NGS) analysis pipelines for the characterization of RNA and DNA molecules of interest for vaccine research and development, and their mechanism of action. • Execute a wide range of traditional computational tasks, such as sequence identity and variant calling analysis, vector integration site analysis, gene expression profiling (bulk, single cell, spatial) from data generated across sequencing platforms, e.g. short and long read sequencers. • Analyze, interpret, and record experimental results and present them in written/oral communications. • Build statistical models and/or machine learning algorithms to extract features of interest. • Develop, and execute new methods and protocols and proactively incorporate new technology or techniques into practice with minimal supervision. • Collaborate with scientists throughout the organization to support NGS activities. • Perform complex data management tasks with supervision. • Lead vaccine development-related scientific investigations and publish the work in scientific journals and patent filings. Basic Qualifications: • Degree in bioinformatics, computational biology, systems biology, data or computer science, applied math, statistics, or related scientific field. • PhD with 3+ years of post-doc and/or job-related experience, MS with 6+ years of experience, or BS with 9+ years of experience. • Five or more years of academic or industry experience in computational biology or bioinformatics, along with genomics, epigenomics, or transcriptomics. • Five or more years of experience in programming (R and Python) and computational environments (Linux, HPC, cloud computing). • Five or more years of experience handling NGS data. • Five or more years of experience in next-generation sequencing technologies (Illumina, Pacific Biosciences, Oxford Nanopore) and their applications, e.g., bulk RNA-seq, single cell omics, immune repertoire profiling. Preferred Qualifications: • Proficiency in single cell and spatial omics data analysis and interpretation, using data generated from commercially available technologies such as 10x Genomics, Parse Bio, Scale Bio. • Proficiency in long-read sequencing data analysis from PacBio or ONT platforms. • Working knowledge of molecular and cell biology. • Effective written and oral communication skills as well as presentation skills. Fluency in English. • Must be detail oriented; possess problem solving skills, and the ability to handle multiple tasks. • Able to efficiently manage uncertainty, changes in priorities and timeline restrictions. • Experience in advanced statistics and AI/ML. • Hands-on experience in molecular and cell biology related to NGS, including but not limited to: Nucleic acid extraction, PCR, library preparation, and sequencing. • Experience in developing fully custom NGS analysis pipelines. #Vx-Cam #Li-GSK Please visit GSK US Benefits Summary t o learn more about the comprehensive benefits program GSK offers US employees. Why GSK? Uniting science, technology and talent to get ahead of disease together. GSK is a global biopharma company with a special purpose - to unite science, technology and talent to get ahead of disease together - so we can positively impact the health of billions of people and deliver stronger, more sustainable shareholder returns - as an organisation where people can thrive. We prevent and treat disease with vaccines, specialty and general medicines. We focus on the science of the immune system and the use of new platform and data technologies, investing in four core therapeutic areas (infectious diseases, HIV, respiratory/ immunology and oncology). Our success absolutely depends on our people. While getting ahead of disease together is about our ambition for patients and shareholders, it's also about making GSK a place where people can thrive. We want GSK to be a place where people feel inspired, encouraged and challenged to be the best they can be. A place where they can be themselves - feeling welcome, valued, and included. Where they can keep growing and look after their wellbeing. So, if you share our ambition, join us at this exciting moment in our journey to get Ahead Together. If you require an accommodation or other assistance to apply for a job at GSK, please contact the GSK Service Centre at 1-877-694-7547 (US Toll Free) or +1 801 567 5155 (outside US). GSK is an Equal Opportunity Employer. This ensures that all qualified applicants will receive equal consideration for employment without regard to race, color, religion, sex (including pregnancy, gender identity, and sexual orientation), parental status, national origin, age, disability, genetic information (including family medical history), military service or any basis prohibited under federal, state or local law. Important notice to Employment businesses/ Agencies GSK does not accept referrals from employment businesses and/or employment agencies in respect of the vacancies posted on this site. All employment businesses/agencies are required to contact GSK's commercial and general procurement/human resources department to obtain prior written authorization before referring any candidates to GSK. The obtaining of prior written authorization is a condition precedent to any agreement (verbal or written) between the employment business/ agency and GSK. In the absence of such written authorization being obtained any actions undertaken by the employment business/agency shall be deemed to have been performed without the consent or contractual agreement of GSK. GSK shall therefore not be liable for any fees arising from such actions or any fees arising from any referrals by employment businesses/agencies in respect of the vacancies posted on this site. 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Overview Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. With a track record of global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy and COVID-19 vaccines, Fred Hutch has earned a reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality. At Fred Hutch we value collaboration, compassion, determination, excellence, innovation, integrity and respect. Our mission is directly tied to the humanity, dignity and inherent value of each employee, patient, community member and supporter. Our commitment to learning across our differences and similarities make us stronger. We seek employees who bring different and innovative ways of seeing the world and solving problems. The Bioinformatics Analyst I-II will provide data analysis services to researchers in the Dhodapkar lab, particularly focusing on single cell genomics, integration of high-dimensional immunologic data and genome sequencing. This position requires the ability to work independently, manage multiple overlapping demands, and communicate effectively with faculty, post-doctoral fellows, and research staff on a wide range of topics in biology, analytical biochemistry, sound experimental design, and data science. The Bioinformatics Analyst works closely with Shared Resources cores, especially Genomics and Hutch Data core, to ensure that data quality is high and that users have access to advice and continuing dialog as they review results. Given the large volumes and diverse types of data generated and integrated in Bioinformatics projects, practical applied programming skills are also essential. At Fred Hutchinson Cancer Center, all employees are expected to demonstrate a commitment to our values of collaboration, compassion, determination, excellence, innovation, integrity, and respect. Responsibilities • Analyze large sequence datasets from diverse workflows including exome capture, RNA-seq, single cell sequencing, ATAC-seq, and CRISPR screens. • Work with Hutch scientists to refine computational research questions and develop analytical processes that can be applied to these genomic datasets. • Consult with researchers on sound experimental design. • Identify appropriate bioinformatics tools to meet the needs of proposed projects. • Partner with researchers who are developing novel assays to design appropriate processing and analysis workflows. • Review current literature to identify and adopt software and methodologies, making new analysis capabilities available to the team. • Provide figures and written sections to document methods and results for manuscripts, presentations, and grant applications. • Collaborate with colleagues in the Genomics Shared Resource and the Hutch Data Core to ensure the integrity and consistency of primary data, track experimental methods and metadata, define standardized analysis pipelines, and provide support as stakeholders analyze and interpret results. • Train laboratory members and collaborators on analytic workflows. • Upload and maintain datasets, workflows, and code (for example GEO, Github). • Other duties as assigned. Qualifications MINIMUM QUALIFICATIONS Bioinformatics Analyst I: • Bachelor’s degree in bioinformatics, computational biology, genetics, or related field. • Some experience in computational analysis of large, complex sequence-based molecular data sets. • Demonstrated proficiency in R and Python 3 are essential. • Familiarity with workflow and scheduling software (e.g., Slurm). • Excellent written and verbal communication skills. Bioinformatics Analyst II: • Bachelor’s degree in bioinformatics, computational biology, genetics, or related field with at least three years’ direct experience in computational analysis of large sequence-based molecular data sets. • Direct experience must include best-practice germline & somatic variant calling from exome capture data, analysis of bulk RNA-seq data with multiple contrasts, analysis of multimodal single-cell profiling data, epigenetic profiling, gene set enrichment, and integration of data across multiple modalities (e.g., epigenetic profiling and RNA-seq). • Effective use of shell scripting and significant fluency in R and Python 3 are essential. • Facility with commonly used Bioconductor packages, ggplot, tidyverse etc. • Ability to generate and customize common data visualizations (PCA plots, volcano plots, Circos plots, etc). • Familiarity with workflow and scheduling software (e.g. Slurm). • Excellent written and verbal communication skills are absolutely required. PREFERRED QUALIFICATIONS Bioinformatics Analyst I: • A year of more of direct experience in computational analysis of large, complex sequence-based molecular data sets. Bioinformatics Analyst II: • Master’s degree in bioinformatics, computational biology, genetics, or related field. • Two+ years of experience in software development, data engineering, data science, or related field with a track record of manipulating, processing, and extracting value from large datasets. • Experience with single cell transcriptomic analyses and associated pipelines. (e.g. Seurat). • Direct experience includes whole exome sequencing, and integration of data across multiple modalities (e.g., TCR-seq, CITE-seq, ChIP-seq, ATAC-seq, and CRISPR/Cas9 knockout screens). Bioinformatics Analyst I: The annual base salary range for this position is from $77,976 to $102,211, and pay offered will be based on experience and qualifications. Bioinformatics Analyst II: The annual base salary range for this position is from $78,894 to $118,310, and pay offered will be based on experience and qualifications. Fred Hutchinson Cancer Center offers employees a comprehensive benefits package designed to enhance health, well-being, and financial security. Benefits include medical/vision, dental, flexible spending accounts, life, disability, retirement, family life support, employee assistance program, onsite health clinic, tuition reimbursement, paid vacation (12-22 days per year), paid sick leave (12-25 days per year), paid holidays (13 days per year), paid parental leave (up to 4 weeks), and partially paid sabbatical leave (up to 6 months). Additional Information We are proud to be an Equal Employment Opportunity (EEO) and Vietnam Era Veterans Readjustment Assistance Act (VEVRAA) Employer. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability (physical or mental), marital or veteran status, genetic information, sexual orientation, gender identity, political ideology, or membership in any other legally protected class. We desire priority referrals of protected veterans. If due to a disability you need assistance/and or a reasonable accommodation during the application or recruiting process, please send a request to Human Resources at hrops@fredhutch.org or by calling 206-667-4700.

Bioinformatics Scientist II – AI Applications The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science. The mission of the Allen Institute for Immunology is to advance the fundamental understanding of human immunology through the study of immune health and diseases where excessive or impaired immune responses drive pathological processes. The Institute will employ a multi-disciplinary team approach in collaboration with academic centers of human immunology to generate novel mechanistic insights into the immune synapse in health and in diseases such as autoimmunity or oncology. The Institute will simultaneously provide a foundational data set and tools for future immunological research as well as a novel collaboration portal for the broader scientific community. The Allen Institute for Immunology is seeking a Bioinformatics Scientist II – AI Applications to train AI models using our enormous multimodal omics data. Reporting to the Director of Informatics & Computational Biology at the Allen Institute for Immunology, the ideal candidate is a self-motivated team player who can work closely with immunologists and bioinformaticians, is an expert in applying AI methodologies for biological/medical research and has a track record of training transformer models. The successful candidate will also have excellent communication skills that can represent our efforts to our stakeholders internally and in external forums. At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment. We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions. Essential Functions • Train AI models (e.g. transformers and variational autoencoders) based on multimodal OMICS data, including but not limited to: spatial transcriptomics, scRNA-seq, scATAC-seq, CITE-seq, TEA-seq, flow cytometry, and proteomics • Apply AI methodologies to generate testable hypotheses for new biological insights, and identify potential biomarkers and/or drug targets for disease of interest • Write reports, research papers, patent applications, and other documents • Represent our efforts to our stakeholders internally and in external forums • Contribute to a rigorously scientific, cohesive and efficient team environment Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned. Required Education and Experience • PhD in computer science, applied mathematics, bioinformatics, biostatistics, computational biology, or closely related disciplines; or equivalent combination of education and experience • Three (3) + years of post-degree experience Preferred Education and Experience • Demonstrated experience in training AI models, including but not limited to: large language models (LLMs), transformers, variational autoencoders, neutral networks, etc. • Experience in applying AI methodologies for biological/medical research • Demonstrated experience in leading research projects • Familiar with OMICS technologies • Foundational knowledge of AI methodologies and bioinformatics • Experience with R and/or Python • Strong publication record • Familiar with advanced statistical methods and machine learning for biomarker discovery • Experience working in a cross-disciplinary, team-based environment • Experience working with outside collaborators to achieve defined objectives • Familiarity with cloud computing and/or Linux • Experience using Git or similar version control system • Excellent written and verbal communication skills and organizational skills • Good problem-solving skills, curious and eager to take new challenges • Able to work independently as well as in a collaborative high paced environment • The successful candidate must be self-motivated, a team player, attentive to details, and able to handle multiple projects simultaneously Work Environment • May enter laboratory environment - possible exposure to chemical, biological, or other hazardous substances. Physical Demands • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment Position Type/Expected Hours of Work • Occasional evening and weekend hours required • This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State. Travel • Attendance and participation in national and international conferences may be required Additional Comments • **Please note, this opportunity offers relocation assistance** • **Please note, this opportunity offers work visa sponsorship** Annualized Salary Range • $111,300 - $137,700 * • Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable. Benefits • Employees (and their families) are eligible to enroll in benefits per eligibility rules outline in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits. It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.

At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people. Quest Diagnostics Specialty Genetics products provide specific answers that clinicians need to deliver the appropriate diagnostic and prognostic care to their patients. You will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing. This position is in our Bioinformatics Solutions Engineering group, part of the Research and Development organization, in Molecular Genomics & Oncology unit. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment primarily using short and long-read sequencing as the basis of evidence. The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics Solutions Engineering group is a cross-functional unit focusing on end-to-end design, develop, document, validation and launching of new high quality diagnostic tests and services for the benefit our patients. This professional can work in a 100% remote capacity and must be located in the US. • Lead technical design, implementation and delivery of projects aiming to launch new diagnostic tests and services. Act as technical owner for your project, being responsible for the end-to-end solution from technical side. • Work with cross-functional partners from business, operations, IT, R&D lab, geneticists, medical directors, and other bioinformatics stakeholders to create solutions that meet business and operational requirements. • Lead solution architecture and interface design including system architecture for bioinformatics and detailed data flow mapping. • Collaborate with stakeholders to ensure compliance of the solution with internal and external IT security and clinical policies and processes. • Work with bioinformatics domain leaders to select appropriate technology platforms for each step in the diagnostic process. • Oversee end-to-end testing and diagnostic test validation activities with the project team. • Lead the technical documentation and plan and execute handover to operations to ensure effective launch and operation of the solution. • Work with project management and report on progress, analyze risks and escalate issues to ensure accurate project management. Required Work Experience: • BS with 7+ years of experience, MS with 4+ years of experience, or PhD with 3+ years of experience in an industrial or academic setting working with clinical and biological data or equivalent and underlying technologies including bioinformatic methods, database development, query/scripting/programming languages, cloud development, agile methodology, DevOps and other data analysis tools. • At least 5 years of experience working in a regulated industrial life sciences environment. • At least 4 years of professional software development or technical engineering experience Preferred Work Experience / Skills: • Thorough understanding of end-to-end diagnostic process including ordering, wet lab, dry lab, result interpretation and result and data delivery. • Experience with solution design, system architecture, solution architecture, data flow modeling. • Experience in leading technical design and implementation of complex projects. • Experience with sequencing data analysis, bioinformatics, variant data analysis. • Knowledge of bioinformatics tools and workflow managers for sequencing data analysis and quality control. • Experience working with SQL and NoSQL databases. • Experience with designing and working with application programming interfaces (e.g. JSON based RESTful APIs). • Experience with designing and implementing solutions in the cloud. AWS experience is preferred. • Experience of working in clinical diagnostics setting (regulations, controlled processes, diagnostic test validation, environment management). • Solid understanding of human genetics and oncology in diagnostic setting. • Solid understanding of web lab process for DNA sequencing and working with or developing LIMS systems. • Infrastructure management: Terraform, AWS CDK. • Architecture design: Microsoft Visio, DrawIO, similar for crafting architecture diagrams. • Programming Languages: Python, javascript/typescript, R, etc. • Containerizing: Docker • Web Frameworks: Python Flask, React Native, Bootstrap • Reporting: R Markdown, Jupyter Notebook • Visualization: Experience with any of ggplot2/tidyverse, Plotly, matplot lib, Tableau, d3.js • Source Control: Git • CI/CD: Gitlab CI/CD, Github CI/CD Education: Bachelor’s Degree Required Master’s Degree or PhD Preferred Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets or any other legally protected status.

About the position We are seeking a passionate scientist with a background in "omics" data analysis to join our team at Washington University School of Medicine. This position is part of a collaboration between the laboratories of Dr. Mayssa Mokalled and Dr. Aaron Johnson. The successful candidate will utilize innovative bioinformatics, machine learning, and statistical approaches to support NIH-funded research projects focused on the mechanisms regulating spinal cord repair and muscle regeneration. The project encompasses conducting analyses on next-generation sequencing data, as well as single-cell genomics, single-cell transcriptome data, and spatial transcriptomics. Highly motivated individuals will have the opportunity for advancement within this dynamic research environment. The Mokalled and Johnson labs are committed to mentoring and nurturing a creative, thoughtful, and collaborative lab culture. Located in the Department of Developmental Biology at Washington University School of Medicine in St. Louis, these laboratories are part of an internationally recognized research institution consistently ranked among the top five medical schools in the country. The extreme collegiality of Washington University, combined with the large Regenerative Medicine Community and extensive infrastructural and core facility support, creates a vibrant research environment in many areas of regenerative biology. This is an especially exciting time to join the Mokalled and Johnson labs, as they are expanding into fully funded and new research directions at the cutting edge of spinal cord and muscle regeneration. This position also offers opportunities for publications and conference presentations, enhancing the professional development of the appointee. Responsibilities • Implements algorithms and computer software for analyzing omics-based data sets, including high-throughput, massively parallel genomic/proteomic/clinical data. , • Develops data management and analysis solutions that aid in the storage, investigation, and dissemination of large data sets. , • Coordinates research projects with other investigators and institutions. , • Participates in developing hypotheses and experimental design. , • Assists with reporting of methods, data, and results. Requirements • Bachelor's degree in computer science, bioinformatics, biostatistics, or related field plus two years of experience; OR a master's degree in computer science, bioinformatics, biostatistics, or related field; OR combined education and experience of seven years. , • Good understanding of computational biology. , • Ability to analyze and interpret large complex data sets, such as genome sequencing, microarray gene expression studies, human genetic studies, and model organism studies. , • Expertise in standard bioinformatics tools. Nice-to-haves • Analytical, reasoning, and problem-solving skills. , • Ability to communicate data in a clear, concise manner. Benefits • Up to 22 days of vacation, 10 recognized holidays, and sick time. , • Competitive health insurance packages with priority appointments and lower copays/coinsurance. , • Free Metro transit U-Pass for eligible employees. , • Forgivable home loan of up to $12,500 for closing costs and down payment for homes in eligible neighborhoods. , • Defined contribution (403(b)) Retirement Savings Plan with university contributions starting at 7%. , • Wellness challenges, annual health screenings, mental health resources, mindfulness programs, and employee assistance program (EAP). , • 4 weeks of caregiver leave to bond with a new child. , • Tuition coverage for employees and their families, including dependent undergraduate-level college tuition up to 100% at WashU and 40% elsewhere after seven years.

What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients. Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible. The Senior Bioinformatics Scientist will work in a collaborative, cross-functional environment to drive the development of existing and new sequencing technologies. In this role, they will design and implement pipelines for data quality assessment, provide actionable insights from experimental data, and contribute to defining Illumina’s R&D data quality and product strategy. Responsibilities: • Plan and execute quality assessments for existing and novel sequencing technologies. • Collaborate with subject matter experts across R&D functions to understand, define, and communicate sequencing technology requirements for research and clinical applications. • Design, deploy, and optimize pipelines for secondary analysis and quality assessment of sequencing data. • Contribute to the development of automated testing infrastructure. • Drive the analysis, integration, modeling, and interpretation of experimental data. • Translate complex analysis results into actionable recommendations for technology development and improvement. Present results clearly and effectively to both technical and non-technical stakeholders. • Stay current on the latest publications and relevant research and identify established methods that should be incorporate into method development. Requirements: • Strong understanding of next-generation sequencing technologies and their underlying principles. • Proficient programming skills with experience in one or more languages, such as Python or R. • Experience working with Unix/Linux and High Performance Computing (HPC) environments. • Proficiency with common bioinformatics algorithms and methods. Hands on experience of quality control and analysis of data generated from a variety of omics, such as WGS, scRNA, somatic profiling, proteomics, methylation, etc. • Solid understanding of statistical and biological concepts; strong data analysis and visualization skills. • Strong data analysis and visualization skills. Desired: • Experience working with cloud environments (e.g., AWS). • Experience with workflow management languages, such as Nextflow, WDL, etc. • Familiarity with containerization tools, such as Docker, and similar technologies. • Excellent communication skills and a proven track record of collaborating with diverse teams. Education: • Masters/PhD in bioinformatics, computer science, data science, engineering, mathematics or equivalent • Typically requires a minimum of 3 years of related experience with a Master’s degree; or a PhD with 0-3 years of experience; or equivalent experience #LI-HYBRID The estimated base salary range for the Sr Bioinformatics Scientist role based in the United States of America is: $126,800 – $190,200. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off. At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and demonstrate our collective commitment to diversity and inclusion in the communities we live and work. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. If you require accommodation to complete the application or interview process, please contact accommodations@illumina.com. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship. Tagged as: Computer Science, Data Science, Life Sciences

Scientist I – Computational Biology and Bioinformatics The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science. Join the Seattle Hub for Synthetic Biology (SeaHub), a new initiative at the intersection of academic creativity and start-up style execution. Our mission is to reimagine living cells and genomes as devices for recording biology and diagnostic information over time, as well as for encoding real-time therapeutic decision-making. Take off with us as we imagine — and create — a kind of cellular flight recorder that can also seize the controls. Be part of a small dynamic team on the ground floor of a new program with world-class scientists. SeaHub is looking for a Scientist I, Computational Biology and Bioinformatics for the “Read” team. The computational biologist should have a very strong background in each of two areas: 1) next-generation genomic technology development methodology and 2) writing ad hoc and bespoke bioinformatics scripts in Python and R to do detailed bioinformatics analyses of next-generation sequencing data. The role will include leading the effort to process and analyze large amounts of diverse sets of sequencing data (both short-read and long-read) to draw conclusions from wet lab experiments, in close collaboration with teams focused on expanding our abilities to engineer cells and genomes to autonomously “Write,” “Sense,” and “Act” at a molecular level. The successful candidate will play a key role in advancing our ability to record lineage and signaling information in the genomes of mammalian cells. This position requires a collaborative mindset, timeline-management abilities, and the ability to work cross-functionally with other research teams to drive project success. At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment. We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions. Essential Functions • Develop next-generation sequencing analysis scripts and pipelines that run on cloud-based architectures (CodeOcean, AWS) • Manage cloud-based data transfer and storage on AWS and other cloud-based servers • Independently perform in-depth bioinformatics analyses on generated sequencing data from wet lab experiments and work with experimental teams to guide project direction • Develop and disseminate written reports summarizing data processing and analysis results and findings with a reasonable turnaround time • Develop bespoke computational biology tools and bioinformatics scripts as needed to advance internal research projects • Follow industry software development and bioinformatics best practices - participate in code reviews, version code, track issues, and write proper documentation • Troubleshoot technical barriers to progress in the reading of synthetic records • Maintain a detailed electronic notebook and create presentations to summarize progress and frame internal decision-making • Mentor and motivate others to perform the above functions Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned. Required Experience and Education • PhD in genetics, genomics, computational biology, bioinformatics, or related field; or equivalent combination of education and experience • Very strong coding ability in R and python Preferred Education and Experience • 0 – 5 years relevant post-doc experience • Expertise in functional genomics and screening, single cell genomics, synthetic biology, or related domains, including demonstrated mastery of molecular biology • Track-record of working as part of a team and understanding the importance of team dynamics • Understanding how data is generated from wet lab experiments in a molecular biology / cell culture laboratory • Expertise with AWS and CodeOcean cloud computing • Outstanding scientific achievement • Experience with molecular biology, mammalian cell culture, stem cell culture, developmental biology or immunology, genomics, and mouse genetics • Experience with lineage tracing algorithm development • Excellent written and verbal communication skills • Strong project management and organizational skills • Excellent analytical and problem-solving skills combined with capacity for complex, detail-oriented work Physical Demands • Fine motor movements in fingers/hands to operate computers and other office equipment Position Type/Expected Hours of Work • This role is currently working onsite and is expected to work onsite for the majority of the working hours. We are a Washington State employer, and the primary work location for Allen Institute employees is 700 Dexter Ave N.; any remote work must be performed in Washington State. Travel • The successful applicant may be invited to attend occasional national and international conferences Additional Comments • **Please note, this opportunity offers relocation assistance** • **Please note, this opportunity offers work visa sponsorship** Annualized Salary Range • $90,900 - $112,400 * • Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable. Benefits • Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institute’s Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits. It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.