Bioinformatics Jobs

The Walter Reed Army Institute of Research (WRAIR) is offering a post-Bachelor's fellowship in the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) Branch. The Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) is a unique entity that serves as the primary surveillance organization for antibiotic-resistant bacteria across the Military Healthcare System (MHS) . The laboratory receives and processes (routine ID, Antibiotic Susceptibility Testing and Whole Genome Sequencing) ~1,000 new isolates of ESKAPE+ pathogens every month from military hospitals across the world, and routinely collaborates with other U.S. Government agencies, allied nations, and academic research institutions. What will I be doing? As an ORISE participant, you will join a community of scientists and researchers to perform comparative genomic analysis of hundreds of epidemiology-linked isolates (ongoing outbreaks in military hospitals) of MDR Enterococcus spp. Staphylococcus spp., Klebsiella spp., Acinetobacter spp., Pseudomonas spp., Enterobacter spp., and Escherichia coli. A variety of bioinformatic tools and software will be utilized to analyze bacterial genomes for the purpose of outbreak investigations and local, national, and international bacterial epidemiology. Within this research, you will have the chance to develop new and innovative methods for analyzing bacterial genomes and will have the opportunity to make significant contributions to this emerging field while conducting research in one of the most comprehensive sequencing laboratories in the USA. Why should I apply? Under the guidance of a mentor, you will gain hands-on experience to complement your education and support your academic and professional goals. Along the way, you will engage in activities and research in several areas. These include, but are not limited to: • Gaining hands-on knowledge of working with both short-read and long-read DNA sequences using the Illumina Miseq and Nextseq systems and the Oxford Nanopore MinIon platform. • Conducting analyses using the most state-of-the-art software and bioinformatics tools and developing hands-on programming experience using Linux, Python, R. • Establishing a fundamental understanding of translational, military-relevant scientific research. • Expanding your network of scientific colleagues and seeking collaborations within the U.S. Department of Defense, academia, and commercial companies. Where will I be located? Silver Spring, Maryland What is the anticipated start date? The Walter Reed Army Institute of Research is ready to make appointments immediately. Exact start dates will be determined at the time of selection and in coordination with the selected candidate. Applications are reviewed on an ongoing basis and internships or fellowships will be filled as qualified candidates are identified. What is the appointment length? This appointment is a twelve month research appointment, with the possibility to be renewed for additional research periods. Appointments may be extended depending on funding availability, project assignment, program rules, and availability of the participant. What are the benefits? You will receive a stipend to be determined by Walter Reed Army Institute of Research. Stipends are typically based on a participant’s academic standing, discipline, experience, and research facility location. Other benefits may include the following: • Health Insurance Supplement (Participants are eligible to purchase health insurance through ORISE) • Relocation Allowance • Training and Travel Allowance About WRAIR The Walter Reed Army Institute of Research (WRAIR) aims to conduct biomedical research that is responsive to U.S. Department of Defense and U.S. Army requirements. WRAIR conducts basic science, applied science, and animal and human subjects research to deliver lifesaving products including knowledge, technology and medical material that sustain the combat effectiveness of the Warfighter. Areas of focus include tropical infectious diseases and HIV, medical care on the battlefield and post-traumatic stress disorders. For more information about the WRAIR, please visit www.wrair.army.mil. About ORISE This program, administered by Oak Ridge Associated Universities (ORAU) through its contract with the U.S. Department of Energy (DOE) to manage the Oak Ridge Institute for Science and Education (ORISE), was established through an interagency agreement between DOE and DoD. Participants do not enter into an employee/employer relationship with ORISE, ORAU, DoD or any other office or agency. Instead, you will be affiliated with ORISE for the administration of the appointment through the ORISE appointment letter and Terms of Appointment. Proof of health insurance is required for participation in this program. Health insurance can be obtained through ORISE. For more information, visit the ORISE Research Participation Program at the U.S. Department of Defense.

• Applications will be reviewed on a rolling-basis. CDER Office/Lab and Location: A bioinformatics research opportunity is currently available with the Office of New Drugs/Office of Hematology and Oncology Products, Center for Drug Evaluation and Research (CDER), Food and Drug Administration (FDA) located in Silver Spring, Maryland. Research Project: This project is a collaborative effort between multiple CDER offices and will provide critical information to FDA/CDER regarding the practical application of Next Generation Sequencing (NGS) from tissue acquisition to patient outcome. Through multiple collaborations (including with Johns Hopkins University and the National Cancer Institute), we will assess the use of NGS technology to answer critical research questions in cancer such as drug-induced adverse events and patient-specific indicators of disease or outcome. The main objective of this program is to assess critical parameters involved in the adoption of NGS technology for cancer care. These parameters include, but are not limited to, tissue processing, laboratory protocols, bioinformatics and variant calling, data processing and related statistical analyses. Under the guidance of a mentor, the participant will be involved in the following: • analyzing various bioinformatics approaches to understand best-in-practice NGS analytics and novel methodologies • examining current SOPs and protocols and emerging tools to understand best-in-practice approaches for NGS analysis and downstream bioinformatics • collaborating with a multi-disciplinary team including clinicians, sequencing biologists, programmers, and regulators, and engaging with multiple investigators for individual projects This project is critical to our public health mission and will prepare the participant for a successful career transition into regulatory science research. This program, administered by ORAU through its contract with the U.S. Department of Energy to manage the Oak Ridge Institute for Science and Education, was established through an interagency agreement between DOE and FDA. The initial appointment is for one year, but may be renewed upon recommendation of FDA contingent on the availability of funds. The participant will receive a monthly stipend commensurate with educational level and experience. Proof of health insurance is required for participation in this program. The appointment is full-time at FDA in the Silver Spring, Maryland, area. Participants do not become employees of FDA, DOE or the program administrator, and there are no employment-related benefits. Completion of a successful background investigation by the Office of Personnel Management is required for an applicant to be on-boarded at FDA. OPM can complete a background investigation only for individuals, including non-US Citizens, who have resided in the US for a total of three of the past five years. FDA requires ORISE participants to read and sign their FDA Education and Training Agreement within 30 days of his/her start date, setting forth the conditions and expectations for his/her educational appointment at the agency. This agreement covers such topics as the following: • Non-employee nature of the ORISE appointment; • Prohibition on ORISE Fellows performing inherently governmental functions; • Obligation of ORISE Fellows to convey all necessary rights to the FDA regarding intellectual property conceived or first reduced to practice during their fellowship; • The fact that research materials and laboratory notebooks are the property of the FDA; • ORISE fellow’s obligation to protect and not to further disclose or use non-public information.

The Walter Reed Army Institute of Research (WRAIR) aims to conduct biomedical research that is responsive to U.S. Department of Defense and U.S. Army requirements and delivers lifesaving products including knowledge, technology and medical material that sustain the combat effectiveness of the Warfighter. For more information about WRAIR, please visit: https://www.wrair.army.mil/ The successful candidate will employ a variety of bioinformatic tools and software to analyze bacterial genomes for the purpose of outbreak investigations and local, national, and international bacterial epidemiology. The successful candidate will collaborate extensively with internal and external researchers on the molecular genetics of antibiotic resistant bacteria. In particular, the successful candidate will analyze and research the global dissemination of antibiotic resistant bacteria and participate in real-time surveillance for these organisms throughout the military healthcare system. The participant in this program will gain extensive educational experience that will greatly enhance his/her career opportunities. In particular, the participant will gain hands-on knowledge of working with both short-read and long-read DNA sequences using the Illumina Miseq and Nextseq systems and the PacBio RSII and MinIon platforms. This combination of short-read and long-read sequence experience is extremely difficult to find. Furthermore, the participant will be conducting analyses using the most state-of-the-art software and bioinformatics tools, such as Geneious, and will also develop hands-on experience using Linux. Under the mentorship of WRAIR staff, the selected candidate will help establish fundamental understanding of translational, military-relevant scientific research. The selected candidate will be highly encouraged to begin expanding their network of scientific colleagues and seek collaborations within the U.S. Department of Defense, academia, and commercial companies. Furthermore, the participant will be challenged to develop new and innovative methods for analyzing bacterial DNA, and will have the opportunity to make significant contributions to this emerging field while conducting research in one of the most comprehensive sequencing laboratories in the USA. Appointment Length An ORISE appointment period can be a short-term (less than 2 weeks), summer (10-12 weeks), or yearlong appointment. Appointments may be extended depending on funding availability, project assignment, program rules, and availability of the participant. Participant Benefits Participants will receive a stipend to be determined by WRAIR. Stipends are typically based on the participant’s academic standing, discipline, experience, and research facility location. Other benefits may include the following: • Health Insurance Supplement. Participants are eligible to purchase health insurance through ORISE. • Relocation Allowance • Training and Travel Allowance Nature of Appointment The participant will not enter into an employee/employer relationship with ORISE, ORAU, DOD, or any other office or agency. Instead, the participant will be affiliated with ORISE for the administration of the appointment through the ORISE appointment letter and Terms of Appointment.

Office of Cellular Therapy and Human Tissue (OCTHT) Center for Biologics Evaluation and Research (CBER) Food And Drug Administration (FDA) Department of Health and Human Services (HHS) Become a part of an agency that touches the lives of every American! The FDA’s Center for Biologics Evaluation and Research (CBER), Office of Cellular Therapy and Human Tissue (OCTHT) is recruiting Bioinformatics Review Scientists as Staff Fellows. OCTHT is strongly committed to bringing scientists, patient advocates, and the public together in partnership to develop novel advanced therapies for the 21st Century, while protecting human subjects and ensuring product safety and quality. OCTHT oversees the development and regulation of a wide variety of cutting-edge biological products including cell therapy products, tissue-engineered products, gene therapy products, and medical devices used in the production of these products. Review Scientists are an integral part of OCTHT’s fast paced regulatory science review and oversight program. Successful candidates will work with a team of dynamic multi-disciplinary scientists and clinicians and apply bioinformatics expertise to perform assessments of scientific and regulatory information of cell and gene therapy products including genome editing products submitted to CBER. The candidates may also have opportunities to contribute to the development of FDA’s regulatory policy and guidance on bioinformatics in emerging therapeutic areas such as genome editing products, next-generation sequencing (NGS)-based precision medicine, and individualized cancer vaccines. RESPONSIBILITIES: The selected candidate will be responsible for: • Evaluating NGS and bioinformatics analysis data relevant to the safety of genome editing products particularly regarding off-target effects and genomic modifications • Evaluating NGS and other genomics and bioinformatics datasets and pipelines relevant to the development of advanced individualized precision medicine products • Assessing and ensuring data suitability for regulatory purposes, identifying critical components in the data, and determining acceptable data quality attributes and thresholds • Performing independent data analyses using internally developed bioinformatics tools as well as open source and third-party genomics software and prediction algorithms • Reviewing experimental design, data acquisition methods, and interpreting results • Developing and implementing bioinformatics data standards and data quality assessment programs for scientific and regulatory reviews performed in CBER • Communicating results and interpretation to a diverse audience, including FDA scientists, collaborators, and external stakeholders BASIC QUALIFICATIONS: This position is multidisciplinary, and applicants will be required to meet the specific qualification requirements of one of the applicable occupational series: General Natural Resources Management and Biological Sciences (RG-0401), Microbiology (RG-0403), Computer Science, RG-1550, Statistics (RG-1530). ADDITIONAL QUALIFICATIONS: Ph.D. degree in Bioinformatics, Computational Biology, Genetics, Computer Science, Genomics, Biology, Statistics, or a related field is required, and a strong publication record is preferable. Candidate must have strong collaborative skills, excellent written and oral communication skills, and show clear evidence of leadership potential. Additionally, candidates who have a good general understanding of cell biology, molecular biology, and human genetics are preferred. Knowledge of federal regulations applicable to biological products and drugs is helpful but not required for consideration. Research and development (R&D) experience in genome editing- or NGS-based therapeutics is a plus; but, this not an R&D position. PREFERRED SPECIALIZED EXPERIENCE: • Developing tools and/or implementing bioinformatics pipelines to analyze NGS-based assays for cell and gene therapies and genome editing Using bioinformatics tools for identifying off-target nomination sites (e.g., GUIDE-Seq, Digenome-Seq, SITE-Seq, CIRCLE-Seq, CHANGE-Seq, PEM-Seq, DISCOVER-Seq) Using bioinformatics tools and complex analytical pipelines including diverse sequencing primary analysis tools (e.g., samtools, bedtools, GATK, BWA, Bowtie, IGV), secondary analysis tools (e.g., muTect, VarScan, VarDict), and statistical or machine learning algorithms (e.g., DESeq2, clustering, t-SNE) • Using bioinformatics tools or pipelines for identifying and predicting neoantigens and their immunogenicity for individual cancer patients using NGS technology Using publicly available data sources (e.g., TCGA, ENCODE, 1000 Genomes, COSMIC, dbSNP, ESP, gnomAD) and diverse genomic annotations Working in the JupyterLab environment Developing and running Python code and/or R code Working in the Linux environment • Working in the JupyterLab environment Developing and running Python code and/or R code Working in the Linux environment FOREIGN EDUCATION: If you are using education completed in foreign colleges or universities to meet the qualification requirements, you must show that the education credentials have been evaluated by a private organization that specializes in interpretation of foreign education programs and such education has been deemed equivalent to that gained in an accredited U.S. education program; or full credit has been given for the courses at a U.S. accredited college or university. For further information, visit the U.S. Department of Education website for Foreign Education Evaluation. SALARY: Salary is commensurate with education and experience. LOCATION: Silver Spring, MD CONDITIONS OF EMPLOYMENT: This position will be filled through the Service Fellowship program. The appointment provides up to (4) years with opportunities for renewal. Applications will ONLY be accepted from U.S. citizens and/or permanent residents (green card). No previous Federal experience is required. Appointment does not confer any entitlement to a position in the competitive service, and there is no entitlement to Merit Systems Protection Board (MSPB) appeals rights. • One-year probationary period may be required. Official Transcripts required Background and/or Security investigation required. If applicant is an U.S. Citizen, males born on, or after, December 31st, 1959 must be registered with the Selective Service System or have an approved exemption. Visit www.SSS.gov for more info. Prohibited financial interest restrictions may apply. For additional information on the prohibited financial interests, please visit the FDA Ethics and Integrity Office website at FDA Ethics and Integrity Office. The COVID-19 vaccination requirement for federal employees pursuant to Executive Order 14043, does not currently apply. Non-US and permanent residents are required to have resided in the United States for a minimum of three of the last five years. HOW TO APPLY: Submit electronic resume or curriculum vitae with a cover letter containing a brief summary of career interest and scientific accomplishments, a statement of how your education and experience would be applicable to this position, and the names/contact information of three references to Rebecca Escobar at Rebecca.Escobar@fda.hhs.gov. Applications and all supporting documentation will be accepted through January 10, 2025. Please reference Job Code: OTP-25-01-FDA ADDITIONAL INFORMATION: For additional information on CBER Careers, please visit: • CBER Careers • Scientific Careers at the FDA HHS/FDA is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or protected veteran status DEPARTMENT OF HEALTH AND HUMAN SERVICES IS AN EQUAL OPPORTUNITY EMPLOYER WITH A SMOKE FREE ENVIRONMENT

Haystack Oncology at Quest Diagnostics is seeking to grow its laboratory informatics team as we expand our assay portfolio and introduce cutting edge diagnostic technology to the public. As a Bioinformatics Engineer - LIMS, you will be responsible for developing, configuring, maintaining, and optimizing key functionality within our cloud-based enterprise Laboratory Information Management System (LIMS) that manages the generation, analysis, quality control, and interpretation of clinical data produced by diagnostic NGS assays. The ideal candidate will possess technical development experience within a LIMS platform, a rounded understanding of clinical laboratory processes and FDA regulations, strong analytical and problem-solving skills and a collaborative and continuous improvement mindset. This is a salaried position and weekend work may be required to satisfy project timelines and to support end-users. This position can work 100% remote and may require up to 10% travel as needed. Professional must be located in the US and is expected to be available during normal business hours in the Eastern and Central US time zones in order to provide support for laboratory sites in these regions. • Work extensively within our cloud-based StarLIMS system to develop and configure frontend and backend solutions that further automate our scientific and technical processes. • Develop new or modify existing code using StarLIMS scripting languages, HTML5, Jscript, .NET libraries, and Python following industry best practices. • Develop scientific reports using SQL, Crystal Reports, and StarLIMS QBE. • Gather and analyze requirements provided by cross functional stakeholders and translate into functional requirements that allow for the development of technical solutions. • Manage workload in Jira and provide timely and accurate status updates on project-based issue tickets that are either assigned or self-assigned. • Document system configurations, procedures, and any changes for reference and compliance purposes. • Both individually and as a part of a team, troubleshoot, debug, and test technical solutions • Provide ongoing support and training to laboratory staff and stakeholders on LIMS usage and best practices. • Respectfully and clearly communicate in English both textually and verbally with stakeholders. • Other duties, as assigned, that will contribute to the success of our company and the data systems we deploy. • Bachelors' or greater degree in Bioinformatics, Computer Science or other STEM-related disciplines. • Minimum 3 years of experience in the configuration and customization of an enterprise LIMS system is required. Experience with StarLIMS is preferred. • Minimum 3 years of experience in the development of custom code using scripting and/or programming languages. • Minimum 3 years of experience with relational databases and reporting tools, including Crystal Reports. • Experience with system integration techniques including REST APIs, web services, and middleware. • Strong understanding of laboratory workflows, data management, and compliance standards. • Experience with laboratory testing and scientific equipment. • Professional experience with a bug/issue tracking system. • Understanding of software design controls and SDLC. • Ability to work effectively with minimal direct supervision in a multiple discipline environment. • Ability to manage multiple tasks and assignments simultaneously. • Ability to adapt quickly to changing priorities in a fast-paced environment. • Excellent analytical, troubleshooting and problem-solving abilities. Proficient in diagnosing and providing solutions for bugs and issues. • Excellent communication and interpersonal skills, both verbal and written in English, with the ability to translate technical information for non-technical stakeholders. • Certificates in IT related topics are a plus. Education: Bachelor’s Degree(Required) Master’s Degree Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets

About the Research Investigating and onboarding novel organisms and engineering novel properties into chassis biosystems requires management and analysis of bioinformation. The successful candidate will work across a number of teams to provide bioinformatic support to genetic, proteomic, biochemical, pathway, and systems biology research projects. Purpose: Microbial bioinformatics to include data analysis, predictive and descriptive modeling of genomic, metagenomictranscriptomic, proteomic, and metabolic datasets, relationships and phenomena. • Experience/Skills:* • Advanced degree (PhD or Masters with equivalent experience) in biological or chemical sciences/engineering, with focus on combined theoretical/experimental approaches to understand and engineer microbial consortia. • Must have experience with analysis of multi-omics data driving toward development of whole-system models of microbial consortia. • Experience with microbial engineering, genome-scale metabolic modeling, and experimental design are preferred. • Must have expertise in R and/or Python as well as Linux. • Must be able to obtain a secret clearance. • Able, interested, and motivated to work in a multidisciplinary environment. • Able to work on multiple sub-projects simultaneously. • Excellent English skills in speech and writing. • Overarching Position Description:* The Biotechnology Branch of the US Army Research Laboratory seeks a contract Bioinformatician to join a multidisciplinary team of microbiologists, biological engineers, computational biologists, chemists, and materials scientists performing research on microbial consortia for materials conversion. The contract Bioinformatician will be responsible for processing and analyzing large-volume sequencing, transcriptomic and proteomic data, and will contribute to the design of the –omics experiments that generate these data. In addition, this team member will build, maintain, and refine genome-scale metabolic models describing individual organisms as well as multi-organism consortia, in order to help guide the team's efforts to understand key metabolic features and relationships of natural and designed material-converting microbial consortia. Interacting and developing technical collaborations with external leaders in the field and maintaining a keen awareness of the current literature and developments in the field are also important components of this position. • Specific Tasks and Duties:* Assist with the design of genomic and metagenomic sequencing experiments. • Design and implement novel state-of-the-art analysis pipelines and methods to distill large sequencing and –omics datasets into the most significant and actionable results aligned with the experimental objectives. • Construct and analyze results from single- and multi-organism genome-scale metabolic models to predict or constrain the space of expected products and metabolic relationships between organisms in consortia. • Communicate results in presentations, written reports, open journal publications, and patent applications. • Maintain current awareness of the relevant technical landscape by reading literature and participating in technical conferences or symposia. • Identify potential external collaborators. Develop strategic and mutually beneficial collaborative relationships to advance Army capabilities and accelerate accomplishment of project goals. ARL Advisor: Valerie E. Martindale ARL Advisor Email: valerie.e.martindale.civ@army.mil About HRED The Human Research and Engineering Directorate (HRED) is ARL’s principal center for research and development directed toward optimizing Soldier performance and human-autonomy teaming. Research within HRED focuses on how to improve Soldier performance in a dynamic and changing battlefield. As technology and autonomous systems become an increasingly integral part of Soldier teams, it is critical to determine how these systems can work with and be adapted to the Soldier and their capabilities. Autonomous systems must be able to be integrated into Soldier teams and move from tools to teammates. Critical to this is an understanding of how humans and human teams perform and change in dynamic environments and situations. HRED leverages human-robot interaction, human-informed machine learning, human cognition and adaptive teaming to improve human-autonomy teaming for future Army teams. About ARL-RAP The Army Research Laboratory Research Associateship Program (ARL-RAP) is designed to significantly increase the involvement of creative and highly trained scientists and engineers from academia and industry in scientific and technical areas of interest and relevance to the Army. Scientists and Engineers at the CCDC Army Research Laboratory (ARL) help shape and execute the Army's program for meeting the challenge of developing technologies that will support Army forces in meeting future operational needs by pursuing scientific research and technological developments in diverse fields such as: applied mathematics, atmospheric characterization, simulation and human modeling, digital/optical signal processing, nanotechnology, material science and technology, multifunctional technology, combustion processes, propulsion and flight physics, communication and networking, and computational and information sciences. A complete application includes: • Curriculum Vitae or Resume • Three References Forms • An email with a link to the reference form will be available in Zintellect to the applicant upon completion of the on-line application. Please send this email to persons you have selected to complete a reference. • References should be from persons familiar with your educational and professional qualifications (include your thesis or dissertation advisor, if applicable) • Transcripts • Transcript verifying receipt of degree must be submitted with the application. Student/unofficial copy is acceptable If selected by an advisor the participant will also be required to write a research proposal to submit to the ARL-RAP review panel for : • Research topic should relate to a specific opportunity at ARL (see Research Areas) • The objective of the research topic should be clear and have a defined outcome • Explain the direction you plan to pursue • Include expected period for completing the study • Include a brief background such as preparation and motivation for the research • References of published efforts may be used to improve the proposal A link to upload the proposal will be provided to the applicant once the advisor has made their selection. Questions about this opportunity? Please email ARLFellowship@orau.org.

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 Genomic Diagnostic Laboratory (GDL) of the Children’s Hospital of Philadelphia is seeking a highly motivated Supervisory Bioinformatics Scientist to manage our Bioinformatics team consisting of Bioinformatics Scientists, Bioinformatics Engineers, and RIA Programmers. This is an exciting opportunity to join our laboratory where we use a wide variety of molecular and cytogenetic test methodologies to provide accurate, timely diagnostic testing that has a direct impact on patient care. The team also supports cutting edge R&D efforts including new clinical test development and clinical research. The Supervisory Bioinformatics Scientist is a key member of the leadership team in the GDL, collaborating with other lab leaders including the Director of Bioinformatics, clinical directors, managers, and supervisors). The successful candidate will have a strong human genetics, bioinformatics, and management background that will be applied to training, clinical work, R&D, and troubleshooting. Good documentation practices as well as strong organizational and communication skills are essential. Job responsibilities include scheduling work duties, providing semi-annual performance reviews, assuring that all accreditation requirements are in full compliance, and participating in quality improvement initiatives. We seek a leader who has an interest in strategic planning to develop and improve our bioinformatics pipelines and other tools to support our expanding test menu. This position can be worked fully on-site at our campus in Philadelphia, PA, or as a hybrid role with an expectation of on-site presence at least once a week, and additional on-site presence possible based on the needs of the lab. In addition to many of the subject matter expert responsibilities of the Principal Bioinformatics Scientist, the Supervisory Bioinformatics Scientist will also: • Build and supervise a team responsible for the architecture, development, testing and production rollout of integrated biomedical data resources and applications. • Balance competing priorities and resource allocation across a portfolio of matrixed projects and collaborations. • Promote common standards and best-practice use of multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research. • Serves as the data integration team lead on larger complex projects that include informatics, clinical and translational researchers. • Propose staffing plans for multi-year strategic data resource initiatives. • Train, mentor, and hold junior staff accountable to the results of modern technology development methodologies such as code test coverage, continuous integration, monitoring. • Educate staff, students, and trainees (fellows, post-docs) on appropriate staffing and expertise levels for application of data integration methods in the clinical and translational research environment. What you will do • A Supervisory Bioinformatics Scientist functions as both subject matter expert and team manager. The responsibilities echo those of a Principal Bioinformatics Scientist, but include direct supervision of team members and projects. A Supervisory Bioinformatics Scientist will: • Directly lead and mentor junior staff in a direct supervisory capacity. • Guide and develop the skills and expertise of junior staff • Build project budgets by estimating time and effort costs • Hold data integration and technical teams accountable to high-level project goals and timelines, mapping detailed project plans into these timelines. • Recruit, hire, and retain a focused team of any of Bioinformatics Scientists, Bioinformatics Engineers, and Bioinformatics Programmers. • Provide bioinformatics academic and thought leadership for joint collaborations with CHOP PIs. Education Qualifications • Master's Degree Required • Doctorate Bioinformatics, Computational Biology, Computer Science, Information Science, Informatics, Biomedical Engineering, Biological Science or a related discipline Preferred Experience Qualifications • At least seven (7) years Experience in bioinformatics analysis, bioinformatics database development, bioinformatics database administration, bioinformatics data management, or related discipline, with progressively more complex projects in a biomedical science or healthcare environment. Required • At least one (1) year Small team supervisory experience. Required Skills and Abilities • Experience in bioinformatics and statistical data analysis on highly dimensional data types such as derived from genomics and observational clinical or human subjects research data. • Expert knowledge of relational database management systems such as PostgreSQL, MySQL, Oracle required. • Expert knowledge of bioinformatics applications and algorithms. • Expert knowledge of one or more of the following required: Python/Django, R, Perl, Scala, Ruby or other scripting languages. • Expert biological domain knowledge. • Must exhibit excellent oral, presentation, and written communication skills. • Experience with source code management, application development, and project lifecycle management. • Project management experience of complex matrix projects required. • Proficiency in the areas of bioinformatics analysis, statistical modeling, data integration, and bioinformatics thought leadership in the larger biomedical community. 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

Research Computing at Boston Children’s supports basic, translational, and clinical research by providing researchers with access to digital tools and technologies. Our computing environment consists of high-performance computing clusters, virtual machines, PetaByte-scale high-performance storage and cloud platforms. We work with BCH scientists to develop solutions in support of cutting-edge research ranging from genomics to epigenetics and transcriptomics, proteomics and metabolomics. The Senior Bioinformatics Data Scientist will work with PhD-level bioinformatics scientists and researchers who have single-cell RNA-seq, single-cell ATAC-seq, spatial transcriptomics, bulk RNA-seq and ChIP-seq data to investigate mouse and human diseases as well as with other pediatric scientists at BCH. The primary responsibilities will be building pipelines for the analysis, integration and sharing of these data. You will analyze, integrate different types of next-generation sequencing data and interpret the results and will have the opportunity to publish high-profile papers with prominent authorship depending on the intellectual contribution. The ideal candidate should have enthusiasm for developing collaborative relationships and a desire to foster the use of bioinformatics data in research studies. Responsibilities include: • Providing computational support services to Boston Children's Hospital scientists and clinicians by applying a wide range of bioinformatics tools, methods and technologies. • With minimal supervision and direction, completing highly complex assignments in the required timeframe; consistently adhering to and Promoting standard operating procedures and best practices; maintaining and upgrading a wide range of Research Computing tools, methods, and technologies, migrating data, documenting changes, and adjusting internal processes; resolving highly complex problems associated with assignments and seeking supervisor assistance when needed. • Routinely leading, co-leading, or participating in complex bioinformatics projects with other members from the BCH research community; setting goals and objectives for projects and demonstrating achievement of those goals and objectives; • Training staff and researchers; effectively tailoring presentations; developing, implementing and maintaining knowledge management systems. To qualify you must have: • Minimum of 4-year Bachelor's degree in STEM. A minimum of one year of position-specific experience, which might potentially include experience acquired through MSc or Ph.D. studies. Preference for candidates with a Ph.D. in Bioinformatics, Computational Biology or related. • Extensive knowledge of the use of bioinformatics computations in high-performance computing environments, including open-source bioinformatics software and pipelines to support diverse bioinformatics analyses such as single-cell RNA-seq, bulk RNA-seq, ChIP-seq, methylation, etc. • Extensive knowledge of technologies used in support of biomedical research, such as programming languages (R and Python), databases (SQL), version control (Git), scientific workflow tools and high-performance computing clusters. • Ability to resolve a wide range of complex Research Computing assignments in support of biomedical research. Ability to routinely lead complex projects and coordinate project teams; readiness to seek advice and guidance when needed and to operate effectively in collaboration with scientists and clinicians; ability to follow, improve and create technical documentation and standard operating procedures. • Strong publication record. Ability to effectively convey messages through written communication that are tailored to target audience; meeting discussions and one-on-one verbal communications are clear and effective; ability to conduct effective meetings, to present in departmental and hospital forums, and to develop training instructions and manuals. #LI-Remote

Payroll Title: BIOINFORMATICS PROGR 5 Department: PEDIATRICS Hiring Pay Scale $145,200.00 - $217,100.00 / Year Worksite: La Jolla Appointment Type: Career Appointment Percent: 100% Union: Uncovered Total Openings: 1 Work Schedule: Days, 8 Hour Shifts, Monday-Friday #133493 Lead Bioinformatics Programmer- Hybrid Filing Deadline: Thu 1/9/2025 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply. UCSD Layoff from Career Appointment: Apply by 12/11/2024 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/23/2024. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will work a hybrid schedule which includes a combination of working both onsite at Campus and remote. DESCRIPTION Department of Pediatrics is one of the largest departments within the UCSD School of Medicine with comprehensive clinical programs, extensive basic science and clinical research, and diverse educational opportunities for students, residents and fellows. The internationally renowned faculty play a major role in medical and graduate student training, providing educational and programmatic offerings that span several disciplines and provide diversity to meet the interests of a broad spectrum of students and scholars. More than one hundred trainees at the graduate student and postdoctoral level, as well as more than 300 professional, research and administrative staff who along with the department administrators interact closely with the faculty. The diverse mix of ages, backgrounds, and talents creates a robust work environment with challenging career opportunities and a commitment to continued growth potential. We constantly seek to recruit highly motivated, technologically-advanced and interested individuals to become a part of our dynamic cutting-edge research, clinical, and educational environment. The Knight lab in the Departments of Pediatrics, Bioengineering, Computer Science & Engineering, and the Halicioglu Data Science Institute uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally. The Lead Bioinformatics Programmer is responsible for leading software development and data analysis teams in high impact projects including data management and analysis for multi-institutional projects. The Lead Bioinformatics Programmer is charged with the architecture, design and implementation of large, complex workflows, web application portals and analytic systems. Conceives, develops, recommends and incorporates new or existing architecture, and/or new strategies to integrate systems and applications. Organizes and presents discussions and training workshops. Leads a team of bioinformatics professionals. Is accountable for multiple large, complex systems or subsystems. Functions as a highly specialized bioinformatics programming professional with an expert understanding of computational algorithms to identify and resolve a wide range of highly complex issues where analysis of situations or data requirements have little or no precedent. Project scope is broad and may extend beyond the university. Is considered a subject matter expert of the organization and often recognized as an expert externally in the field. Leads a team of bioinformatics professionals. Performs other duties as assigned. MINIMUM QUALIFICATIONS • Eleven (11) years of related experience, education/training, OR a Bachelor's degree in biological science, computational/programming, or related area plus seven (7) years of related experience/training. • Expert knowledge of bioinformatics methods, applications programming, web development and data structures. • Advanced analytical skills in independent, inductive, and deductive reasoning. Demonstrated ability to efficiently assess a broad spectrum of technical and resource requirements and proven skill to identify, define and delegate the efforts necessary to address those requirements in a high-performance computing setting. • Demonstrated skill and experience in leading to a team of programmers, meet deadlines and demonstrate highly developed problem solving skills. • Expert in bioinformatics programming design, modification, and implementation, with extensive knowledge of relational databases, web interfaces, and operating systems. • Highly developed project management skills. • Extensive knowledge and experience in Biology, Computational Biology, Bioinformatics, and modern biology with its applications in relevant research fields. • Highly developed interpersonal skills in order to work with both technical and non-technical personnel at all levels internally and externally to the organization. • Ability to communicate technical information in a clear and concise manner. • Highly developed ability to interface with management on a regular basis. • Expert knowledge of web, application and data security concepts and methods. • Exceptional writing and oral presentation skills. Excellent writing skills appropriate to the creation of the clear and persuasive scientific proposals and clear communications to colleagues in computational science and allied fields, as well as to technical and clerical employees. Proven ability in writing proposals and acquiring funding for research and development. SPECIAL CONDITIONS • Employment is subject to a criminal background check. • Remote work during evenings and weekends may be required. • Must be willing and able to travel. Pay Transparency Act Annual Full Pay Range: $145,200 - $289,000 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $69.54 - $138.41 Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable). Apply Now If employed by the University of California, you will be required to comply with our Policy on Vaccination Programs, which may be amended or revised from time to time. Federal, state, or local public health directives may impose additional requirements. If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable. UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community. UC San Diego is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. For the University of California’s Affirmative Action Policy please visit: https://policy.ucop.edu/doc/4010393/PPSM-20 For the University of California’s Anti-Discrimination Policy, please visit: https://policy.ucop.edu/doc/1001004/Anti-Discrimination UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information. UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening. Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts a conditional offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; received notice of any allegations or are currently the subject of any administrative or disciplinary proceedings involving misconduct; have left a position after receiving notice of allegations or while under investigation in an administrative or disciplinary proceeding involving misconduct; or have filed an appeal of a finding of misconduct with a previous employer. a. "Misconduct" means any violation of the policies or laws governing conduct at the applicant's previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, discrimination, dishonesty, or unethical conduct, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct: • UC Sexual Violence and Sexual Harassment Policy • UC Anti-Discrimination Policy • Abusive Conduct in the Workplace

About the Research Investigating and onboarding novel organisms and engineering novel properties into chassis biosystems requires management and analysis of bioinformation. The successful candidate will work across a number of teams to provide bioinformatic support to genetic, proteomic, biochemical, pathway, and systems biology research projects. Purpose: Microbial bioinformatics to include data analysis, predictive and descriptive modeling of genomic, metagenomictranscriptomic, proteomic, and metabolic datasets, relationships and phenomena. • Experience/Skills:* • Advanced degree (PhD or Masters with equivalent experience) in biological or chemical sciences/engineering, with focus on combined theoretical/experimental approaches to understand and engineer microbial consortia. • Must have experience with analysis of multi-omics data driving toward development of whole-system models of microbial consortia. • Experience with microbial engineering, genome-scale metabolic modeling, and experimental design are preferred. • Must have expertise in R and/or Python as well as Linux. • Must be able to obtain a secret clearance. • Able, interested, and motivated to work in a multidisciplinary environment. • Able to work on multiple sub-projects simultaneously. • Excellent English skills in speech and writing. • Overarching Position Description:* The Biotechnology Branch of the US Army Research Laboratory seeks a contract Bioinformatician to join a multidisciplinary team of microbiologists, biological engineers, computational biologists, chemists, and materials scientists performing research on microbial consortia for materials conversion. The contract Bioinformatician will be responsible for processing and analyzing large-volume sequencing, transcriptomic and proteomic data, and will contribute to the design of the –omics experiments that generate these data. In addition, this team member will build, maintain, and refine genome-scale metabolic models describing individual organisms as well as multi-organism consortia, in order to help guide the team's efforts to understand key metabolic features and relationships of natural and designed material-converting microbial consortia. Interacting and developing technical collaborations with external leaders in the field and maintaining a keen awareness of the current literature and developments in the field are also important components of this position. • Specific Tasks and Duties:* Assist with the design of genomic and metagenomic sequencing experiments. • Design and implement novel state-of-the-art analysis pipelines and methods to distill large sequencing and –omics datasets into the most significant and actionable results aligned with the experimental objectives. • Construct and analyze results from single- and multi-organism genome-scale metabolic models to predict or constrain the space of expected products and metabolic relationships between organisms in consortia. • Communicate results in presentations, written reports, open journal publications, and patent applications. • Maintain current awareness of the relevant technical landscape by reading literature and participating in technical conferences or symposia. • Identify potential external collaborators. Develop strategic and mutually beneficial collaborative relationships to advance Army capabilities and accelerate accomplishment of project goals. ARL Advisor: Valerie E. Martindale ARL Advisor Email: valerie.e.martindale.civ@army.mil About HRED The Human Research and Engineering Directorate (HRED) is ARL’s principal center for research and development directed toward optimizing Soldier performance and human-autonomy teaming. Research within HRED focuses on how to improve Soldier performance in a dynamic and changing battlefield. As technology and autonomous systems become an increasingly integral part of Soldier teams, it is critical to determine how these systems can work with and be adapted to the Soldier and their capabilities. Autonomous systems must be able to be integrated into Soldier teams and move from tools to teammates. Critical to this is an understanding of how humans and human teams perform and change in dynamic environments and situations. HRED leverages human-robot interaction, human-informed machine learning, human cognition and adaptive teaming to improve human-autonomy teaming for future Army teams. About ARL-RAP The Army Research Laboratory Research Associateship Program (ARL-RAP) is designed to significantly increase the involvement of creative and highly trained scientists and engineers from academia and industry in scientific and technical areas of interest and relevance to the Army. Scientists and Engineers at the CCDC Army Research Laboratory (ARL) help shape and execute the Army's program for meeting the challenge of developing technologies that will support Army forces in meeting future operational needs by pursuing scientific research and technological developments in diverse fields such as: applied mathematics, atmospheric characterization, simulation and human modeling, digital/optical signal processing, nanotechnology, material science and technology, multifunctional technology, combustion processes, propulsion and flight physics, communication and networking, and computational and information sciences. A complete application includes: • Curriculum Vitae or Resume • Three References Forms • An email with a link to the reference form will be available in Zintellect to the applicant upon completion of the on-line application. Please send this email to persons you have selected to complete a reference. • References should be from persons familiar with your educational and professional qualifications (include your thesis or dissertation advisor, if applicable) • Transcripts • Transcript verifying receipt of degree must be submitted with the application. Student/unofficial copy is acceptable If selected by an advisor the participant will also be required to write a research proposal to submit to the ARL-RAP review panel for : • Research topic should relate to a specific opportunity at ARL (see Research Areas) • The objective of the research topic should be clear and have a defined outcome • Explain the direction you plan to pursue • Include expected period for completing the study • Include a brief background such as preparation and motivation for the research • References of published efforts may be used to improve the proposal A link to upload the proposal will be provided to the applicant once the advisor has made their selection. Questions about this opportunity? Please email ARLFellowship@orau.org.