Bioinformatics Jobs

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

Location: Hyde Park Campus Job Description... • Develops, applies, documents, and maintains computational tools, both for own use and to support analysis by biologist colleagues without formal computational training; critically evaluate computational solutions. • Develops customized computational solutions supporting new kinds of assays and experiments; understands the analytical needs of new experiments, working closely with wet-lab experimental biologists. • Implements and optimizes successful algorithms and methods to be shared for use by the broader community. • Develops figures and reports, which provide transparency into the data quality and characteristics, and automates the production of such reports as routine components of computational analysis pipelines. • Reports data to supervisor and team, attends team meetings to share results, plan projects and experiments, and ensures that projects support current team goals. • Maintains and organizes computational infrastructure and resources. • Contributes to generation of protocols, publications, and intellectual property. • Develops, tests, debugs, and maintains new and existing application software. • Evaluates new technologies and software products to determine feasibility and desirability of incorporating their capabilities within research projects. • Participates in the product development life cycle, providing professional assistance to the design of front-end applications and database systems back-end schema. Analyzes high-level system specifications and makes sure that all application development standards are met. • Develops and presents technical training materials and web-based documentation. Ensures timely systems support and updates. Assists in conducting information security assessments and risk analysis of computing environment. • Performs other related work as needed. Preferred Qualifications Education: • PhD in computer science, computational biology, bioinformatics, quantitative science or related field. Experience: • Practical experience in data analysis, preferably in an independent project in an academic research laboratory setting. Technical Skills or Knowledge: • Fluency in Unix, standard bioinformatics tools (Python, R, or equivalent), and a programming language (C/C++, Java). • Background in statistics and machine learning. • Proficient in SLURM or other job scheduler, and/or bioinformatics tools. • Excellent communication skills and the ability to interact professionally with all levels of staff and external contacts in a fast-paced environment. • Exceptional organization and time management skills. • Trained in biology or immunology; inclination to acquire such knowledge. • Identify and gain expertise in appropriate new technologies and/or software tools. Preferred Competencies • Understand and translate researchers' scientific goals into computational requirements. • Work well with faculty and researchers. • Function as part of an interactive team while demonstrating self-initiative to achieve project's goals and Research Computing Center's mission. • Strong analytical skills and problem-solving ability. Application Documents • Resume/CV (required) • Cover Letter (required) The University of Chicago is an Affirmative Action/Equal Opportunity/Disabled/Veterans Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, status as an individual with a disability, protected veteran status, genetic information, or other protected classes under the law. For additional information please see the University's Notice of Nondiscrimination. Staff Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-5800 or submit a request via the Applicant Inquiry Form. The University of Chicago's Annual Security & Fire Safety Report (Report) provides information about University offices and programs that provide safety support, crime and fire statistics, emergency response and communications plans, and other policies and information. The Report can be accessed online at: securityreport.uchicago.edu. Paper copies of the Report are available, upon request, from the University of Chicago Police Department, 850 E. 61st Street, Chicago, IL 60637

Passionate about making a difference in the world of cancer genomics? With the advent of genomic sequencing, we can finally decode and process our genetic makeup. We now have more data than ever before, but providers don't have the infrastructure, time, or expertise to make sense of this data. We're on a mission to connect an entire ecosystem to redefine how genomic data is used in clinical... settings. We are seeking a highly motivated and capable bioinformatics scientist to manage data operations and quality assurance for bioinformatics data delivered to our external clients and research partners. This position requires extensive experience with cancer genomics, precision medicine, bioinformatics pipelines, and pharma/research client delivery work-flows. Top candidates will also have experience deploying bioinformatics code and retrieving relevant data from relational databases. Duties And Responsibilities • Field questions and requests from internal stakeholders and external customers - including pharmaceutical clients and research partners - regarding the Tempus bioinformatics pipeline. • Use SQL, Python, Bash, etc., to retrieve relevant data from various bioinformatics resources, to support data delivery. • Engage in cross-functional analysis with various teams within Tempus, including other scientists and clinicians, delivery teams, and operations team management to analyze cancer clinical sequencing data relevant to Partner/Pharma clients and respond to their specific questions. • Communicate findings in a clear and logical manner to help stakeholders make scientific decisions based on your data analysis. • Produce high quality and detailed documentation for all projects. Required Experience • Advanced degree in bioinformatics, computational biology, genomics, or related field. • Familiarity with relational database querying (MySQL, postgres). • Familiarity with Python and/or R. • Familiarity with statistical modeling. Ideal Candidates Will Possess • PhD in Bioinformatics and/or computational biology • Pharma work experience • Thorough understanding of bioinformatics data analysis pipelines. • Demonstrated programming ability in relevant bioinformatic programming language(s) • Work experience in cancer genetics, precision medicine, or molecular biology • Significant work experience handling next-generation sequencing data • Self-driven and works well in interdisciplinary teams • Experience with communicating insights and presenting concepts to a diverse audience • Strong background in statistical models and analyzing and resolving problematic data • Familiar with cloud computing a plus

Department BSD PED – Section Administrator: Hematology, Oncology, and Stem Cell Transplantation... About the Department The Section of Pediatric Hematology/Oncology provides care for patients and families with acute and chronic medical conditions, or other hematologic diseases, requiring the specialty knowledge and skills of Hematology, Oncology and Stem Cell Transplantation. Job Summary The Piunti Lab is looking for a Bioinformatics Specialist; the job administers programs and support all phases of bioinformatics activities by helping devise or modify procedures to solve biological complex problems. The Bioinformatics Specialist is responsible for all aspects of research projects and research facilities. Plans and conducts clinical and non-clinical research; facilitates and monitors daily activities of research projects. Directs engineering and technical support activities to develop and maintain tools and computational methods needed to gather and analyze data. Responsibilities • Knowledge and experience in basic and advance analyses of NGS data (ChIP-seq, RNA-seq, ATAC-seq, Hi-C, Bisulfite sequencing, etc.). • Participates in creating data algorithms and specialized computer software to identify and classify components of a biological system (i.e. create a pipeline for data analyses and an accessible internal repository for sequencing data). • Applies basic application of computational tools and information technology to gather, analyze and visualize data in biology and biomedical research (i.e. generating easy-to-interpret graphs that can be used for publications or presentations at conferences). • Interprets data analysis of high throughput genomics, proteomics and genetic data generally concerning chromatin biology projects. • Plans own resources to implement or modify existing web-based bioinformatics tools. • Designs and perform formal evaluation of informatics methods and products. • Manipulates publicly accessible, commercial, or proprietary genomic, proteomic, or post-genomic databases. • Performs other related work as needed. Minimum Qualifications Education: Minimum requirements include a college or university degree in related field. Work Experience: Minimum requirements include knowledge and skills developed through 5-7 years of work experience in a related job discipline. Preferred Qualifications Education: • College or university degree in Biology, Biology or Informatics or related disciplines. • Master’s degree strongly preferred. Experience: • Author of at least one research article where the candidate contributed to bioinformatics analyses. • Experience in single cell genomic analyses Working Conditions • Laboratory setting Application Documents • Resume (required) • Cover letter (preferred) • References (preferred) When applying, the document(s) MUST be uploaded via the My Experience page, in the section titled Application Documents of the application. Posting Statement Effective October 15, 2021, the University of Chicago requires COVID vaccination for all students, faculty, and staff members. Individuals may claim exemption from the vaccine requirement for medical or religious reasons. The University of Chicago is an Affirmative Action/Equal Opportunity/Disabled/Veterans Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, status as an individual with a disability, protected veteran status, genetic information, or other protected classes under the law. For additional information please see the University’s Notice of Nondiscrimination. Staff Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-5800 or submit a request via Applicant Inquiry Form. We seek a diverse pool of applicants who wish to join an academic community that places the highest value on rigorous inquiry and encourages a diversity of perspectives, experiences, groups of individuals, and ideas to inform and stimulate intellectual challenge, engagement, and exchange. All offers of employment are contingent upon a background check that includes a review of conviction history. A conviction does not automatically preclude University employment. Rather, the University considers conviction information on a case-by-case basis and assesses the nature of the offense, the circumstances surrounding it, the proximity in time of the conviction, and its relevance to the position. Tagged as: Life Sciences

Northwestern University offers impressively stimulating environment for conducting scientific research. Dr. Ruli Gao’s laboratory at Northwestern University Feinberg School of Medicine harbors both single cell sequencing technologies and computational methodologies under one roof, surrounded by nationally top ranked hospitals and the Robert H. Lurie Cancer Center. Dr. Ruli Gao has significant contribution in tumor evolution fields by developing and applying single cell sequencing technologies and bioinformatic algorithms. These include development of the paradigm shift punctuated copy number evolution (PCNE) model that challenged the Darwinian Gradualism in tumor evolution (Nature Genetics, 2016), the bi-mode chemo-resistance evolution model where adaptive selection of genotypes and acquired reprogramming of phenotypes are activated in parallel (Cell, 2018), the high throughput nanogrid single nuclear RNA sequencing technology that opened the avenue of analyzing single cell... transcriptomes from archival frozen tissue samples (Nature Communications, 2017), and the CopyKat, an integrative Bayesian algorithm to infer single cell genetic architecture from scRNA-seq data (Nature Biotechnology, 2021). The Gao Laboratory is looking for highly motivated postdoc candidates, who are interested in developing and applying novel bioinformatic algorithms for single cell and third generation sequencing data to understand the cellular and molecular mechanisms underlying human cancer and other diseases.Applicants are expected to be recently graduated PH.D. or M.D./PH.D.; Degrees in Bioinformatics, Genetics and Genomics, Computational Biology, or equivalent areas are highly preferred. Interested candidates should directly send his/her CV along with the contact information of three references to Dr. RuliGao (Email: ruli.gao@northwestern.edu

Department: MED-Center for Genetic Med Salary/Grade: EXS/8 ... Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis. This includes database administration, data consolidation, data analysis and management reporting. Utilizes software to generate metrics and develops actionable recommendations. Collaborates with various function teams such as marketing, research, and IT to achieve business results. The Bioinformatics Analyst will work in the Center for Genetic Medicine and the Gottwein lab in the Department of Microbiology and Immunology, performing basic and advanced analyses in bioinformatics using current open-source software and by developing new analytical tools and pipelines. The successful candidate will have a background in bioinformatics, biostatistics, and/or cancer biology and have software development experience, at least to the level of developing scripts for processing data in languages such as Perl, Python, and/or R. The candidate must be comfortable working in a Linux/Unix environment. Typical data sets include single-cell RNA-seq, RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, CRISPR screening results, WES, and WGS. Specific Responsibilities : Strategic Planning • Manages and plans for data/analysis requests and projects. • Provides consultation to customers on appropriate data management, methodological issues, and statistical analyses. • Collaborates with technical staff explaining needs of functional users. Serve on committees related to data structure and governance. Administration • Reviews reports before presentation to ensure quality and accuracy. • Develops and maintains documentation of process for quality assurance and reporting methodology • Defines, develops and communicates new standards and best practices. Development • Develops queries and quality metrics. • Interprets results using a variety of techniques, ranging from simple data aggregation via statistical analysis to complex statistical analysis. • Determines data structure for local datasets. Performance • Develops and documents standards for data quality and regulatory compliance pertaining to reporting. • Ensures quality and compliance by reviewing reports Supervises • Provides work direction and/or supervises staff such as team members, subordinates, contractors, vendors, students, etc. • Recommends staff hires/terminations. • Coaches and mentors staff. • Manages projects ensuring timelines and deliverables are met and meet expectations. 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. • Three to four years of relevant work experience in analyzing next generation sequencing data from projects involving RNA-seq, single-cell RNA-seq, ChIP-seq, and/or variant analysis. • Experience in computing in a Linux/Unix environment. • Experience in at least 1 scripting language such as perl, python, or shell scripting. • Willingness and capability to share knowledge with other members of the team. • Please highlight requirements: • Programming Languages and Frameworks • Perl • Python • Shell Scripting • Analytical • Critical thinking • Data mining • Data modeling • Decision making • Judgment • Metadata creation and management • Problem solving • Troubleshooting • Project • Collaboration and teamwork • Organizational skills • Planning Minimum Competencies: (Skills, knowledge, and abilities.) • Demonstrated ability to learn about new technologies. • Demonstrated ability in working with open-source bioinformatics software and publically available databases. • 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: • BS or MS in Bioinformatics, Biostatistics or Statistics with a cancer biology background. • Experience in Cancer Informatics. • Experience with high-dimensional data mining and machine learning. • Experience working in an academic or health care computing environment. • Ability to solve complex bioinformatics problems. Preferred Competencies: (Skills, knowledge, and abilities) • Record of taking the initiative to solve problems and working with high standards. • Familiarity with software versioning tools. Benefits: At Northwestern, we are proud to provide meaningful, competitive, high-quality health care plans, retirement benefits, tuition discounts and more! Visit us at https://www.northwestern.edu/hr/benefits/index.html to learn more. Work-Life and Wellness: Northwestern offers comprehensive programs and services to help you and your family navigate life’s challenges and opportunities, and adopt and maintain healthy lifestyles. We support flexible work arrangements where possible and programs to help you locate and pay for quality, affordable childcare and senior/adult care. Visit us at https://www.northwestern.edu/hr/benefits/work-life/index.html to learn more. Professional Growth & Development: Northwestern supports employee career deve

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 seeking a highly motivated and capable bioinformatics scientist 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 experience deploying bioinformatics code within a clinical setting. Duties And 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. • Work in interdisciplinary groups of scientists, engineers, and product developers 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 • 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. • 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 • Self-driven and works well in interdisciplinary teams • 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