Bioinformatics Jobs

Division: Biostatistics and Bioinformatics Shared Resource The University of Miami is among the top research universities and academic medical centers in the nation, and one of the largest private employers in South Florida. With more than 16,000 faculty and staff, the University strives for excellence, and is driven by a powerful mission to transform and impact the lives of its students... patients, members of the community, and people across the globe. The University is committed to fostering a culture of belonging, where everyone feels valued and has the opportunity to add value. Through values of Diversity, Integrity, Responsibility, Excellence, Compassion, Creativity, and Teamwork (DIRECCT) the U community works together to create an environment driven by purpose, excellence, community, and service. Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center? This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University of Miami. The Associate Scientist (Bioinformatician) will provide up to date bioinformatics and molecular informatics data analysis and expertise for clinical, laboratory and epidemiological studies. This analysis includes but is not limited to: gene expression analysis for transcriptome profiling and/or gene regulatory network building, microRNA target analysis, variant calling, epigenetics data preprocessing and analysis, SNP functionality and pathway analysis, and its visualization. This position will collaborate with Cancer Center investigators on experimental design and subsequent high dimensional data analysis of gene expression, genomics and/or proteomics studies. Duties and Responsibilities: • Individual will be responsible for initiating and maintaining independent research collaborations with SCCC clinicians and basic scientists, and for working collaboratively with members of the division on research or development projects. • Collaborates with Cancer Center members in planning and analyzing data from laboratory-based and epidemiologic investigations. • Collaborates with Cancer Center members in developing cancer-related grant proposals. Carries out and/or supervises corresponding data analysis. • Interacts with internal contacts such as principal investigator, research project team, clinicians and data processing and management staff to provide the statistical input required in the design, conduct and analysis of scientific research studies. • Collaborates with Cancer Center members on writing manuscripts or publication, and in preparing abstracts and poster for scientific presentation. • Stays current with new bioinformatics methodology applicable to cancer studies, and incorporates major useful advances into proactive. • Supports the BBC Biostatistics Division and other members of the core on bioinformatics aspects of Cancer Center research-related to clinical trials, epidemiologic studies, and laboratory-based investigation. • Other duties as assigned. Qualifications: A Ph.D. degree or equivalent experience, with a minimum of 5 years of post-doctoral experience with bioinformatics and molecular informatics data analysis in support of basic, translational, clinical, and/or epidemiological studies. Must enjoy working with others, have initiative, and be reliable. Attention to detail and multitasking abilities are critical, with the ability to work both independently and as part of a team. Proficiency in R/Python programming and excellent English communication skills (both verbal and written) are required. Prefer experience with statistical and computational methodology development with application in genomics studies, with single-cell RNA/DNA sequencing and metagenomics data analysis, with integrative multi-omics data analysis, and spatial genomics data analysis. Prefer strong critical thinking and problem solving skills with proven ability to apply creative approaches to complicated questions. Application Instructions: For more information or to apply for this position, please go to: Full Job Posting: https://umiami.wd1.myworkdayjobs.com/en-US/UMCareerStaff/job/Miami-FL/Associate-Scientist-Bioinformatician-_R100054919-1 Job Posting Contact: Yuguang Ban, yuguang.ban@med.miami.edu

Job Description Would prefer onsite in Cambridge, but can be remote... • Project involves developing multi-omics directed graph networks based on causal inference framework based on multiple data types (e.g., clinical, RNA-seq, epigenetic, proteomic, and/or genetic data). • Must be expert in at least one area of causal inference such as interpretable machine learning or data fusion problem, e.g., to reduce space of plausible causal relationships and how data from multiple sources can be combined to make causal inferences. • Experience with machine learning in the context of causal inference, so that the predictive models are more than just a black box, is strongly desired. • Ideal candidate is experienced in both genomic data, causal inference, and machine learning, but the latter two are the most important. Skills / Qualifications Required • PhD Student / Master's degree In Statistics, Physics, Computer Science or related area with 2-3 years' experience • Causal Inference • Bayesian DAGs • Machine Learning • Data preprocessing for multiple data types • Genomics experience • Programing skills (python javascript c+), experience analyzing real word data and experience utilizing deep neural network

Basepair develops SaaS to manage, analyze and interpret next generation sequencing (NGS) data. Scientists and physicians working in molecular diagnostics, biopharma, assay development at top universities like Harvard, Stanford, NYU, UCSD, etc. use Basepair to make breakthrough medical discoveries and provide better medical care to patients. Founded by a scientist from Harvard Medical School... Basepair is driven by the mission to use technology to improve healthcare. Our team is analytical, fast-paced and informal. We are funded by venture capital and NIH, and we are growing rapidly. We are looking for a technically skilled and detail-oriented scientist to join our bioinformatics team remotely. Your goal is to develop, validate and update best-in-class NGS pipelines. You will communicate with existing and prospective users to answer questions about our software, perform custom analyses, and help guide strategic scientific direction for Basepair. You will be the face of Basepairs bioinformatics expertise, conducting webinars, publishing content, etc. Requirements • Develop, validate and update best-practices pipelines for variant calling, gene expression, epigenetics, single cell RNA-Seq, etc. • Have knowledge of public datasets and consortiums • Perform custom bioinformatics analysis for users • Conduct webinar, QnA, etc. to introduce NGS pipelines to bench scientists • Write white papers and blogs • Represent Basepair at conferences and meetings What you will need for this position • Masters or PhD with 3+ years of experience in bioinformatics, computational biology or related field • 2+ years of experience of building NGS pipelines • 2+ years of Python programming, data visualization, ability to read and modify other peoples source code • Proficiency in Linux, setting up servers, installing packages, bash scripting, etc. • Ability to work independently, prioritize tasks and manage your time productively • Excellent communication skills, including scientific writing Additional Desired Qualifications • Experience with cloud computing (AWS), docker, etc • Proficiency in R • Experience with CWL, WDL • Expertise with front end software development using JavaScript, e.g., React, d3.js, etc. • Familiarity with molecular biology and NGS library preparation techniques • Previous startup and remote work experience is a plus Benefits This is an opportunity to make a significant impact at an early stage startup. Were a small team working closely together to make peoples lives better! Your voice will be heard and you will have the autonomy to set your vision. We strongly encourage ongoing learning to be the best in your position. We provide a competitive salary, meaningful equity, excellent healthcare and other benefits. While half the team works out of our New York office, we are a remote-friendly company. We want to hire the best talent, and people who work at Basepair can live and work from anywhere they want

The Sylvester Comprehensive Cancer Center & the Department of Molecular and Cellular Pharmacology are actively seeking a full-time Bioinformatics Analyst to work on the UHealth campus. The Bioinformatics Analyst will design, build, and maintain bioinformatic pipelines and tools and integrate them with Sylvester’s internal end-user data analytics platform. The candidate will be performing their... activities within an interdisciplinary team of research scientists, data engineers and full-stack developers and will be using state-of-the-art software development practices. The ideal candidate should have a passion for data science and be comfortable with building production-ready solutions that will enhance the research activities of the university’s members. Responsibilities • Develop and maintain production pipelines for analyzing high-throughput NGS data: (e.g. bulk/single-cell RNA-seq, WGS/WES, ATAC-seq) • Develop visualization and computational tools for the exploration and analysis of large scale multi-omic datasets • Integrate algorithms and pipelines with Sylvester’s internal end-user data analytics platform • Write standard operating procedures and other relevant documentation Requirements • Bachelor's degree, or MS in bioinformatics, computational biology, statistics, data science, computer science, or a related field, or equivalent practical experience • Fluency in R or python and Unix (bash) • Experience with NGS data analysis, using common bioinformatics tools (BWA, STAR, Picard, GATK etc.) • Experience using bioinformatics workflow management systems (e.g. Cromwell) and pipeline workflow languages (e.g. WDL) • Familiarity with version control (Git) • Highly motivated, strong work ethic, and able to work independently and with a team • Excellent skills in communication, organization, and time management Preferred Qualifications • 1 – 2 years experience in bioinformatics • Experience developing and implementing scalable data management and infrastructure • Experience with Cloud Computing Environments (e.g. Azure) • Familiarity with relational (e.g. PostgreSQL) and/or NoSQL databases (e.g. MongoDB) • Familiarity with container technologies (e.g. Docker

The Gateway Institute for Brain Research is looking for a Computational Systems Biologist hire to help drive the biological understanding of neurological diseases. The position will support Gateway’s in vitro and in vivo experimentation to discover novel genetic modifiers, small molecules, biologics, and potential therapeutic targets for use in Parkinson’s Disease. Responsibilities... • Creation of computational pathway models built from external as well as internal data. • Analysis of gene expression data and scaling of information results to understand what molecular events are taking place in both diseased as well as normal tissue. • Creation and utilization of data visualization approaches for relaying analysis findings • Partner with Disease area biology experts in project teams • Actively communicate results, experiment design and outcomes to colleagues Required Qualifications • Requires MS or PhD. degree in biology, chemistry, computer science, physics or other relevant science • 2+ years of General experience in the field; laboratory and related research experience a plus. • Must possess computer programming skills, mathematical, instrumentation, interpersonal, communication, and documentation skills. Skills in R, Python, or Matlab. • Ability to give and follow written and oral instructions; ability to communicate effectively with others; ability to react and perform in scientific situations; ability to exercise analytical judgment on work to be done and meet job demands. • Must exhibit a solid understanding of computational approaches Salary Based On Experience And Scientific Skills 401K, Dental, Health, Vision - Available three months after employment Job Type: Full-time

Current Employees: If you are a current Staff, Faculty or Temporary employee at the University of Miami, please click here to log in to Workday to use the internal application process. To learn how to apply for a faculty or staff position using the Career worklet, please review this tip sheet... Transforming Lives The University of Miami is among the top research universities and academic medical centers in the nation, and one of the largest private employers in South Florida. With more than 16,000 faculty and staff, the University strives for excellence, and is driven by a powerful mission to transform and impact the lives of its students, patients, members of the community, and people across the globe. The University is committed to fostering a culture of belonging, where everyone feels valued and has the opportunity to add value. Through values of Diversity, Integrity, Responsibility, Excellence, Compassion, Creativity, and Teamwork (DIRECCT) the U community works together to create an environment driven by purpose, excellence, community, and service. The Department of Molecular & Cellular Pharmacology has an exciting opportunity for a Full Time Bioinformatics Analyst. The Bioinformatics Analyst works with research staff to extend capabilities in bioinformatics and improve understanding of genetic variation in human health and disease. The Bioinformatics Analyst maintains and performs analysis with existing pipelines while assisting and benchmarking the development of novel methods. Maintain and expand current computational infrastructure of Sylvester’s internal end-user data analytics platform. Monitors system logs and activity on both the on-premise and cloud-based computational infrastructure of the platform. Design, manage, and maintain tools to streamline operational processes. Oversee key elements of the platform’s data and software infrastructure. Researches, installs, and tests software updates and patches to support applications and various operating systems. Provides scripting and programming support to Sylvester’s internal end-user data analytics platform. Runs and maintains existing next generation data analysis pipelines. Assists senior bioinformatics analysts in pipeline and algorithm development and validation. Extracts features of interest from data relating to specific biological questions. Contributes to the maintenance of genomic and clinical databases. Performs statistical and integrative data analysis on genomics and clinical data. Works along-side other team members and data analysts. Follows standard operating procedures, documentation, and scripts to generate reports. Adheres to University and unit-level policies and procedures and safeguards University assets. Department Specific Responsibilities • Develop and maintain production pipelines for analyzing high-throughput NGS data: (e.g. bulk/single-cell RNA-seq, WGS/WES, ATAC-seq) • Develop visualization and computational tools for the exploration and analysis of large scale multi-omic datasets • Integrate algorithms and pipelines with Sylvester’s internal end-user data analytics platform • Write standard operating procedures and other relevant documentation • Runs and maintains existing next generation data analysis pipelines. • Assists senior bioinformatics analysts in pipeline and algorithm development and validation. • Extracts features of interest from data relating to specific biological questions. • Contributes to the maintenance of genomic and clinical databases. • Performs statistical and integrative data analysis on genomics and clinical data. • Works along-side other team members and data analysts. • Follows standard operating procedures, documentation, and scripts to generate reports. • Adheres to University and unit-level policies and procedures and safeguards University assets. This list of duties and responsibilities is not intended to be all-inclusive and may be expanded to include other duties or responsibilities as necessary. Core Qualifications Education: Bachelor’s Degree in Bioinformatics, computational biology, statistics, data science, computer science, or a related field or 7 years of equivalent work experience in relevant technical domain or Associate’s Degree and 4 years of equivalent engineering work experience in relevant technical domain Experience: Required: • Minimum of 1 year of experience • Fluency in R or python and Unix (bash) • Experience with NGS data analysis, using common bioinformatics tools (BWA, STAR, Picard, GATK etc.) • Experience using bioinformatics workflow management systems (e.g. Cromwell) and pipeline workflow languages (e.g. WDL) • Familiarity with version control (Git) Preferred: • 1 – 2 years experience in bioinformatics • Experience developing and implementing scalable data management and infrastructure • Experience with Cloud Computing Environments (e.g. Azure) • Familiarity with relational (e.g. PostgreSQL) and/or NoSQL databases (e.g. MongoDB) • Familiarity with container technologies (e.g. Docker) • Familiarity with machine learning frameworks (e.g. Scikit-learn, Tensorflow), developing and deploying machine learning models Knowledge, Skills and Attitudes: • Ability to analyze, organize and prioritize work under pressure while meeting deadlines • Ability to work independently and/or in a collaborative environment • Skill in collecting, organizing, and analyzing data • Ability to recognize, analyze, and solve a variety of problems • Ability to exercise sound judgment in making critical decisions • Ability to process and handle confidential information with discretion • Proficiency in computer software #LN-AL1 The University of Miami offers competitive salaries and a comprehensive benefits package including medical, dental, tuition remission and more. UHealth-University of Miami Health System, South Florida's only university-based health system, provides leading-edge patient care powered by the ground breaking research and medical education at the Miller School of Medicine. As an academic medical center, we are proud to serve South Florida, Latin America and the Caribbean. Our physicians represent more than 100 specialties and sub-specialties, and have more than one million patient encounters each year. Our tradition of excellence has earned worldwide recognition for outstanding teaching, research and patient care. We're the challenge you've been looking for. Patient safety is a top priority. As a result, during the Influenza ("the flu") season (September through April), the University Of Miami Miller School Of Medicine requires all employees who provide ongoing services to patients, work in a location (all Hospitals and clinics) where patient care is provided, or work in patient care or clinical care areas, to have an annual influenza vaccination. Failure to meet this requirement will result in rescinding or termination of employment. The University of Miami is an Equal Opportunity Employer - Females/Minorities/Protected Veterans/Individuals with Disabilities are encouraged to apply. Applicants and employees are protected from discrimination based on certain categories protected by Federal law. Click here for additional information. Job Status: Full time Employee Type: Staff Pay Grade: r7

The Department of Neurological Surgery at Northwestern University Feinberg School of Medicine is seeking a faculty candidate interested in the interface of bioinformatics, machine learning, and the medical sciences. As the acquisition of biomedical data has become increasingly scalable, the challenge has shifted from obtaining data to identifying relevant data and analyzing and interpreting it... relative to the existing corpus of research. Often data is collected across multiple modalities including various imaging and ‘omics platforms, each with its own associated databases. Our goal is to develop tools that leverage the multilayered nature of the data to establish relationships between modalities and direct experiments using machine learning.Qualifications: Ph. D. in Biophysics/Physics, Applied Mathematics, Computer Science, Statistics, Quantitative/Computational Biology, or related field. Strong background in statistics, experience implementing machine learning algorithms, and demonstrated ability to extract datasets from publicly available sources. Experience building analysis pipelines for ‘omics data. Fluency with R/Python is a plus. Research Objectives: Develop machine learning algorithms to direct biomedical experiments, integrate knowledge from multiple biomedical data modalities to obtain a coherent understanding, collaborate with medical researchers to design experiments and analysis approaches. Benefits: Competitive salary commensurable with experience; travel, computer, and relocation funds; and interdisciplinary research environment. Interested applicants must send a current curriculum vitae, a cover letter containing a short summary of research experience and aspirations, and names and contact information for at least three professional references to Maciej Lesniak, MD Professor and Chair, Department of Neurosurgery, Northwestern Medicine (maciej.lesniak@northwestern.edu) Position opened until filled. Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, underrepresented racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Hiring is contingent upon eligibility to work in the United States

Shift - Typically between 9AM-5PM Central Time. Job Description... • We have an exciting contract opportunity for a Bioinformatics Programmer to support bioinformatics pipeline development in GRC. • Primary responsibility is the development of existing processing pipelines implemented in CWL (e.g., Bulk RNAseq, Germline/Somatic Variant) for deployment in Linux HPC environments, as well as the updating of relevant user documentation. • Candidate will work with stakeholder users to enable utilization of CWL pipelines on their project data. • If candidate harbors strong skills/interest in pipeline deployment in AWS, there is also a need to connect these pipelines to a highly-scalable internal Genomics Data Platform. • Ideal candidate must have strong CWL workflow development skills, preferably in a bioinformatics environment. • Data engineering and software development roles in Bioinformatics settings. Skills • Proficient in CWL workflow development • Containerization technology (e.g., Docker, Singularity) • Programming in a Linux HPC environment with Python and BASH • Version control with git • Strong ability to communicate with group members as well as stakeholders Years of experience, education, and/or certification • B.S. or M.S. in Computational Biology, Bioinformatics, Computer Science, or comparable field. Nice to have (but not required) • Comfortable working with NGS data (mainly short read technology

Passionate about precision medicine and advancing the healthcare industry? Recent advancements in underlying technology have finally made it possible for AI to impact clinical care in a meaningful way. Tempus' proprietary platform connects an entire ecosystem of real-world evidence to deliver real-time, actionable insights to physicians, providing critical information about the right treatments... for the right patients, at the right time. We are looking for a highly motivated and capable bioinformatics team lead with extensive experience and interest in translational cancer research and genomics algorithm development. This position requires experience with scientific programming, relational data systems, algorithms development, and statistical modeling. Top candidates will also have leadership experience in NGS pipeline development in a clinical setting. Responsibilities • Design and conduct analysis to improve variant calling, classification and analysis systems. • Translate insight from model systems into predictors and classifiers of therapeutic response and prognosis in clinical cancer care. • Collaborate with scientists, and clinicians to design and perform analyses on cancer clinical sequencing data in order to improve quality of care. • Lead an interdisciplinary group of scientists and engineers to translate research into clinically actionable insights for our clients. • Develop algorithms used to gain insight into cancer variation through analysis of next generation sequencing data • Communicate with outside scientific teams as well as product and bioinformatics leadership • Produce high quality and detailed documentation for all projects. Preferred Qualifications • Must have completed a Ph.D. in Cancer Biology or Molecular Biology related to cancer. • At least 5 years of post-doc experience • Computational skills using R, Bioconductor, and/or Python. Ideal Candidates Will Possess • Experience in cancer genetics, immunology, or molecular biology • Experience working with next-generation sequencing data • Leadership experience in NGS pipeline development in a clinical setting. • Self-driven and works well in interdisciplinary teams • Experience leading a team of scientists or software engineers • Experience with communicating insights and presenting concepts to a diverse audience • Demonstrated programming ability • Background in predictive or prognostic algorithm development • Strong background in the development of statistical models

Job ID: 41513 Location: Chicago, Illinois... Department: MED-Biochem&Molecular Genetics Salary/Grade: EXS/8 Job Summary: A Bioinformatician position is available in the Shilatifard laboratory in the Department of Biochemistry and Molecular Genetics at Northwestern University. Experience in the Next Generation Sequencing (NGS) is a pre-requisite, with background in bioinformatics, biostatistics, or computational biology. Bioinformatician will support current projects analyzing ChIP-seq, RNA-seq and PRO-seq data and will assist in scaling the rapidly growing genomics platform by building state-of-the-art bioinformatics solutions. The successful candidate will work under a supervision of the Lead Bioinformatician to design, implement, and validate NGS bioinformatics pipelines and maintain NGS database. This position requires proficiency in R, Python or Perl, and familiarity with bash scripting. The laboratory is located at the downtown Chicago campus in the vibrant Streeterville neighborhood along the shore of Lake Michigan. Specific Responsibilities: Strategic Planning • Performs data management, data analysis and other bioinformatics-related tasks in coordination with other computing and bioinformatics staff. Assures that quality control criteria are met. • Adheres to detailed work plans and timelines. Provides timely status reports. • Collaborates with technical staff, instructs rotating students and new members of the laboratory staff as needed. Administration • Reviews reports before presentation to ensure quality and accuracy. • Prepare manuscripts on related data analysis. • Management of the related data produced at the Core Facility Development • Supports bioinformatics operations and supports NGS projects in the Shilatifard Lab at the direction of the Lead Bioinformatician. • Support current Next Generation Sequencing projects with datasets including ChIP-seq, Total RNA-seq, Nascent RNA-seq, and GRO-seq. Miscellaneous • Performs other duties as assigned. Minimum Qualifications: • Successful completion of a full 4-year course of study in an accredited college or university leading to a bachelor's or higher degree; OR appropriate combination of education and experience. • 4 years data analysis/report writing, or similar experience required. • Please see information highlighted in tables below. Minimum Competencies: (Skills, knowledge, and abilities.) • Demonstrated ability to learn about new technologies • Demonstrated ability in working with commercial software • Outstanding interpersonal skills and ability to work with individuals and groups • Ability to multitask, work and learn independently, and be self-motivated • A record of taking the initiative to solve problems and working to high-quality standards Preferred Qualifications: • PhD or Master's degree in Bioinformatics, Biostatistics or Computer Science with biology background. • Proficient in Unix, with experience R, Python or Perl. • Familiarity with at least one database language such MySQL, Oracle etc. is preferred. • Background in statistics is preferred • Willingness and capability to share knowledge with other members of the team Preferred Competencies: (Skills, knowledge, and abilities) • Record of taking the initiative to solve problems and working with high standards • Outstanding interpersonal skills • Familiarity with software versioning tools • Please highlight requirements: • Infrastructure • Linux Operating System • SQL/MySQL/Postgres • Programming Languages and Frameworks • Perl • Python • Shell Scripting • R • Analytical • critical thinking • Debugging • problem solving • Troubleshooting • Project • Code documentation • collaboration and teamwork • facilitate collaboration • organizational skills The Northwestern campus sits on the traditional homelands of the people of the Council of Three Fires, the Ojibwe, Potawatomi, and Odawa as well as the Menominee, Miami and Ho-Chunk nations. We acknowledge and honor the original people of the land upon which Northwestern University stands, and the Native people who remain on this land today. Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Click for information onEEO is the Law