Bioinformatics Jobs

About GREGoR Stanford Site : GREGoR Stanford Site (GSS), is one of 6 sites in the National Institutes of Health (NIH)’s Genomics Research to Elucidate the Genetics of Rare disease (GREGoR) Consortium. The GSS (https://gregor.stanford.edu/) mission is to provide a platform for functional genomics research and validation to improve diagnosis in Mendelian disease through integrated analysis of... multi-omics data. GSS is led by co-PIs Dr. Stephen Montgomery (Department of Pathology), Dr. Matthew Wheeler (Division of Cardiovascular Medicine) and Dr. Jon Bernstein (Division of Medical Genetics). At GSS, research participants who remain undiagnosed after exome sequencing will undergo short read and long read genome sequencing, transcriptome sequencing, methylation assays, metabolomics and/or lipidomics assays. State-of-the art computational algorithms and new methods will be applied and developed to prioritize the variants and genes. The data will be analyzed in a secure and scalable manner using a HIPAA compliant cloud platform like AnVIL and Google Cloud Platform (GCP). Novel causal variants and genes will be validated through state-of-the-art targeted approaches including massively parallel reporter assays, induced-pluripotent stem cell assays and CRISPR engineered cellular and mouse models. About the Position: We are seeking a highly talented and motivated Bioinformatics Engineer to support our GSS pipeline and data analysis team. Your role will focus on the development of pipelines and tools for comprehensive analysis of large amounts of molecular data generated by the GSS, with special emphasis on genomics, transcriptomics, and metabolomics datasets. You will also establish and support cloud infrastructure for storage and computation of the multi-omics data. Your ability to understand biological experiments, strong experience in the analysis of large-scale biological datasets, proficiency with programming languages and experience in high-performance computing environments or cloud will be a key resource in enabling high-quality data to flow through our systems to enable diagnosis and discovery of new disease-gene associations. A complete application will include CV and cover letter. Duties include: • Development of pipelines and tools for the comprehensive analysis of large amounts of multi-omics data being generated by the GSS. • Establish and maintain the cloud infrastructure for GSS on AnVIL and GCP. • Interact with GREGoR team members as well as external tool developers to implement new tools, algorithms, and updates. • Develop intuitive reports for molecular pipelines for tracking progress and quality metrics. • Track reports for problems with pipeline analysis and underlying data. • Extract relevant data from a variety of sources, including RESTful API services, databases and medical records. • Serve as a resource for bioinformatics inquiries from the clinical team members to access data or results from local cluster/cloud/external provider. • Work with stakeholders across the consortium to best understand data structures to model metadata schemas. • Mentorship to Junior Analysts with regards to primary analysis • Document and report as needed to fulfill grant and regulatory obligations. • – Other duties may also be assigned Due to the nature of the work, this position will be fully onsite. Desired Qualifications: • Graduate degree (Ph.D or M.S) that emphasizes bio/medical informatics, engineering, computer science and statistics are preferred. • Relevant work experience preferred, two or more years. • Domain expertise in analysis and running pipelines and bioinformatic tools for at least one of the following ‘omes: genomics, transcriptomics, metabolomics, atac-seq, proteomics. • Proficiency in Python and/or R and Linux bash scripting. • Experience with pipeline languages like WDL or snakemake or nextflow. • Proven track record of data and infrastructure management in a HPC (High Performance Computing) cluster or cloud computing like Google Cloud Platform or AWS. • Experience with container systems such as setting up virtual machines and docker instances. • Experience and knowledge of code management such as github. • Experience in systems biology approaches for data integration is a plus • Experience in developing tools and statistical methods for large-scale data analysis is a plus. • Biological domain knowledge (rare disease) is a plus. • Experience on bioinformatics and/or software development team-based projects. • Willingness to work in a highly collaborative environment. Experience as part of large NIH consortiums is a plus. • Ability to quickly adapt and learn the latest tools and skills. • Strong communication skills (e.g., put together reports and presentations). • Ability to work independently (e.g., find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results). Education & Experience (Required): Bachelor’s degree and three years of relevant experience or combination of education and relevant experience. Experience in a quantitative discipline such as economics, finance, statistics or engineering. Knowledge, Skills and Abilities (Required): • Substantial experience with MS Office and analytical programs. • Excellent writing and analytical skills. • Ability to prioritize workload. Tagged as: Data Science

Why Mayo Clinic Mayo Clinic is the nation's best hospital (U.S. News & World Report, 2022-2023) and ranked #1 in more specialties than any other care provider. We have a vast array of opportunities ranging from Nursing, Clinical, to Finance, IT, Administrative, Research and Support Services to name a few. Across all locations, you’ll find career opportunities that support diversity, equity and... inclusion. At Mayo Clinic, we invest in you with opportunities for growth and development and our benefits and compensation package are highly competitive. We invite you to be a part of our team where you’ll discover a culture of teamwork, professionalism, mutual respect, and most importantly, a life-changing career! Mayo Clinic offers a variety of employee benefits. For additional information please visit Mayo Clinic Benefits. Eligibility may vary. Position description Under general supervision and guidance: - The analyst/programmer is responsible for the support of moderately complex software-based systems in the supported areas. - Contributes to the design, development, implementation, and maintenance of custom software, or the installation and maintenance of purchased software systems. - Produces documentation such as systems requirements, designs, and plans as requested by the work unit leadership. - Work will be reviewed for quality, timeliness, and adequacy at predetermined milestones. Qualifications Working towards a PhD in Computer Science or related Informatics field with a GPA of 3.0 or greater. Additional qualifications Experience with Java, SQL, and XML. Exemption status Non-exempt Compensation Detail $24.42 - $30.00 / hour Benefits eligible No Schedule Part Time Hours / Pay period 40 Schedule details Monday - Friday 20 hours a week Weekend schedule N/A Remote Yes International Assignment No Site description Mayo Clinic is located in the heart of downtown Rochester, Minnesota, a vibrant, friendly city that provides a highly livable environment for more than 34,000 Mayo staff and students. The city is consistently ranked among the best places to live in the United States because of its affordable cost of living, healthy lifestyle, excellent school systems and exceptionally high quality of life. Recruiter Stephanie Baird EOE As an Affirmative Action and Equal Opportunity Employer Mayo Clinic is committed to creating an inclusive environment that values the diversity of its employees and does not discriminate against any employee or candidate. Women, minorities, veterans, people from the LGBTQ communities and people with disabilities are strongly encouraged to apply to join our teams. Reasonable accommodations to access job openings or to apply for a job are available

A pharmaceutical company in Illinois is actively seeking a dynamic and hardworking professional to join their staff as their new Bioinformatics Analyst. In this role, the Bioinformatics Analyst will support computational research priorities associated with oncology discovery programs. Responsibilities... The Bioinformatics Analyst will be responsible for: • Querying public cancer genomics resources for mutation/expression distributions • Assessing normal expression, interpreting germline associations between targets and relevant diseases, • Assessing internally generated proteomic/transcriptomic datasets • Informing discovery peers on computational opportunities for ongoing programs • Providing feedback on experimental design • Communicating results to diverse scientific backgrounds Qualifications • Ph.D.; or a Master’s degree with 1+ year of industry work experience; or a Bachelor’s degree with 8+ years of experience in bioinformatics, computational biology, computer science, engineering, or cancer biology • Oncology experience • Experience processing omics (transcriptomics, proteomics, genotypes, etc.) or other high-dimensional data • Strong understanding of principles behind raw data processing and downstream analysis for common NGS data types • R experience • Experience with Linux, on-premise HPC, or AWS • Exceptional communication and collaboration skills Desired skills • Prior experience in the pharmaceutical industry or a related field • Familiarity with public genomics data repositories (Genomic Data Commons, SRA/GEO, ENA/EBI, TCGA, GTEx) • Experience with Python

GRAIL is a healthcare company whose mission is to detect cancer early, when it can be cured. GRAIL is focused on alleviating the global burden of cancer by developing pioneering technology to detect and identify multiple deadly cancer types early. The company is using the power of next-generation sequencing, population-scale clinical studies, and state-of-the-art computer science and data science... to enhance the scientific understanding of cancer biology, and to develop its multi-cancer early detection blood test. GRAIL is headquartered in Menlo Park, CA with locations in Washington, D.C., North Carolina, and the United Kingdom. GRAIL, LLC is a wholly-owned subsidiary of Illumina, Inc. (NASDAQ:ILMN). For more information, please visit www.grail.com . In this role, you will analyze some of the largest, richest genomics datasets in the world to identify biological patterns and guide assay and classifier development. Working closely with scientists, clinicians, and engineers, you will develop algorithms and tools to investigate the biology of tumor-derived cell-free DNA and to translate your insights into new assay and classification strategies. Your efforts will contribute to exciting biological discoveries, influential scientific publications, and impactful products for the early detection of cancer! You will: • Design and implement computational methods to identify and exploit opportunities to improve assay and classifier performance. • Collaborate closely with assay scientists to plan experimental studies and interpret results. • Work with a team of versatile bioinformaticians and data scientists to apply machine learning and statistical methods to large, sophisticated genomics datasets to generate biological insights. • Present project updates and results regularly at technical meetings. • Interact cross-functionally with other teams including software, clinical, operations, research, product development, and external collaborators. Your background should include: • M.S. or Ph.D. in bioinformatics, computational biology, statistics, biological sciences, cancer biology, genetics, genomics, computer science, physics, engineering, mathematics, or equivalent preparation and experience. • Familiarity with genomics and next generation sequencing. • Proven expertise in at least one programming language (such as R, Python, or Go) and proficiency within a Linux environment. • Preferred, familiarity with git or other version control systems. • Knowledge of statistical and machine learning tools and their application to genomics datasets. • Being self-directed with the ability to multitask in a sophisticated environment. • Capacity to thrive in a highly team-driven environment with a strong collaborative mentality. • Desire to teach and learn from others. • Strong written and verbal communication skills. • Comfort working with cloud-based systems such as G-Suite and AWS. GRAIL is an Equal Employment Office and Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status. We will reasonably accommodate all individuals with disabilities so that they can participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. Following extensive monitoring, consideration of business implications, and advice from internal and external experts, GRAIL US has made the decision to require that all U.S. employees be “Fully Vaccinated” with the COVID-19 vaccine. “Fully Vaccinated” is defined as two weeks after both doses of a two-dose vaccine (e.g. Pfizer or Moderna) or two weeks since a single-dose vaccine (e.g. Johnson & Johnson) has been administered. Absent a qualifying exemption, all GRAIL US employees are to comply with this requirement, including providing documentation of such vaccination status, as a condition of employment. Anyone unable to be vaccinated, either because of a sincerely held religious belief or a medical condition or disability that prevents them from being vaccinated, can request a reasonable accommodation for consideration by GRAIL

Hiring Department: Biochemistry and Molecular Genetics Location: Chicago, IL USA... Requisition ID: 1015318 Posting Close Date:1/16/22 About The University Of Illinois Chicago UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has nearly 260,000 alumni, and is one of the largest employers in the city of Chicago. Description: The laboratory of Dr. Jalees Rehman in the Department of Biochemistry and Molecular Genetics at the University of Illinois, College of Medicine (Chicago) has openings for a highly motivated post-doctoral position with research track record in any of the following areas: computational biology, bioinformatics, data science or genomics. The willingness to develop new analytical approaches and experiment with novel concepts is expected. Our laboratory develops novel computational approaches to infer cellular functions in health and disease by analyzing single cell RNA-sequencing, single cell multi-omic and spatial transcriptomic data. Our laboratory consists of a computational team and a wet lab team, working on a broad range of topics such as immunology, inflammation, vascular biology, neurobiology, SARS-CoV-2 infections and stem cell biology. Examples of our recent publications include Jambusaria A, eLife (2020) and Gao S, Genome Research (2021). Computational team members routinely interact and co-publish with wet lab scientists via mutually beneficial collaborations. We provide a strong mentoring environment that helps post-doctoral fellows forge their own career paths at the interface of computational biology and biomedical research questions. Eligible postdocs within the first two years of completing their doctoral degree will be given the opportunity of submitting an NIH K99/R00 award which represents a key path towards independence. Postdoctoral fellows who are not eligible for the K99/R00 award will be provided other mentored career development opportunities for careers in academia or industry. The salary range is $62,000 - $70,000 and commensurate with prior experience Duties & Responsibilities • Developing novel research projects in computational biology under the guidance of the principal investigator • Analyze, interpret, and integrate multi-omic datasets. • Work in close collaboration with wet-lab scientists and develop analysis pipelines • Prepare scientific results for publication in peer-reviewed journals and/or grant applications. • Communicate results at internal and external scientific conferences. • Assist in the training of graduate students. Qualifications: • PhD degree in computational biology, bioinformatics, mathematics, computer science, biostatistics, genomics or a related field. • At least one first authored, original research publication focusing on developing novel analytical approaches in computational biology, bioinformatics or genomics. • Experience with the analysis of RNA-sequencing data • Strong programming skills in R or Python Preferred Qualifications • Experience with the development of novel software packages in R or Python. • Expertise in machine learning / deep learning • Experience with analyzing single cell RNA-sequencing, single cell ATAC-sequencing data or spatial transcriptomics data • Multiple publications (first-authored as well as co-authored) that involve the development or application of computational approaches in genomics To Apply Applicants should email a single pdf file containing a cover letter With Brief Description Of Research Experience And Future Interests, curriculum vitae , and list of three references • Send to jalees@uic.edu The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, COVID-19 vaccination requirement, and employment eligibility review through E-Verify. The university provides accommodations to applicants and employees. Request an Accommodation

Responsibilities I will be working on migrating BioInformatics Datawarehouse and processes to GCP... Qualifications Masters in Computer Science, Experience working with Python, Bioinformatics Data, Pipelines, and Cloud

Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. The primary goals of the CBFG are to... establish a research nexus that integrates leading-edge developments in computational sciences, next-generation genomics and epigenomics, and to use functional biology to improve our understanding of disease etiology applied to personalized health. The Knott laboratory at Cedars-Sinai Medical Center is searching for a Postdoctoral Scientist with a strong background in tumor biology and the immune microenvironment to lead single cell-based omics studies of immunotherapy clinical trials being carried out at the medical center. The scientist will manage a team of laboratory technicians through the processing of clinical trial biopsies for profiling with single cell RNA and ATAC sequencing as well as other emerging technologies. Additionally, our laboratory analyzes the clinical samples with spatial profiling methods such as Co-Detection by Indexing, which allows us to directly study interactions between neighboring cells within the tumor that may govern the response to therapy. We are currently analyzing trials to study the effects of combination immunotherapies in patients with triple negative and estrogen receptor positive breast cancers. We are also beginning trials in patients with early as well as late stage Her2 positive disease. We expect all analyses of these cutting-edge clinical trials will result in high-profile publications in top-tier scientific journals. To learn more, please visit: Knott Research Lab | Cedars-Sinai. Are you ready to be a part of breakthrough research? Working independently but in close cooperation and in consultation with Dr. Knott and other Research Scientists, the Postdoc will perform routine and complex laboratory procedures throughout training period. May develop, adapt, and implement new research techniques and protocols, analyze and interpret data. #jobs Primary Job Duties and Responsibilities: • May assist in preparation of grant proposals, but is not responsible for generating grant funds. • May participate in publications and presentations as author or co-author. • Designs and performs experiments. Will keep appropriate experimental records and documentation and analyze the results with the Principal Investigator. • Analyzes, interprets, summarizes and compiles data. • Operates and maintains equipment and instruments. Education: • Doctorate Degree in Cancer Biology, Immunology or a related field, required. Experience and Skillset: • Acquires thorough technical and theoretical knowledge of research project and objectives during one to five (1-5) year post-doctoral appointment. • Experience analyzing murine or human tumor microenvironments with single cell resolution methods. • Molecular biology skills are also required, as this scientist will be responsible for guiding laboratory technicians through specific analytical techniques mentioned. • Ability to interpret high-dimensional data and a willingness to work in a collaborative setting with clinicians, immunologists and computational scientists is essential. • Works independently on research projects designed by a mentor (typically the PI) within area of specialization. • Demonstrated aptitude to perform experimental protocols and procedures, including detailed data collection, and analysis, and operation and maintenance of specialized equipment. • Knowledge of safety standards and maintenance of specialized equipment. Working Title: Postdoctoral Scientist - Knott Lab - Bioinformatics & Functional Genomics Department: BMS - Bioinfo & Func Genomics Business Entity: Academic / Research Job Category: Academic/Research,Academic/Research Job Specialty: Postdoctoral Position Type: Full-time Shift Length: 8 hour shift Shift Type: Day

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 hiring a Bioinformatics Research Scientist for the Probe Bioinformatics Group to join our growing team of world class scientists and engineers. The Probe Bioinformatics team is embedded within the Probe Development group, which is responsible for the identification, validation, and maturation of affinity reagents (probes) that are being used in protein decoding experiments on the Nautilus platform. The incumbent will work hand in hand with internal and external experimentalists from diverse backgrounds and experience levels to develop sound experiments and lead subsequent data curation, storage, and analysis. We are looking for someone who is comfortable interacting with bench scientists as well as fellow-bioinformaticians and software engineers to improve existing data and analytics infrastructure. The successful applicant will also leverage their own ideas and expertise to develop new innovative approaches to propel the development of affinity reagents forward. This position will report to the Probe Bioinformatics team lead and is located in San Carlos, CA, San Diego, CA, or Seattle, WA. A minimum of three days in office, preferred. Responsibilities • Work closely with experimentalists from affinity reagent discovery teams to answer key research questions with the goal of continuously improving processes and success rates • Routinely analyze statistical trends in high-throughput data and perform correlations across experiments to inform direction of research • Provide technical expertise for the design of experiments and the resulting data capture and curation steps to maximize knowledge gained • Develop automated pipelines for the ingestion, curation, and analysis of experimental data • Work collaboratively on shared code bases, contributing personal work following high code quality standards • Contribute to Nautilus’ self-service reporting infrastructure by creating compelling visualizations based on queried data Qualifications • PhD in Bioinformatics or related field with a minimum of 2-4 years of relevant industry experience or a BS/MS and 8-10 years of experience in a related field is required • Demonstrated the ability to employ statistical tools for the analysis of complex data sets to identify trends and correlations • Proficient with Python, Jupyter notebooks, and related analytics packages, such as numpy, pandas, scipy, etc • Good working knowledge of relational databases and SQL • Comfortable working independently with a minimum of supervision as well as being part of a larger team • Excellent interpersonal skills and the ability to effectively communicate complex technical topics to a non-technical audience • Excellent at time management, well organized, and have the proven ability to prioritize your work effectively • Thrive in an environment that requires you to have multiple areas of responsibility and manage these effectively Preferred Skills • Experience with Django (backend) and a frontend frameworks such as Angular or React. • Experience with AWS (VPC, EC2, S3, Athena, RDS, Batch, ECR, Lambda, Step Functions) • Knowledge of machine learning techniques for the identification of patterns in NGS data • Experience with testing frameworks such as pytest or unittest and developing code in a production environment • Familiarity with Mode Analytics Nautilus Team Culture • We are curious go-getters: this is a team of life-long learners who aren’t afraid to tackle the big challenges and we embrace the journey • We are detail oriented: we do great science by working smart & with diligence where we learn from our trials and mistakes • We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness #LI-Onsite

Primary Duties and Responsibilities: • Perform data analysis on genomic data... • Extract features of interest from data. • Assist in pipeline development and optimization, algorithms development and validation. • Assist in management of genomic data and annotation resources. • Contribute to presentation of methods, results, conclusions, and recommendations. • Work closely with Research and Development on internal and external projects. Required Skills/Abilities: • Experience with one or more of the following: Python, Perl, and R. • Knowledge in basic biological processes and genomics. • Familiarity with public genomics databases. • Working knowledge of laboratory protocols relevant to sequence analysis. • Excellent verbal and written communication skills. • Ability to multi-task and shift priorities according to company needs in a fast-paced environment. Education and Experience Requirements: • M.S. in statistics, bioinformatics, genomics or computational biology or equivalent experience. Preferred Skills/Abilities: • Experience with NGS and/or high-throughput technologies. • Experience with analysis of sequence variants. • Knowledge in statistics, modeling, and machine learning. Mikey Ryerson Mikey@peoplewithchemistry.com 858-429-6069

The Senior Scientist Bioinformatics operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. They will demonstrate deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. They will provide support for the BGM strategy and interpretation to other SBUs and clients. Key Accountabilities... • Responsible for the development of analytical pipelines and implementation of data management strategy for omics and/or genetics domains for the client. • Liaise with stakeholders in the client’s human genetics and computational biology group to provide clear guidance on data ingestion needs. • Provide data processing support through standardized pipelines, data transformations to fit pipeline requirements and establish data quality checks where required. • Support defining quality control and analytical requirements where necessary to include specification of data types, formats, and data structure along with the defining of experimental metadata. Skills: • Hands-on experience managing and analyzing large-scale genetic/genomic data and performing data transformations and quality control of data where required • Experience with several specialized data types and analytical pipelines (e.g., GWAS, eQTL, Single Cell and Bulk RNA-Seq), whilst maintaining awareness of additional pipelines outside the specialized modality (e.g., ATAC-Seq, Variant Calling, Pooled CRISPR) to facilitate data integration as needed • Working knowledge of relational and distributed databases (i.e., MySQL, Hadoop, NoSQL) • A good practical knowledge of programming languages to manipulate large datasets (Python, R, Perl) • Experience working in a Unix environment • Skilled in Microsoft Office tools including Excel, PowerPoint, and Word • Strong ability to simultaneously manage several projects consisting of technical and non-technical goals • Strong organizational, problem solving and analytical skills • Professional attitude, self-motivated, client focused work ethic with ability to handle confidential matters and data • Able to work independently and organize own workload • Willingness to work in a matrix environment and to value and promote the importance of teamwork • Strong interpersonal, verbal, and written communication skills • Clear and precise communication in English Knowledge and Experience: • Two or more years’ experience in pharmaceutical industry, CRO or academia desired • Strong knowledge of genomics and preferably drug development. • Experience in genetic analysis, bioinformatics, and computational programming • Experience in preparing data for analysis by others • Knowledge of data standards for exchange of human genetic, phenotypic, and clinical data Education: • Master’s Degree with 5 - 8 years of experience or a doctoral degree with 2 - 5 years of relevant professional working experience (including post-doc), in one of the following subjects: Bioinformatics, Biostatistics, Computer Science, Life Sciences Employment is contingent on disclosure of your COVID-19 vaccination status and, if relevant, proof of vaccination. #LI-REMOTE