Bioinformatics Jobs

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. Data-driven computational approaches are a critical driver across all therapeutic areas at Lilly. At Lilly Research Labs (LRL), we are expanding our efforts in bioinformatics, creating a centralized bioinformatics hub that works with bioinformatics groups across different therapeutic areas and functions to provide centralized scientific resources, enable state-of-the art infrastructure and tools, and bring new technologies to Lilly. We are... searching for a talented and experienced scientist to join the Lilly Omics Hub that operates in an interdisciplinary manner within a tightly integrated research community at Lilly. The successful candidate will have a flexible, learning mindset to design customer-aligned solutions; they will work in a highly dynamic team, creating workflows to process and analyze high-dimensional data. This will include development of self-service analytics tools to enable and facilitate the real-time analysis of scientific data within our research community. This position will work closely with internal and external partners to find new ways to accelerate bioinformatics efforts across LRL and will represent LRL bioinformatics to internal and external partners. Minimum Qualifications • Bachelor’s/Master’s/PhD in computer science, bioinformatics, or equivalent experience • 2+ years of software development experience, including experience in computer science, bioinformatics or other applied science • Documented track record delivering and deploying large-scale informatics production solutions in the cloud using AWS/Azure and Docker • Experience implementing bioinformatics pipelines using scalable cloud solutions Familiarity with Nextflow is a plus • A strong knack for creating visually appealing UX/UI, and ability to abide by clear design rules • Understanding of NGS technology, and downstream -omics data analysis (RNAseq, ATACseq, ChIPseq, etc) • Familiarity with designing, maintaining and implementing relational databases. Experience with NoSQL databases a plus • Proficiency in working within a Linux/Unix environment Additional Information: • Location is flexible, within the US • Lilly currently anticipates that the base salary for this position could range from between $80,000 to $240,000 and will depend, in part, on the successful candidate’s qualifications for the role, including education and experience. Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).  Of course, the compensation described above is subject to change and could be higher or lower than the range described above.  Further, Lilly reserves the right to amend, modify , or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees. Eli Lilly and Company, Lilly USA, LLC and our wholly owned subsidiaries (collectively “Lilly”) are committed to help individuals with disabilities to participate in the workforce and ensure equal opportunity to compete for jobs. If you require an accommodation to submit a resume for positions at Lilly, please email Lilly Human Resources ( LillyRecruitingCompliance@lists.lilly.com ) for further assistance. Please note This email address is intended for use only to request an accommodation as part of the application process. Any other correspondence will not receive a response. Lilly is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status. Our employee resource groups (ERGs) offer strong support networks for their members and help our company develop talented individuals for future leadership roles. Our current groups include: Africa, Middle East, Central Asia Network, African American Network, Chinese Culture Network, Early Career Professionals, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinos at Lilly, PRIDE (LGBTQ + Allies), Veterans Leadership Network, Women’s Network, Working and Living with Disabilities. Learn more about all of our groups. #WeAreLilly

Postdoctoral and Associate Research Scientist positions in Bioinformatics, Multi-Omics Data Science and Computational Proteogenomics for Immunotherapy and Cancer Vaccine Research. Postdoctoral and Associate Research Scientist Positions in Etienne Caron Lab at Department of Immunobiology, Yale School of Medicine. The Caron Lab seeks exceptional Postdoctoral and Associate Research Scientist... candidates with a passion for innovation in immunotherapy and cancer vaccine research using computational proteogenomics and immunopeptidomics approaches. The overarching goal of the Caron Lab is to develop and apply mass spectrometry-based immunopeptidomics and systems immunology approaches to understand the generation, composition and dynamics of both the self and nonself immunopeptidome, as well as its interaction with T cells, with the goal of innovating treatments and preventive strategies for a broad range of immune-related diseases. Responsabilities: • Develop and apply computational pipelines and innovative bioinformatics approaches for the discovery of novel tumor-specific antigens, PTMs, and both canonical and non-canonical actionable T cell epitopes from large immunopeptidomics datasets, • Collaborate with other researchers (academic and industry), • Train other lab members, • Publish high impact factor publications, • Present at conferences, locally, nationally and internationally, • Actively contribute to the lab's activities, including preparation of manuscripts and research grants. Qualifications: • Ph.D. in bioinformatics, systems immunology or related field, • Demonstrated expertise in the integration and analysis of large multi-omics datasets (WGS, RNAseq, ribo-seq, proteomics, immunopeptidomics), • Knowledge in T cell biology and neoantigen prediction algorithms, • Demonstrated expertise in the development of computational pipelines and databases, • Strong communication skills in English (spoken and written), • Demonstrated excellence in time management and teamwork. Opportunities and Benefits: The selected candidates will have the opportunity to gain expertise in mass spectrometry, systems immunology, spatial immunopeptidomics, T-cell epitope discovery, immunology, and vaccine design. The selected candidates will also have the opportunity to become active players within several Yale Centers, including the Yale Center for Immuno-Oncology (YCIO), Center for Infection and Immunity (CII), and Center for Systems and Engineering and Immunology (CSEI). Strong support will be given to pursue independent directions. Compensation and benefits will be according to Yale policies. About the Caron Lab: Dr. Caron is an Assistant Professor at Yale University. Over the last five years, the Caron Lab has published 14 immunopeptidomics manuscripts including 10 as corresponding papers in Journal of Experimental Medicine, Cell Systems, Cancer Discovery, and other high-profile journals. Dr. Caron is co-founder and former chair (2015-2020) of the Human Immunopeptidome Project. He has a total citation of >4400 times to date and is the recipient of multiple Awards and Recognitions. Please see https://medicine.yale.edu/profile/etienne-caron/ for more information. If interested, please send your CV and motivation letter to etienne.caron@yale.edu. Yale University is an Affirmative Action/Equal Opportunity Employer. Yale values diversity among its students, staff, and faculty and strongly welcomes applications from women, persons with disabilities, protected Veterans, and underrepresented minorities

• Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and... comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals. • We seek an enthusiastic and highly motivated bioinformatics associate to join our cancer genomics research group. This individual will join oncologists, computational biologists and research scientists on our effort aimed at studying the relationships between cancer causing genomic alterations and clinical outcome. This position will provide ample opportunities for professional development and the acquisition of cutting-edge skills in basic and translational cancer genomics research, research planning and strategy, and data analysis and interpretation. • This individual will analyze cancer genomic data generated at Dana Farber using software tools within our team and by generating their own statistical analysis code. This individual will collaborate with oncologists, computational biologists and research scientist to study alterations in patients’ somatic genomes in order to assist in finding new cancer treatments and cures. • Works in teams with oncologists, research scientist and molecular biologists to define and execute computational approaches. • Performs computational analysis of next generation sequencing data, somatic copy number alterations, expression profiling, and biological pathways using in house algorithms. • Generates own code to conduct various other statistical analyses including those to discover relationships between cancer alterations and clinical correlates. • Presents data at project team meetings. • Assists in drafting of scientific manuscripts. • This employee will be located at both the Dana-Farber Longwood Medical Area campus and at the Broad Institute in Cambridge. At Dana-Farber Cancer Institute, we work every day to create an innovative, caring, and inclusive environment where every patient, family, and staff member feels they belong. As relentless as we are in our mission to reduce the burden of cancer for all, we are equally committed to diversifying our faculty and staff. Cancer knows no boundaries and when it comes to hiring the most dedicated and diverse professionals, neither do we. If working in this kind of organization inspires you, we encourage you to apply. • Required: B.S./B.A. in the life sciences, physical sciences, or computational sciences. Some coding knowledge of either R, Matlab, and/or python. The ability to work in teams, excellent communication and data presentation skills. • Preferred: Background in molecular genetic data. Understanding of statistical methods and working in cloud computing and UNIX environments. • We will consider May 2024 graduates. Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law. EEOC Poster

Understanding the location and functions of genes within an organism's genome is useful for scientists to learn more about the relationship between organisms. We look at several features of fruit fly genomes as part of the Genomics Education Partnership. We use online software to make judgements about start and stop sites on exons within the genomes. Students can participate remotely, though sessions with the PI are needed for training and initial workthroughs.

Personal Genome Diagnostics (PGDx), a part of LabCorp, is Empowering the Fight Against Cancer by unlocking actionable information from the genome. We are developing an innovative portfolio of tissue-based and non-invasive liquid biopsy genomic products for laboratories worldwide. We are seeking a highly motivated and curious Bioinformatics Software Engineer to join our Bioinformatics Core in the... Baltimore, MD area. Every part of our organization relies on software. As a Bioinformatics Software Engineer you will be producing software and documentation that will directly impact our products, customers and patients. RESPONSIBILITIES: • Actively participate in all facets of design, development, testing, and maintenance of robust software and systems to support PGDx products and services. • Strategize with leadership to solve challenging problems • Follow the software development lifecycle in an agile environment • Contribute to software and project requirements • Contribute to the architecture and design of software • Provide technical leadership and expertise for staff • Ensure data and software quality by designing and implementing test methodologies • Ensure the security of the information systems, software, communication lines, and equipment • Provide reports to managers and staff on systems and software, including capabilities, performance, and security Required Qualifications: • 2+ years of professional software engineering experience • Bachelor’s degree in Bioinformatics, Biology, Computer Science, Software Engineering, or a related major • Confident in a Linux environment • Team-first attitude and entrepreneurial spirit • Ability to deliver within fixed deadlines • Excellent problem-solving skills and ability to learn quickly on the job • Interest in Cancer Biology Preferred Qualifications: • Bioinformatics • NextGen Sequence data analysis • Sequence alignment • Pipeline development • Big data management • Algorithm development • Machine Learning concepts and techniques • Software Engineering • Programming Languages including Python, PERL, R, C/C++, Java, BASH • Web-technologies including Angular, React, JavaScript • Web-service frameworks including Django, RESTful APIs • Workflow systems • Database Services including SQL, NoSQL • Master’s degree/PhD in related field preferred • Familiarity with concepts in genomics and bioinformatics analysis of cancer. • Experience with agile software development methodology and practices, git source control, and Atlassian tools (JIRA, Confluence, Bitbucket, Bamboo). Pay Range: $88,552 to $144,291. Benefits: All job offers will be based on a candidate’s skills and prior relevant experience, applicable degrees/certifications, as well as internal equity and market data. Regular, full-time or part-time employees working 20 or more hours per week are eligible for comprehensive benefits including: Medical, Dental, Vision, Life, STD/LTD, 401(K), ESPP, Paid time off (PTO) or Flexible time off (FTO), Company bonus where applicable. For more detailed information, please click here. Labcorp is proud to be an Equal Opportunity Employer: As an EOE/AA employer, Labcorp strives for diversity and inclusion in the workforce and does not tolerate harassment or discrimination of any kind. We make employment decisions based on the needs of our business and the qualifications of the individual and do not discriminate based upon race, religion, color, national origin, gender (including pregnancy or other medical conditions/needs), family or parental status, marital, civil union or domestic partnership status, sexual orientation, gender identity, gender expression, personal appearance, age, veteran status, disability, genetic information, or any other legally protected characteristic. We encourage all to apply. For more information about how we collect and store your personal data, please see our Privacy Statement

Bioinformatics Data Manager POSITION SUMMARY... SFARI Cohorts and Data Collections Since its beginning, SFARI (Simons Foundation Autism Research Initiative) has partnered with families and clinical centers across the country to build large and diverse cohorts of well-characterized individuals with autism or with specific genetic alterations associated with neurodevelopmental risk. These include the Simons Simplex Collection (SSC), Simons Searchlight, Autism Inpatient Collection, and SPARK. The principles of community-based participatory research have been key to all cohort activities. The Simons Foundation Informatics group manages the collection and distribution of large-scale aggregate and deidentified clinical and genomic data from these cohorts, which are made available to autism researchers through SFARI Base, a clearinghouse for autism and autism-related research data and biospecimens supported by SFARI. Bioinformatics Data Manager The Bioinformatics group at the Simons Foundation is seeking a dedicated full-time bioinformatics data manager. The ideal candidate has outstanding attention to detail, with experience in data science or bioinformatics, and will be at the forefront of the Foundation's open data initiatives. This critical position is responsible for overseeing an extensive and ever-expanding collection of genomics (over 170K whole-exomes and genomes) and biomedical data across Simons Foundation autism cohorts and neuroscience collaborations. The data manager will be instrumental in enhancing data accessibility and utility for both internal staff and external investigators, aligning with the principles of open data and science. The data manager will be part of the bioinformatics team and will collaborate with informatics' engineering team, the SFARI science team, and external investigators. Key responsibilities include meticulous handling and processing of incoming data, such as genomic sequencing or biosensor data, as well as performing detailed quality control checks and downstream bioinformatics analyses. Additionally, the candidate will be responsible for preparing regular data releases and facilitating coordination among different teams, contributing to the Foundation's dynamic and collaborative environment. ESSENTIAL FUNCTIONS/RESPONSIBILITIES Data releases Maintain the Bioinformatics quality control pipeline, used to verify consistency with phenotypic data and ensure the integrity of released genomic data Execute existing variant calling pipelines, which will be included in data releases Package whole-exome and whole-genome data for regular curated and rapid releases Manage ad hoc genetic data releases for various SFARI cohorts and datasets Data organization Coordinate data receipt from external investigators, vendors, and research groups Perform incoming data cleaning, including deidentifying sample identifiers, organizing data files, and ensuring consistent metadata Manage the organization of raw, cleaned, and released data on our local cluster environment Harmonize our large collection of heterogeneous datasets hosted on SFARI Base Data sharing and support Support data sharing for SFARI investigators and collaborations, such as the Autism Rat Consortium (ARC), and Simons Sex Differences Collaboration (SSDC) Respond promptly to dataset questions from external investigators Support data access for cloud platforms MINIMUM QUALIFICATIONS Education B.S. or M.S. in data science, bioinformatics, or a related discipline. Required Experience At least 4+ years' relevant work experience Extensive experience with Linux/bash Experience working in an HPC environment Experience with Python Experience with version control using git / GitHub Basic skills in data analysis and statistics Strong organizational skills and outstanding attention to detail Effective oral and written communicator Ability to thrive in collaborative environments Desired Experience Enthusiasm for open science and collaboration Experience with genomics data processing and analysis Experience writing technical documentation Experience with cloud storage solutions (AWS, Google Cloud, Terra) Working knowledge of SQL Familiarity with data privacy and security regulations in the healthcare or research domain REQUIRED APPLICATION MATERIALS Resume Cover letter stating your interest in the position. Links to code repositories or GitHub, if available COMPENSATION AND BENEFITS The full-time annual compensation range for this position is $130,000 – $145,000, depending on experience. In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package. THE SIMONS FOUNDATION'S DIVERSITY COMMITMENT Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law. To apply, visit: https://simonsfoundation.wd1.myworkdayjobs.com/simonsfoundationcareers/job/160-Fifth-Avenue/Bioinformatics-Data-Manager_R0001472-1 Copyright 2022 Jobelephant.com Inc. All rights reserved. Posted by the FREE value-added recruitment advertising agency jeid-de464cd3bfa68740ae6589b41f02285c

• Develops and manages a specific bioinformatics, computational biology or quantitative genomics project within the research program under the supervising faculty member. • May prepare and submit funding applications within the content areas of the supervisor with permission of the supervisor. • May manage a small research group; conducting reviews and evaluating work... • Leads discussions regarding experimental design, data analysis and interpretation of results. • May represent the supervising faculty member in leading the research group as needed. • Responsible for gathering preliminary data for grant applications, completion of objectives of funded external grants, and preparation of completed work for publication. • Contributes to writing grant applications or manuscripts. • May serve on research committees. • Collaborates and leads genomics and bioinformatics analysis for clinical faculty and other investigators. • Performs literature searches to gather information pertaining to research projects or analytical methods in order to develop new protocols, research projects or grant applications for the work group. • Advises other research employees regarding technical and analytical problems within area of expertise. • Participates in work group meetings and formal seminars to present, explain, and discuss research interests. • Makes presentations to extramural audiences at national meetings and academic institutions. Work is typically performed in an office environment. Accountable for satisfying all job specific obligations and complying with all organization policies and procedures. The specific statements in this profile are not intended to be all-inclusive. They represent typical elements considered necessary to successfully perform the job

The Wistar Institute is a world leader in early-stage discovery science in the areas of cancer, immunology, and infectious disease. Wistar is committed to accelerating research advances from bench to bedside through brilliant science and distinctive approaches to collaboration among scientific investigators and academic and industry partners. Wistar's dynamic environment supports the advancement... of discoveries that will change the future of human health. The Wistar Institute is committed to diversity, equity and inclusion (DEI). All candidates must share our commitment to DEI. The Wistar Institute is especially interested in qualified candidates who can contribute, through their research, mentoring, and/or service, to the diversity and excellence of our academic/research community. The Wistar Institute has multiple openings for Bioinformatics Analysts to join the Bioinformatics Shared Resource of our NCI-designated Cancer Center. The Bioinformatics Core provides Wistar investigators with expertise in computational analyses of biomedical research data as well as database management and software applications support. The Bioinformatics Analyst will: • Apply and develop bioinformatics approaches for analysis of data from high-throughput experiments conducted by Wistar Institute scientists, including but not limited to bulk and single cell next generation sequencing and other various types of genomics and proteomics data. • Design, implement, and evaluate new bioinformatics programs to extend the services and capabilities of the facility. • Develop and implement application for management, analysis and representation of different types of data, including interface implementations of scientific algorithms and to write comprehensive reports. • Execute special projects as assigned and attend project meetings as appropriate. Master's degree in Bioinformatics/Mathematical/Physical/Computational Sciences or related fields required, PhD preferred. Minimum of one-year prior experience in Bioinformatics data analysis and scientific software development for high throughput data (next generation sequencing, proteomics, other platforms) is preferred. Experience in programming languages (e.g. Python or Perl) and experience in R or Matlab statistical environments is required. The ideal candidate will have experience with analysis of most next generation sequencing approaches, including bulk and single cell RNA-seq, CHIP/CUT&RUN/ATAC-seq, HiCHIP/HiC data analyses. Relational database development and website integration knowledge is a plus. The Wistar Institute is located in the University City area of Philadelphia, in the heart of the University of Pennsylvania Campus. Wistar provides resources to its faculty and staff that enable them to conduct cutting edge collaborative research and provides for outstanding intellectual environments and state-of-the-art facilities. We offer a competitive salary and an excellent benefits package. For more information about The Wistar Institute visit our website at www.wistar.org. It is the policy of the Institute to provide equal employment opportunities to all individuals regardless of race, citizenship, ethnicity, color, creed, religion, marital status, national origin, ancestry, sex, age, veteran status, mental or physical disability (including HIV and AIDS), pregnancy, caregiver status, domestic or sexual violence victim status, sexual orientation, gender identity and expression, or on the basis of genetic information, or any other characteristic protected by federal, state, or local law, with respect to all terms and conditions of employment. Other details Apply Now

SHIFT: Day (United States of America ... Seeking Breakthrough Makers Children’s Hospital of Philadelphia (CHOP) offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation. At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care—and your career. CHOP’s Commitment to Diversity, Equity, and Inclusion CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children. We strongly encourage all candidates of diverse backgrounds and lived experiences to apply. A Brief Overview The bioinformatics group in the Department of Biomedical and Health Informatics (DBHI) at The Children’s Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team of Bioinformatics Scientists supporting ongoing basic and translational research within the Division of Oncology and Center for Childhood Cancer Research (CCCR). The candidate will be embedded in the CCCR, a highly collaborative environment, and will primarily be focused on supporting scientific teams and projects as a bioinformatics domain expert. The candidate will attend selected lab meetings and interact daily with principal investigators and individual lab members on a project-by-project basis. Additionally, the candidate will work with a principal investigator overseeing the bioinformatics group in the CCCR and our extended bioinformatics group in DBHI to stay current on emerging technologies and algorithms. The successful candidate will preferably have a PhD degree in Bioinformatics, Computational Biology, or a related field, and must have demonstrable skills in coding in R and/or Python, though both are preferred. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments, experience in the analysis of sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusion transcripts, copy number analyses, or ATAC sequencing), as well as experience in other types of bioinformatics analyses, particularly those involving next-generation sequencing. The successful candidate will have experience with established algorithms/pipelines for processing genomics data, and the ability to learn and apply new methods. They will also be able to conceive and develop innovative solutions for a variety of computational challenges of these data. Creative data visualization skills are important for this position. The Bioinformatics Scientist II position is a position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of bioinformatics tools and methods to bench and clinical research problems in various biomedical domains. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. Activities occur with a moderate degree of supervision with some latitude for independent judgment, development of bioinformatics workflows and processes, and presentation of results. The Bioinformatics Scientist II will begin to apply best practices in collaborative science as a bioinformatics domain expert. Academic output, while not a primary focus of this position, is also expected with a moderate degree of supervision. The Bioinformatics Scientist II is primarily focused on supporting scientific teams and projects as a bioinformatics domain expert. The Bioinformatics Scientist II must be able to perform all responsibilities listed in the Bioinformatics Scientist I job description. All responsibilities listed in this description are additional. What you will do • Pre-Analysis (20%): Contribute to the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support. • Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan. • Contribute to the development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances. • Advocate for specific collaboration requirements for continual advancement of shared pipeline and code resources. • Provide collaboration-specific transparency for data processing and pre-analysis, including sample- and cohort-level status. • Coding (20%): Code and generally support code and applications on behalf of collaborative project and/or team. • Within the context of the collaboration or project, develop and apply best practices to code development. • Establish requirements with the project team. • Review existing applications and code sources (both commercial and open source) and selection of best strategy for development or adoption. • Advocate for chosen strategy to project team by showing value of approach • Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations. • Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews. • Data Analysis (20%): Analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data primarily under the direction of the collaborative project team. • Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings. • Incorporate more advanced applications and methods into analysis. • Develop at least one specialty analytical or biomedical area that serves the collaborative team. • Collaboration (20%): Establish role within collaborative project team as primary bioinformatics resource. • Contribute to and influence project-level management by serving as bioinformatics point. • Define and promote boundaries of support by assessing all stakeholders, including bioinformatics management, collaborator expectations, and funding levels and mechanisms. • Regularly discuss satisfaction and expectations with collaborators; continually advocate for clear understanding of role. • Develop new collaborations with high degree of supervision. • Academic Output (20%): Develop presentations, grant sections, and manuscript sections with subsequent review by peers and mentors. • Regularly contribute to bioinformatics-focused manuscripts and publications. • Regularly contribute to podium presentations and posters. • Contribute to bioinformatics sections of grant and award proposals. Education Qualifications • Bachelor's Degree Required • Master's Degree biological or computational discipline Preferred Experience Qualifications • At least three (3) years experience in applied bioinformatics, genomics, and computational work Required • Experience with management and analysis of complex data types. Required • At least four (4) years of experience in applied bioinformatics, genomics, and computational work Preferred • Experience with Python, Perl, or other languages Preferred • Experience with pipeline or workflow development frameworks Preferred • Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture. Preferred Experience • Four (4) or more years of experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation. • Knowledge of cancer biology and/or genomics Skills and Abilities • Strong UNIX/LINUX expertise required. • Proficiency in R or similar commonly used bioinformatics language required. • Proficiency in various open source and commercial bioinformatics resources and software required. • Knowledge of the working mechanism of microarray, NGS, mass spectrometry, or other high-throughput technologies and awareness of their strengths and weaknesses, as well as applicability to a specific biological problem is preferred. • Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required. • Ability to correctly select and perform statistical tests for most types of genomic data, and to properly interpret their results in the scenario of a specific study is preferred. • Ability to interact with biologists and clinicians during a scientific discussion is required. • Accountability and attention to timelines. • Excellent organization and communication skills with an emphasis on strong presentation skills. • Ability to independently plan and execute analyses of moderate complexity required. • Ability to provide objective validation of results required. • Ability to work in a team environment. To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine. Learn more. Employees may request exemptions for valid religious and medical reasons. Start dates may be delayed until candidates are immunized or exemption requests are reviewed. EEO / VEVRAA Federal Contractor | Tobacco Statement

SHIFT: Day (United States of America ... Seeking Breakthrough Makers Children’s Hospital of Philadelphia (CHOP) offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation. At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care—and your career. CHOP’s Commitment to Diversity, Equity, and Inclusion CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children. We strongly encourage all candidates of diverse backgrounds and lived experiences to apply. A Brief Overview The bioinformatics group in the Department of Biomedical and Health Informatics (DBHI) at Children’s Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team to support ongoing basic and translational research within the Center for Childhood Cancer Research (CCCR) and the Department of Anesthesiology and Critical Care Medicine. The candidate will be embedded in the laboratories of Dr. Caroline Diorio and Dr. Robert B. Lindell and will support scientific projects focused on immune dysregulation disorders related to infection, or due to cancers or cancer therapies. Major areas of focus will be CAR-T and cytokine release syndrome/immune effector cell associated neurotoxicity syndrome, and the immunologic phenotypes of sepsis. The candidate will attend lab meetings and interact daily with principal investigators and individual lab members. Additionally, the candidate will work with a principal investigator overseeing the bioinformatics group in the CCCR and our extended bioinformatics group in DBHI to stay current on emerging technologies and algorithms. The successful candidate will preferably have a MS degree in Bioinformatics, Computational Biology, or a related field, and must have demonstrable skills in coding in R and/or Python, though both are preferred. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments and will be expected to analyze data generated from proximity extension assays (i.e. Olink), bulk RNA sequencing, and multiparameter flow cytometry. Additionally, the successful candidate is expected to have experience with single cell RNA sequencing somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusion transcripts, or copy number analyses as well as experience in other types of bioinformatics analyses, particularly those involving next-generation sequencing. The successful candidate will have experience with established algorithms/pipelines processing genomics data, and the ability to learn and apply new methods. They will also be able to conceive and develop innovative solutions for a variety of computational challenges of these data and develop creative data visualizations. Strong communication, time-management, and presentation skills are essential. Knowledge of cancer biology and/or genomics is preferred. The Bioinformatics Scientist I position is an entry level position for a non-PhD level professional. The focus of the position is development, maintenance, and evolution of the tools that support management and analysis of genomic, proteomic, and other complex molecular data types. This includes the support of internal bioinformatics software, implementation and modifications of existing algorithms, and execution of routine tasks of limited complexity within the general area of bioinformatics analysis. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. All activities occur with a moderate to high degree of supervision and the individual will rely on a high degree of peer-to-peer mentorship. The Bioinformatics Scientist I is primarily focused on the support of higher level bioinformatics personnel but may have minor direct interaction with collaborators and designees to resolve primarily technical issues and solutions. What you will do • Pre-Analysis (40%): Contributes to the maintenance and development of bioinformatics tool portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provides efficient data management support. • Works with bioinformatics group members to develop functioning pipelines upstream of customized analysis workflows. • Maintains pipelines by staying current with evolving algorithms and standards and incorporating into pipeline. • Executes robust development testing for commonly used applications such as data processing pipelines. • Optimizes performance of applications by working with scientific computing and information systems groups to optimize hardware/software parameters. • Defines and prioritizes requirements for pipeline development over time to incorporate new technologies and platforms via functional communication with bioinformatics group members and bioinformatics end users. • Identifies appropriate open-source and commercial products that serve needs of pipeline and/or customized analyses of end users. • Implements and maintains commercial and open-source software for common bioinformatics and genomics data analysis. • Implements, updates and maintains locally stored data resources required for various analysis tasks. • Provides ad hoc support and one-on-one and group-based training on key bioinformatics software, features, and workflows. • Provides efficient data management support including file transfers, data formatting and manipulation, and basic integration of data from a variety of experimental and reference resources. • Develops and maintains working relationship with data providers such as sequencing cores within CHOP and infrastructure groups such as information systems. • Continually keeps abreast of evolving data generation platform fundamentals, file-specific information representation, and strategic application of code base to optimize value of data. • Maintains working knowledge of available commercial and openly accessible knowledge bases as they apply to bioinformatics analysis. • Coding (30%): Codes and generally supports both ad hoc, single task applications and larger pipeline applications that may combine multiple 3rd party and internally developed applications for genomics/proteomics/other complex data types and projects. • Implements, maintains, and regularly contributes to formal and bioinformatics group-centralized code management system. • Adopts appropriate forking and other strategies for robust code development. Apply to general bioinformatics group code base. • Adopts best practices for code development consistent with larger bioinformatics group. This includes choice of language based on the type of solution being developed, the likely life cycle and downstream usage of the resulting application, and integration with other systems. • Ensures that all routinely used tools (e.g. those included in shared analysis pipelines) are versioned and managed through a source control system. • Ensures that configuration files that provide parameters to algorithms and analysis software are versioned and managed through a source control system. • Develops and implements automated data-driven testing processes that test reproducibility of results between versions of pipeline software. • Develops and implements automated deployment processes that build and configure systems from source control repositories, eliminating the need to manually modify configuration files. • Regularly documents code, troubleshoot, and provide training when necessary. • Data Analysis (10%): Analyzes data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data under supervision from mentors and peers. • Develops robust analysis plans under supervision. • Incorporates QA/QC in analysis workflows. • Delivers analytical endpoints such as feature identification, annotation, characterization, prioritization, etc. • Reports results using, primarily, spreadsheets and, secondarily, abstracted materials such as slides and visuals. • Collaboration (10%): Works with both bioinformatics group members and end users/clients to understand specific needs in bioinformatics and end user-specific domains. • Attends group and team meetings and contributes primarily factual information regarding processes and approach. • Defers to mentors and peers in establishing relationships, but works within boundaries to accomplish analytical goals. • Academic Output (10%): Contributes to presentations, grants, and manuscripts under supervision by mentors and peers. Education Qualifications • Bachelor's Degree Required • Master's Degree biological or computational discipline Preferred Experience Qualifications • At least one (1) year in applied bioinformatics, computational, and genomics/proteomics experience. Preferred Experience • Four (4) or more years of experience in applied bioinformatics, genomics, and computational work. • Knowledge of cancer biology and/or genomics. Skills and Abilities • Strong UNIX/LINUX expertise required. • Experience with R strongly preferred. • Experience with Python, Perl, or other languages preferred. • Experience with pipeline or workflow development frameworks preferred. • Experience with data management preferred. • Familiarity with open source and commercial bioinformatics resources and software preferred. • Experience with genomic data analysis preferred. • Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred. • Knowledge of the working mechanism of microarray, NGS, mass spectrometry, or other high-throughput technologies and awareness of their strengths and weaknesses, as well as applicability to a specific biological problem is preferred. • Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is preferred. • Accountability and attention to timelines. • Excellent organization and communication skills with an emphasis on strong presentation skills. • Ability to work in a team environment. To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine. Learn more. Employees may request exemptions for valid religious and medical reasons. Start dates may be delayed until candidates are immunized or exemption requests are reviewed. EEO / VEVRAA Federal Contractor | Tobacco Statement