Bioinformatics Jobs

The Position Genentech, a member of the Roche group and founder of the biotechnology industry, is dedicated to pursuing groundbreaking science to discover and develop medicines for people with serious and life-threatening diseases. To solve the world's most complex health challenges, we ask bigger questions that challenge our industry and the boundaries of science to transform society. Our... transformational discoveries include the first targeted antibody for cancer and the first medicine for primary progressive multiple sclerosis. Diversity and Inclusion (D&I) are critical to the success of our company and our impact on society. We believe that by championing diversity of background, thought and experience, we can foster a sense of belonging and provide an environment where every employee feels valued, included, and able to contribute their best for the patients we serve. We’re focused on attracting, retaining, developing and advancing our people to their full potential by rewarding bold ways of thinking and integrating inclusive behaviors into every aspect of our work. This position is part of the Pharma Individualized Medicines Team responsible for the process development, manufacture and supply of personalized immunotherapies in collaboration with our global partners. Job Summary: This position is part of the Pharma Cell and Gene Therapy team responsible for the process development, manufacture and supply of next generation immunotherapies in collaboration with our global partners. We are seeking a highly motivated team member to contribute to the ongoing effort to evaluate and operationalize bioinformatics aspects of individualized medicine manufacturing. You will represent the production team at cross-functional team meetings. The successful candidate is expected to effectively communicate and develop collaborative relationships with key stakeholders. You will play a critical role in building compliant, production scale bioinformatics software to enable commercial manufacturing of next generation individualized therapeutics. Responsibilities Provide operational and strategic software engineering support needed for bioinformatics functions within Genentech’s Cell and Gene Therapy programs. You will play a critical role in enabling a new manufacturing paradigm for Roche/Genentech that includes next-generation sequencing and advanced bioinformatics techniques to deliver individualized immunotherapeutics to patients. You will be expected to take ownership, provide guidance and feedback on bioinformatics pipeline development and deployment to cross functional teams. Ensure alignment of bioinformatics milestones with those of the broader team. Serve as the single point of contact to key stakeholders to execute on jointly defined deliverables, from project kick-off to method implementation. Key responsibilities include • Architecting NGS bioinformatics pipelines to run in a cloud infrastructure. • Developing compliant cloud architecture to process patient NGS data. • Testing and deploying a variety of bioinformatics pipelines into a production environment. • Reviewing and refactoring bioinformatics code (in R and Python) according to best software practices. • Software engineering/QA aspects of the production bioinformatics pipelines. ​Qualifications The ideal candidate will meet the following qualifications: • MS/PhD in life sciences or computer science, with minimum 5 years of experience with NGS bioinformatics. • Exceptional coding skills in R and Python, preferably in the context of cancer bioinformatics. • 3 years experience in developing cloud (AWS) based compute platforms. • Experience working with at least one workflow orchestration software (Nextflow, Cromwell, etc) • Experience with developing in cloud environments using Docker or similar containerization packages. • Deep knowledge of the AWS platform, with background in using AWS to deploy infrastructure. • Experience with compute orchestration software such as AWS Batch, Kubernetes, or other. • Experience with deploying infrastructure as code (Terraform, Cloudformation). • Experience with HPC environments. • Strong written and verbal communication skills and ability to effectively communicate with cross-functional teams • Must be detail-oriented with excellent organizational skills to manage multiple projects and meet assigned deliverables. • Strategic agility and ability to adapt to the evolving personalized healthcare environment • Ability to work well on teams and keep relevant stakeholders informed regarding the status of projects. • Comfortable working in a flexible, fast-paced hybrid remote environment. Nice to haves: • Experience with developing, deploying and testing production software in the cloud (preferably bioinformatics software). • Experience with disk and network performance optimization for high throughput workflows. • Understanding of security and compliance requirements in the healthcare space, with some experience meeting those requirements in a cloud environment. • Strong understanding of software quality assurance. This position may be based out of South San Francisco, California, USA, with remote work locations possible in The United States. Relocation benefits are available for this position for candidates willing to relocate to a commutable location in the San Francisco Bay Area. For Colorado-based applicants, the expected salary range for this position is $127,585 - $157,605. For New York state-based applicants, the expected salary range for this position is $115,770 - $178,710. Actual pay will be determined based on experience, qualifications, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance. This position also qualifies for the benefits listed below. Benefits: Roche offers highly competitive benefit plans and programs, including: •Medical, dental and vision insurance •401(k) and 401(k) matching •Paid time off •Roche Long Term Incentive Plan (available at certain position levels) #LI-AD1 #ptcareers #cellandgenetherapycareers# Genentech is an equal opportunity employer, and we embrace the increasingly diverse world around us. Genentech prohibits unlawful discrimination based on race, color, religion, gender, sexual orientation, gender identity or expression, national origin or ancestry, age, disability, marital status and veteran status. Genentech requires all new hires to be fully vaccinated against COVID-19 as of their start date. This requirement is a condition of employment at Genentech, and it applies regardless of whether the position is located at a Genentech campus or is fully remote. If you are unable to receive the vaccine due to a disability or serious medical condition, or because it is prohibited as a result of your sincerely held religious beliefs, you will have an opportunity to request a reasonable accommodation

The Department of Dermatology at Stanford School of Medicine, is seeking a Principal Bioinformatics Scientist to develop software for bioinformatics, computational biology, machine learning and artificial intelligence in order to facilitate biomedical research. The candidate will work with a team of bioinformatics scientists and basic science researchers, postdoctoral researchers, and graduate... students to design analysis plans, implement these plans through bioinformatics programming, present results orally to investigators and publish high impact findings. The candidate will be responsible for managing the computational needs of the labs, with a holistic view of both the software and hardware platforms. The candidate will be responsible for managing the use of on-premise and cloud resources and coordinate with PIs for the budgeting of new computational resources to best suit evolving needs. The candidate will also be responsible to help design, develop and maintain informatics platforms to benefit many researchers with a variety of needs. This position will be based at the Stanford Medical campus and provides hybrid flexibility, subject to operational need. The labs perform cutting-edge research using high-throughput techniques to understand stem cell function, development, cancer, and other biological processes, with a focus on epigenomics. Technologies currently in use include next generation sequencing platforms, spatial genomics, mass spectrometry, custom tiling arrays, and functional genomics screens. We are seeking a candidate with a strong background in bioinformatics, computational biology and machine learning. Previous experience with analysis of high throughput genomics data and developing novel methods or software solutions for a variety of problems is highly desired. Applicants are expected to have expertise in machine learning and good visualization practices. Previous experience in administering Unix-like systems, administering cloud environments and using high-performance computing clusters is needed. Significant experience in software development skills and a good background in biology are also desired. We are looking for a person with outstanding ability to communicate information to both technical and non-technical audiences. The candidate will also need to possess skills to work in cross functional teams and be responsible for guiding the work of junior staff. Duties Include • Propose, conceptualize, design, implement, and develop solutions for difficult and complex applications independently. • Oversee testing, debugging, change control, and documentation for major projects. • Supervise professional staff, as necessary, working on all phases of application development projects. • Engage in long-term strategic planning. • Define complex application development administration and programming standards. • Oversee the support, maintenance, operation, and upgrades of applications. • Troubleshoot and resolve complex technical problems. • Review the physical design of existing systems for optimizing performance. • Lead projects, as necessary, for special systems and application development in areas of complex problems. • Work with other technical professionals to develop standards and implement best practices. • - Other duties may also be assigned Desired Qualifications • PhD in Bioinformatics, Statistics, Computer Science or related field, and three years of relevant experience • Skilled in R and Python, and a statistical analysis software e.g., SAS or SPSS • Experience implementing NGS analysis pipelines and developing novel bioinformatics approaches • Highly skilled in relational databases, data integration and statistical analysis • Experience with designing web sites with good UI/UX design practices • Expert in statistical machine learning and good visualization techniques is desired • Experienced in software development practices and version control systems e.g., GitHub • Experience administering Unix-like systems and cloud environments, and working in HPC environment • Outstanding ability to communicate information to both technical and non-technical audiences Education & Experience (required) Bachelor's degree and eight years of relevant experience, or a combination of education and relevant experience. Knowledge, Skills And Abilities (required) • Ability to quickly learn and adapt to new technologies and programming tools. • Demonstrated experience in designing, developing, testing, and deploying applications. • Strong understanding of data design, architecture, relational databases, and data modeling. • Thorough understanding of all aspects of software development life cycle and quality control practices. • Ability to define and solve logical problems for highly technical applications. • Strong communication skills with both technical and non-technical clients. • Demonstrated experience leading activities on structured team development projects. • Ability to select, adapt, and effectively use a variety of programming methods. • Ability to recognize and recommend needed changes in user and/or operations procedures. Certifications & Licenses None PHYSICAL REQUIREMENTS*: • Constantly perform desk-based computer tasks. • Frequently sit, grasp lightly/fine manipulation. • Occasionally stand/walk, writing by hand. • Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds. • - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job. WORK STANDARDS (from JDL) • 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. As an organization that receives federal funding, Stanford University has a COVID-19 vaccination requirement that will apply to all university employees, including those working remotely in the United States and applicable subcontractors. To learn more about COVID policies and guidelines for Stanford University Staff, please visit https://cardinalatwork.stanford.edu/working-stanford/covid-19/interim-policies/covid-19-surveillance-testing-policy

Position Highlights: Dr. Xuefeng Wang’s Lab (lab.moffitt.org/wang), at H. Lee Moffitt Cancer Center, an NCI Comprehensive Cancer Center and top-ranked cancer research institute, is seeking one new postdoc fellow to join the group and work on an exciting project funded by NIH. The position will remain open until filled... The Ideal Candidate: • Research background/experiences in bioinformatics, computational biology, or statistics. • A highly motivated and independent researcher with a strong quantitative scientific background and programming skills. • Experience in cancer genomics is not required but ability to learn new knowledge is highly desirable. Responsibilities: • Will develop and extend machine learning methods for big cancer Omics data. • Will help discover new predictive biomarkers for cancer prognosis. • Will be responsible for developing novel visualizing that will facilitate interpreting big Omics data in cancer research. Credentials and Qualifications: Required: PhD in Bioinformatics, Statistics/Biostatistics, Data Science, Computer Science, or related fields. Preferred: • Strong programming skills in languages such as R/Python. • Research background in machine learning. • Experience of integration of multi-omics data including whole exome sequencing, RNA-seq, metabolomics, proteomics, etc. • Excellent communication and writing skills. How to Apply: Interested applicants should send a single PDF file that includes a cover letter summarizing their research training and accomplishments, current CV with recent publications, and contact information of at least two references to Dr. Xuefeng Wang at xuefeng.wang@moffitt.org

Managers Note • Remote role • Oncology... • Developing Omic data visualization tool. • Programming in R needed, Python good to have • SQL database • Shiny • Data loading, large data • Experience with Linux, on-premise HPC, or AWS is required Job Description Development of an interactive omics data visualization portal that support oncology area target identification and evaluation needs. The specific deliverables include • Develop streamlined backend omics analysis workflows that populate data into the visualization portal • Mine, integrate, and analyze omics datasets including transcriptomics, proteomics, genotypes, etc. • Build robust omics (expression, mutation, copy number) data base infrastructure and data extraction, transfer, loading process for the front-end visualization portal. • This role will involve cross functionally collaboration with computational oncology, bioinformatics engineering, and oncology discovery research. • We’re looking for candidates with experience in developing data visualization user stories and features to enhance the omics data portal based on end-users feedback & needs. Qualifications • Ph.D. OR a Master’s degree with at least one year of industry work experience in developing data science product OR a bachelor’s degree with six years of experience in bioinformatics, computational biology, computer science, data science, or data engineering, is required. • R is required, Python is a plus • SQL / other database experience required • Experienced in omics data visualization portal development. Shiny is preferred. • Expertise in large data repository ETL process • Experience processing omics (transcriptomics, proteomics, genotypes, etc.) or other high-dimensional data is required. • Experience with Linux, on-premise HPC, or AWS is required • Docker/Nextflow/CWL is preferred • Strong understanding of principles behind raw data processing and downstream analysis for commonNGS data types • Familiarity with public genomics data repositories (Genomic Data Commons, SRA/GEO, ENA/EBI, TCGA, GTEx) a plus • Oncology experience is preferred • Prior experience in the pharmaceutical industry or a related field is preferred

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of... the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines. We are looking for a Senior Bioinformatics Scientist to join our Bioinformatics team. Your work will focus on development of new data acquisition and analytics approaches to be incorporated in future iterations of Nautilus instrumentation. To that end, you will work together with the Platform Integration experimental team to support all phases of research from ideation through proof-of-concept. The role is highly collaborative; success is measured by the degree to which you elevate the capabilities of your peers in pursuit of scientific insight. Frequent activities in this role include consulting with experimentalists on experimental design, implementing data visualizations and statistical approaches to answer key experimental questions, building pipelines to automate common analysis tasks, and designing databases to organize experimental data and enable longitudinal analysis. This role reports to the Associate Director of Bioinformatics and is based in San Carlos, CA. A minimum of three days in office, preferred. #LI-Onsite

Classification Title: Postdoc Aso... Job Description: The Institute of Food and Agricultural Sciences is committed to creating an environment of inclusive excellence that affirms diversity across a variety of dimensions, including ability, class, ethnicity/race, gender identity and expression. Inclusive excellence is the active process of including and respecting everyone as we strive for excellence and equitable outcomes in all we do at the University of Florida. We particularly welcome applicants who can contribute to such an environment through their scholarship, teaching, mentoring, and professional service. We strongly encourage historically underrepresented groups to apply. If an accommodation due to a disability is needed to apply for this position, please call 352-392-2477 or the Florida Relay System at 800-955-8771 (TDD) or visit Accessibility at UF . One postdoctoral position is available in the Zhao lab in the Department of Microbiology and Cell Science at the University of Florida to investigate genetic and epigenetic regulation of meiotic recombination in maize. The fully funded position will use genetic, genomic and bioinformatics approaches to investigate the mechanisms of meiotic recombination in the crop species maize. For more information, please check our latest publication . Duties/Physical Demands • Perform basic genetic and molecular experiments • Collect and prepare samples for high-throughput sequencing • Analyze whole genome resequencing, DNA methylation, small RNA, mRNA, and ChIP sequencing data • Responsible for data presenting and manuscripts writing • Provide guidance and mentoring for graduate and undergraduate students in the lab Knowledge, Skills and Abilities: The expected candidate should be familiar with next- generation sequencing data and have strong skills in the analysis of different types of high- throughput data. Initial appointment will be one year and are renewable up to four years based on performance. Salaries are commensurate with qualifications. Benefits are provided via the University of Florida. In addition to this position, visiting scholars and graduate students are both welcome to join the lab. Expected Salary: Commensurate with Experience and Education Minimum Requirements: Ph.D. (foreign equivalent acceptable) in plant genetics, genomics and bioinformatics. The candidate must be highly motivated. Candidates must be supportive of the mission of the Land-Grant system. Excellent written and oral communications, as well as strong computational skills, are required.Candidates must also have a commitment to IFAS core values of excellence, diversity, global involvement, and accountability. Preferred Qualifications: Favorable consideration may be given to candidates who have experiences with ChIP-seq and ATAC-seq. The candidate is able to work both independently and collaboratively within a multidisciplinary research environment. Special Instructions to Applicants: Application must be submitted by 11:55 p.m. (ET) of the posting end date. • Individuals wishing to apply should go online to Careers at UF and submit: • Cover letter that states applicant’s interest in the position and qualifications relative to the credentials listed above • Curriculum vitae • Contact information (including email addresses) for 3 individuals willing to write letters of recommendation Selected candidate will be required to provide an official transcript to the hiring department upon hire. A transcript will not be considered “official” if a designation of “Issued to Student” is visible. Degrees earned from an education institution outside of the United States are required to be evaluated by a professional credentialing service provider approved by National Association of Credential Evaluation Services (NACES) . Hiring is contingent upon eligibility to work in the US. The University of Florida is a public institution and subject to all requirements under Florida Sunshine and Public Record laws. The University of Florida is an Equal Opportunity Institution dedicated to building a broadly diverse and inclusive faculty and staff. The University and greater Gainesville community enjoy a diversity of cultural events, restaurants, year-round outdoor recreational activities, and social opportunities. Health Assessment Required: No

Position: Bioinformatician Duration: 6-month contract to start, high potential for extension... Location: Remote Services Overview: • Development of an interactive omics data visualization portal (preferably in R-Shiny) that support oncology area target identification and evaluation need • Development of streamlined backend omics analysis workflows that populate data into the visualization portal • Build robust omics (expression, mutation, copy number) database infrastructure and data extraction, transfer, loading process for the front-end visualization portal • Develop data visualization user stories and features to enhance visualization portal based on end-users feedback & needs • Interacting with: Computational Oncology, Bioinformatics Engineering, Oncology Discovery Research Qualifications: • In areas related to Bioinformatics, Computational Biology, Computer Science, Data Science • Advanced degree (Ph.D./MS) preferred but not required • > 1 year of industry work experience in developing data science product in the life science field • Oncology experience preferred • Experience processing omics (transcriptomics, proteomics, genotypes, etc) or other high-dimensional data • Strong experience with Rshiny or similar dashboard systems is required • Good understanding of principles behind raw data processing and downstream analysis for common NGS data types • Familiarity with public genomics data repositories (Genomic Data Commons, SRA/GEO, ENA/EBI, TCGA, GTEx) a plus • R required, Python a plus • Experienced in omics data visualization portal development (Shiny preferred) • SQL / other database experience required • Expertise in large data repository ETL process • Docker/Nextflow/CWL is a plus • Experience with Linux, on-premise HPC, or AWSo Exceptional communication and collaboration skills are required. • Prior experience in the pharmaceutical industry or a related field is preferred

Synlico is taking a different approach to understand biological system and process. The company is seeking talented, ambitious researchers to develop cutting-edge computational tools to understand individual cells and new technologies to enable more accurate prediction of biological system. The company’s research is highly interdisciplinary, involving system biology, genomics, bioinformatics... mathematics, and highly team oriented. The bioinformatics scientist position will utilize single-cell, bulk and spatial transcriptomes as well as other omics data, public and internal, to generate biological interaction networks and model. The candidates will need to Identify and develop optimal algorithms and workflows to analyze large scale single cell/bulk/spatial transcriptomics datasets from internal, publicly available, commercial, and real-world datasets. Qualifications: A Ph.D. in bioinformatics, genomics, computer science or related field with strong hands-on analytical experience of single cell, bulk and spatial transcriptomics data. Experience with machine learning and network modeling approaches applied to biological systems Demonstrated experience working with public database. Established publication record. Ability to work independently and within a team H1B/O-1 will be provided to qualified candidates

Position description We are looking for skilled scientists to join the Bioinformatics team, and help develop advancements that will unlock new capabilities of our genomics lab to deliver impactful health information to hundreds of thousands of patients a year... We leverage proprietary next-generation sequencing (NGS) capabilities, rigorous statistical modeling, and novel algorithms to increase the quality and throughput of our products. The ideal candidate excels at integrating a diversity of computational skills and talents with a drive to push the envelope of what’s possible in genomics. What you'll do • Author innovative approaches and novel methods to detect clinically actionable genetic information and expand the capabilities of our core products • Responsible for our analytical NGS pipeline from raw sequencing data to patient genotypes • Prove through rigorous analysis the validity and performance of our analytical pipeline • Develop characterizations of test performance and quality control metrics to ensure high sensitivity and specificity • Work in collaboration with assay development scientists to develop innovative protocols • Work with multidisciplinary R&D and product teams to bring new products to market • Present research findings and advocate for our technological strengths through internal and external publications and conferences About you • PhD (or equivalent experience) in Bioinformatics, Computational Biology or related discipline • Proven track record of developing robust and innovative solutions to complex problems through novel research, publication record and/or achievements in industry • Ability to apply and leverage advanced statistical methods, modeling, data science to molecular biology • Proficient in at least one major programming language (Python, Java, C++), strength with scientific python libraries or statistical packages (R, MATLAB) • Strength in modern NGS methods and data analysis toolkits • Experience working in a regulated clinical environment (e.g. CAP/CLIA) is a plus • Ability to thrive in a professional atmosphere where collaborative, interdisciplinary teams are central to project success

The Position We are seeking a talented and highly motivated Principal Bioinformatics Scientist to support the development of Roche Diagnostics Molecular Assays that will impact patient care globally. This position requires a broad understanding of assay development on multiple technologies such as microarray, NGS, PCR, and digital PCR. The candidate will work closely with Bioinformatics, wet lab... scientists and internal experts for customer support to develop, maintain, and improve internal algorithms and tools to support the NIPT Ariosa cell-free DNA System (AcfS) and the development of PCR and NGS assays. Responsibilities • Provide hands-on troubleshooting to ensure the AcfS product quality • Collaborate with Bioinformatics and wet lab scientists to develop, improve, and maintain tools for PCR and NGS assay development • Lead scientific analysis efforts to understand customers’ needs • Follow best practices for documentation, software version control, and training of algorithms and tools • Present and communicate team activities/project results across multiple functions in the organization Requirements • Master’s degree in Bioinformatics, Computational Biology, Statistics, Computer Science or a relevant subject area plus a minimum of 3+ years of proven experience • Strong statistics skills and proficiency in using programming languages (R, Python) in both Windows- and Linux- based environments • Very good understanding and proficiency in software version control and HPC • Very good understanding of biology and IVD • Proven track record of supporting scientific informatics efforts. Ability to independently implement informatics solutions • Excellent written and verbal communications and scientific presentation skills • C++ or Java proficiency is a plus • Detail oriented and committed to delivering high quality clinical products #LI-SC3 Who we are At Roche, more than 100,000 people across 100 countries are pushing back the frontiers of healthcare. Working together, we’ve become one of the world’s leading research-focused healthcare groups. Our success is built on innovation, curiosity and diversity. Unless entitled to a reasonable accommodation under applicable law, employees are required to be fully vaccinated against COVID-19 in accordance with customer requirements, the company’s health and safety obligations and/or applicable law or guidelines. Roche is an equal opportunity employer and strictly prohibits unlawful discrimination based upon an individual’s race, color, religion, gender, sexual orientation, gender identity/expression, national origin/ancestry, age, mental/physical disability, medical condition, marital status, veteran status, or any other characteristic protected by law. If you have a disability and need an accommodation in connection with the on-line application process, please email us at US.Accommodation@roche.com