Bioinformatics Jobs

Part-time Bioinformatics Analyst Back Apply Share • Requisition no: 538199 • Work type: Part Time • Location: Medical Center • School/Department: Systems Biology • Grade: Grade 103 • Categories: Information Technology • Job Type: Officer of Administration • Bargaining Unit: • Regular/Temporary: Regular • End Date if Temporary: • Hours Per Week: 20 • Standard Work Schedule: • Building: • Salary Range: $35,000 - $35,000 The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to departmental budgets, qualifications, experience, education, licenses, specialty, and training. The above hiring range represents the University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Position Summary The Department of Systems Biology at Columbia University Irving Medical Center is seeking to hire a part-time Bioinformatics Analyst to work in Dr. Yufeng Shen's lab. The Bioinformatics Analyst will participate in analysis of large-scale genomic data in genetic studies of human conditions and diseases. Responsibilities • Participate in computational and statistical model development for predicting genetic effect of genomic variation. • Participate in computational analysis of large-scale genomic data to identify risk variants and genes in human conditions and diseases, such as autism and neurodevelopmental disorders. • Maintain and improve bioinformatics pipelines for genomic variants annotation. Minimum Qualifications • Bachelor's degree or equivalent in education and experience Preferred Qualifications • Bachelor's degree in Science or Engineering • At least one year of experience in projects with data science or machine learning as a core component • Proficient in Python, git, and modern data science frameworks Equal Opportunity Employer / Disability / Veteran Columbia University is committed to the hiring of qualified local residents. Applications open: Aug 08 2023 Eastern Daylight Time Applications close: Back Apply Share Whatsapp Facebook LinkedIn Email App

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 or any other legally protected status.

Overview The Bioinformatics/Research Software Development group in the Lewis-Sigler Institute for Integrative Genomics (LSI) at Princeton University is hiring a Senior Research Software Development Manager, reporting to the Assistant Director of the Lewis-Sigler Institute for Integrative Genomics. The Bioinformatics/Research Software Development group provides computational research expertise to the faculty, staff, and students in the Lewis-Sigler Institute for Integrative Genomics. The Institute, housed in the Icahn Laboratory, offers a diverse, interdisciplinary intellectual environment with a wide range of research opportunities. The Research Computing team emphasizes collaboration, best practices in software engineering, and flexibility to accommodate the evolving requirements of researchers. The Senior Research Software Development Manager will lead a team of four Research Software Engineers, Bioinformatics specialists, and Database developers, who provide dedicated expertise to researchers to create efficient, scalable, and sustainable research software and services that enable advancements in research. The Senior Research Software Development Manager will have the opportunity to work directly with researchers and faculty to create tailored solutions for a diverse range of projects such as sequence assembly, single cell RNA-Seq, mass spectrometry, and microscopy image analysis. The Senior Research Software Development Manager will play a pivotal role in supporting the research community (Genomics and BioInformatics) in the LSI and will collaborate closely with faculty, researchers, and graduate students to understand their computational research needs and develop innovative solutions. Responsibilities Responsibilities will include: • Team Leadership: Manage and mentor a team of Research Software Engineers, guiding their professional development and ensuring the efficient delivery of projects. • Product Ownership: Represent the team and its efforts to researchers, and the requirements and strategy to developers, assuming responsibility for prioritization of tasks and requirements to keep efforts aligned with goals. • Technical Expertise: Provide technical guidance and expertise to the team, staying up-to-date with the latest advancements in sequencing data analysis and computational biology. • Collaboration: Foster strong working relationships with researchers and faculty, understanding their specific needs and translating them into effective software solutions. • Innovation: Encourage a culture of innovation within the team, exploring new technologies and approaches to address emerging research challenges. • Technical Consultation: Provide expert guidance and support to researchers on software best practices, coding standards, and algorithm optimization. • High-Performance Computing: Assist researchers in utilizing the institution's high-performance computing resources effectively for their computational tasks. • Workflow Automation: Create automated workflows to streamline research processes and improve data analysis efficiency. Qualifications Essential: • Bachelor's or Master's degree in Computer Science, Bioinformatics, or a related field. • 10+ years experience (e.g., graduate school, industry experience, open-source software development, etc.) • Strong programming skills in languages such as Python, R, or C++. • Demonstrated successes working in a collaborative software development environment as well as working independently. • Excellent problem-solving and analytical skills. • Ability to collaborate effectively with researchers from various scientific disciplines. • Experience managing development projects and teams. Preferred: • Experience with specific research domains, such as genomics, mass spectrometry, or data science. • Experience with high-performance computing environments and clusters. • Knowledge of data management principles and tools. • Familiarity with cloud computing platforms and services. • Contributions to open-source software projects. Princeton University is an Equal Opportunity Employer and all qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity or expression, national origin, disability status, protected veteran status, or any other characteristic protected by law. KNOW YOUR RIGHTS Standard Weekly Hours 36.25 Eligible for Overtime No Benefits Eligible Yes Probationary Period 180 days Essential Services Personnel (see policy for detail) No Physical Capacity Exam Required No Valid Driver’s License Required No Experience Level Director #LI-JJ1

Position Summary: Rutgers, The State University of New Jersey is seeking a Bioinformatics Specialist within the Rutgers Cancer Institute-Bioinformatics Department. The primary role of the Bioinformatic Specialist in the Biomedical Informatics Shared Resource ( BISR ) is to provide bioinformatics support for gene expression, spatial transcriptomics, molecular responsiveness testing for cell therapy, Ncounter Nanostring, shotgun metagenomic sequencing, and metabolism-related pathway analysis. The Bioinformatics Specialist is expected to manage requests for all Cancer Institute scientific projects that require bioinformatics support in the areas of genomics, transcriptomics, metagenomics, and metabolomics pathways and charge for these services through the BISR recharge mechanism. Among the key duties for this position are the following: • 10X single-cell RNA sequencing : a. Perform quality checks (QC30 value), determine the cut-off value for rarely expressed genes, and perform FDR-analysis. b. Knowledge of script language (Python, R, Linux, etc.) that enables the development of pipelines for individual projects. c. Understand and interpret borderline QC data. d. Familiarity with scripts that allow for the visual representation of data, including but not limited to river plots, clonal analysis, Partek analysis, dendrograms, heat maps, circos, etc. e. TCR/BCR sequencing, including the determination of clonality. • 10X Visium HD spatial Transcriptomics: a. Runs sequencing alignments with single-cell images using cloud-based or LINUX platforms. b. Generates and prepares data in an easy-to-understand format, such as functional and phenotypic characteristics of cells present in the tissue section. • Molecular Responsiveness testing (MRT- Molecular responsiveness testing for Cell Therapy-clinical samples). Develops, tests, and runs new pipelines on existing NCBI or other databases to detect clonal expansion, single nucleotide polymorphisms, mutations, and HLA-type and analyze tumor cell antigen presentation, T cell function, apoptosis, and inflammatory pathway. The Bioinformatics Specialist should also be efficient in the graphical presentation of data and perform statistical analysis of data, mainly multivariate analysis. • Ncounter Nanostring assays Understands the sufficiency of reads obtained, the false discovery rate, and how to avoid it in analysis and data presentation. Generates graphical data sets and perform data comparisons among groups. • Metabolomics: a. Understands metabolic pathways, biochemistry fundamentals, and how metabolites are generated and processed in human body. b. Knowledge of databases that store metabolite information (e.g., HMDB, KEGG) and experience integrating metabolomics with other omics data. c. Maintains familiarity with software and tools like MetaboAnalyst and others for analyzing metabolomics datasets, including targeted and untargeted metabolomics. d. Works with pathway enrichment analysis tools like KEGG Mapper, or IPA for identifying pathways associated with metabolomic signatures. e. Maintains strong understanding of statistical methods for high-dimensional data, including multivariate analysis linear models, and familiarity with machine learning approaches (supervised and unsupervised) that are often used in metabolomics for biomarker discovery and classification f. Familiarity with techniques for adjusting for potential confounders in metabolomics studies (e.g., host factors, batch effects). Minimum Education and Experience: • Master's Degree in Biology, Computational Biology and/or Computer Science or other related field. • A minimum of two (2) years' work/research experience in bioinformatics, computer science, biology, biochemistry or similar. • Equivalent education, experience and/or training may be substituted for the degree requirement. City: New Brunswick State: NJ Physical Demands and Work Environment: PHYSICAL DEMANDS: • Standing, sitting, walking, talking and hearing. • No special vision requirements. • Lifting up to 25 lbs. WORK ENVIRONMENT: • Flexible Work Arrangement possible per Rutgers University policies. • Office environment. Moderate noise. Posting Number: 25ST0860

Description We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) shared resource facility, to lead genomics, transcriptomics and epigenetics data analysis projects related to Cancer and Developmental biology. The mission of BiNGS is to enhance scholarship and facilitate NGS data analysis in the ISMMS community by providing access to state-of-the-art tools and training. The BiNGS staff support a broad range of biostatistics and bioinformatics analyses for multiple applications spanning bulk ATAC-, RNA-, and ChIP-seq, CUT&RUN and HiC, single cell ATAC- and RNA-seq, single cell Multiome and Spatial Transcriptomics, WGS and WES. BiNGS further provides services for data management, bioinformatics tools development, access to biocomputing resources, web-based app development, and advanced computational training in data analysis. We are focused on delivering a comprehensive, rapid and user-friendly service. More specifically, we are working on multiple projects together with PIs in the Tisch Cancer institute and the broader Mount Sinai community to analyze NGS related datasets. For example, we are working to understand the role of the histone variant MacroH2A in the regulation of chromatin organization in melanoma utilizing micro-C analysis, enhancers analysis, transcriptomic analysis, open chromatin analysis and transcription factor network analysis; in another project, we are working to develop a computational classifier for risk assessments from cancer patients’ biopsies, utilizing WES and ultra-low pass WGS and ML tools. We are seeking a highly motivated junior Bioinformatic Scientist who wants the opportunity to significantly impact the growth and success of our research programs, the bioinformatics core and the services we provide. The candidate will work closely with TCI investigators to facilitate and enhance the processing of their projects. Commitment to accuracy, high attention-to-details, and ability to work independently are critical competencies for the role. The ability to lead projects is a must. We feel that BiNGS presents a unique opportunity for junior bioinformaticians who seek to work with like-minded professionals to expand their data analysis skills; their understanding of transcriptional and epigenetic programs and their role in driving cancer initiation, progression and metastasis, and other diseases; their ability to communicate science clearly and efficiently; and their involvement in reducing racial bias in science through mentorship of URM in Science. Responsibilities • Implement bioinformatics pipelines and perform analysis for WES and WGS datasets. • Utilize existing pipelines for the analysis of bulk RNA-seq. • Integrate data across different datatypes and from publicly available resources (e.g., PCAWG, TCGA, ICGC and GTEx), with experimental data generated by PIs. for example; correlation with gene expression signatures, and Histone PTM enrichment analysis. The ideal candidate will be able to navigate the available datasets and extract meaningful data based on the system he/she works on. • Provide analyses and visualization for presentations and publications. • Participate in the implementation of new software tools to process, analyze and visualize high-throughput multidimensional sequencing data. The candidate will be required to identify the main requirements, identify available tools, implement and test. • Manage the core online database and interactive tools on local HPC and commercially available clouds preferably Amazon Web Services. • Tracking and reporting of ongoing projects. • Provide training to TCI investigators and trainees. Qualifications • B.S. in Biological Sciences, Bioinformatics, Computer Sciences, Statistics or related discipline; M.S. preferred • 3 years experience required • Working experience with genetics or statistics analysis software and online resources. Experience in programming environments such as Matlab, R statistical package, BioConductor, Perl or C++. Employer Description Strength through Unity and Inclusion The Mount Sinai Health System is committed to fostering an environment where everyone can contribute to excellence. We share a common dedication to delivering outstanding patient care. When you join us, you become part of Mount Sinai’s unparalleled legacy of achievement, education, and innovation as we work together to transform healthcare. We encourage all team members to actively participate in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual. At Mount Sinai, our leaders are committed to fostering a workplace where all employees feel valued, respected, and empowered to grow. We strive to create an environment where collaboration, fairness, and continuous learning drive positive change, improving the well-being of our staff, patients, and organization. Our leaders are expected to challenge outdated practices, promote a culture of respect, and work toward meaningful improvements that enhance patient care and workplace experiences. We are dedicated to building a supportive and welcoming environment where everyone has the opportunity to thrive and advance professionally. Explore this opportunity and be part of the next chapter in our history. About the Mount Sinai Health System: Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 48,000 employees working across eight hospitals, more than 400 outpatient practices, more than 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time — discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it. Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes more than 9,000 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked: No. 1 in Geriatrics, top 5 in Cardiology/Heart Surgery, and top 20 in Diabetes/Endocrinology, Gastroenterology/GI Surgery, Neurology/Neurosurgery, Orthopedics, Pulmonology/Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report’s “Best Children’s Hospitals” ranks Mount Sinai Kravis Children's Hospital among the country’s best in several pediatric specialties. The Icahn School of Medicine at Mount Sinai is ranked No. 11 nationwide in National Institutes of Health funding and in the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges. Newsweek’s “The World’s Best Smart Hospitals” ranks The Mount Sinai Hospital as No. 1 in New York and in the top five globally, and Mount Sinai Morningside in the top 20 globally. Equal Opportunity Employer The Mount Sinai Health System is an equal opportunity employer, complying with all applicable federal civil rights laws. We do not discriminate, exclude, or treat individuals differently based on race, color, national origin, age, religion, disability, sex, sexual orientation, gender, veteran status, or any other characteristic protected by law. We are deeply committed to fostering an environment where all faculty, staff, students, trainees, patients, visitors, and the communities we serve feel respected and supported. Our goal is to create a healthcare and learning institution that actively works to remove barriers, address challenges, and promote fairness in all aspects of our organization. Compensation The Mount Sinai Health System (MSHS) provides salary ranges that comply with the New York City Law on Salary Transparency in Job Advertisements. The salary range for the role is $65000 - $87610 Annually. Actual salaries depend on a variety of factors, including experience, education, and operational need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.

POSITION RESPONSIBILITIES We are seeking a highly motivated Bioinformatics Analyst to join the research group of Dr. Robert Burk at Albert Einstein College of Medicine. This role is critical to supporting our ongoing molecular epidemiology and microbiome research, with a strong emphasis on human papillomavirus (HPV)-related neoplasia and the human microbiome (gut, oral, and cervicovaginal). The successful candidate will contribute to projects that have been published in high-impact journals such as Nature Communications and CELL. The ideal candidate will have a strong background in bioinformatics, epidemiology, computational biology, or a related discipline and possess demonstrated experience processing next-generation sequencing (NGS) data. This position provides an opportunity to work at the intersection of genomics, microbiome research, and epidemiology, with direct implications for cancer prevention and infectious disease research. Key Responsibilities: • NGS Data Analysis: Process and analyze high-throughput sequencing data (e.g., amplicon sequencing, bisulfite sequencing, metagenomics, viral integration) and develop bioinformatics pipelines. • Epidemiological Data Integration: Apply bioinformatics methodologies to study host-pathogen interactions, microbial communities, and genomic variations in large-scale epidemiological cohorts. • Phylogenetics & Evolutionary Analysis: Perform phylogenetic tree construction and genomic epidemiology studies for HPV and other microbiome-related investigations. • Data Management & Security: Organize, manage, and curate sequencing datasets, ensuring compliance with clinical data protection and security best practices. • Computational & Statistical Analysis: Utilize R, Python, or other computational tools to perform statistical analyses, epidemiological modeling, and data visualization. • Cross-Disciplinary Collaboration: Work closely with molecular biologists, epidemiologists, and computational scientists to integrate findings into broader translational research efforts. • Reporting & Presentation: Present findings in lab meetings, scientific conferences, and high-impact publications. • Grant & Manuscript Preparation: Contribute to research proposals and manuscript writing to support ongoing and new projects. QUALIFICATIONS • Education: Bachelor’s degree required; Master’s or Ph.D. in bioinformatics, computational biology, epidemiology, or related fields preferred. • Technical Skills: • Proficiency in R, Python, or similar languages for data analysis. • Experience with NGS data processing, microbiome bioinformatics (16S, ITS1, shotgun metagenomics), and HPV genomics. • Familiarity with machine learning/statistical modeling techniques in epidemiology is a plus. • Problem-Solving & Innovation: Strong analytical and critical thinking skills with a proactive approach to problem-solving in bioinformatics and epidemiology. • Communication & Collaboration: Ability to work in a highly interdisciplinary team and clearly communicate complex findings. Why Join Us? • Work on cutting-edge molecular epidemiology and microbiome research with direct public health impact. • Collaborate with leading experts in bioinformatics, genomics, and epidemiology. • Be part of projects published in top-tier journals such as Nature Communications and CELL. • Career development opportunities, including conference participation, grant writing experience, and authorship on high-impact publications. If you are a bioinformatics scientist eager to apply computational approaches to epidemiological and microbiome research, we encourage you to apply! Minimum Salary Range USD $58,500.00/Yr. Maximum Salary Range USD $65,000.00/Yr.

The Bioinformatics Research Scientist performs data analysis, data visualization, statistical analysis, experimental design, database development, mathematical modeling, and novel method development. Provides bioinformatics analysis for investigators and communicates analytical process and results. The Center for Applied Bioinformatics (CAB) at St. Jude Children's Research Hospital is seeking a highly motivated Senior Bioinformatics Research Scientist to join the Transcriptomics Group. CAB is an institutional shared resource dedicated to providing state-of-the-art bioinformatics services to St. Jude investigators. Our Center collaborates with lab scientists and physician-scientists at multiple stages of their research, from study design, data analysis to preparation for presentations, grant proposals, and co-authoring manuscripts. We uphold the highest level of scientific rigor by carefully vetting and documenting all bioinformatics methods and pipelines. The successful candidate will develop and apply innovative analytical approaches to analyze & interpret new and existing multi-omic datasets obtained from both clinical and basic research lab, including bulk tumor/normal, single-cell/nucleus, and spatial-omic profiles. These analyses will contribute to understanding the underlying mechanisms driving pediatric cancers and other human diseases. The candidate will work closely with other bioinformatics personnel within CAB, playing an integral role in exciting research partnerships both within St. Jude and with external collaborators. He/she will contribute to establish the pipelines and best practice to characterize bulk or single cell RNA isoforms and noncoding RNA transcripts with long read sequencing technologies. He/she follows and adheres to best practices in structured transparent project management by tracking progress, identifying roadblocks, and proposing solutions, developing specific milestones for each research goal, and providing informative progress reports and summaries to principal investigators. The Center provides a highly interactive environment with collaborative opportunities across basic and clinical departments. You'll have access to high performance computing clusters, cloud computing environments, innovative visualization tools, highly automated analytical pipelines, and mentorship from experienced scientists. Members of this Center have the opportunities to publish high profile papers with prominent authorship depending on their intellectual contributions. The ideal candidate should have: · A PhD and extensive post-PhD experience in bioinformatics, computational biology, and data science. · A strong CV that includes high-profile publications in the field of computational biology, cancer genomics, and/or single-cell genomics. · Experience analyzing some/all the following platforms: whole-genome/exome sequencing, RNA-seq. ATAC-seq, ChIP-seq/CUT&RUN, single-cell/nucleus RNA-seq, CITE-seq, single cell multiome (ATAC+GEX), spatial transcriptomics, and long-read sequencing (e.g., PacBio and Oxford Nanopore) · Proficiency in relevant programming languages such as R and Python, preferably in a High-Performance Computing (HPC) environment. · Proficiency in tools for ensuring reproducibility of pipelines, such as workflow management systems (e.g., nextflow), and version control (e.g., git). · Proficiency in tool development, including examples documented in public repositories. · Extensive expertise in data integration and harmonization. · Proven problem-solving skills and collaborative nature in fast-paced environment. · Excellent communication and presentation skills. Job Responsibilities: • Provide research support and deliver high-quality results by formulating an efficient analytical approach with the available data. • Deliver data files, and document the analytical process. May participate in manuscript preparation at project's conclusion. • Assist with establishing and documenting protocols or best practices for common research tasks, and in the formulation of analytical plans that use the best approach to address challenging data analysis questions. • Assist in the evaluation and testing of new methods and technologies. • Contribute ideas to automate or improve existing analysis methods. Implement the improvement or work with others to do so. • Participate in the department's developmental projects and interdepartmental team projects. • Perform other duties as assigned to meet the goals and objectives of the department and institution. • Maintains regular and predictable attendance. Minimum Education and/or Training: • Bachelor's degree in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry) or related field. • Master's degree or PhD preferred. Minimum Experience: • Minimum Requirement: Bachelor's degree with 7+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry). • Experience Exception: Master's degree with 5+ years of relevant post-degree experience (OR) PhD with 2+ years of relevant post-degree experience. • Significant experience in at least one programming or scripting language and at least one statistical package, with R preferred. Compensation In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $86,320 - $154,960 per year for the role of Bioinformatics Research Scientist. Explore our exceptional benefits! St. Jude is an Equal Opportunity Employer No Search Firms St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.

Bioinformatics Analyst III (AI), MDPL, CGR Job ID: req4291 Employee Type: exempt full-time Division: Clinical Research Program Facility: Rockville: 9615 MedCtrDr Location: 9615 Medical Center Drive, Rockville, MD 20850 USA The Frederick National Laboratory is operated by Leidos Biomedical Research, Inc. The lab addresses some of the most urgent and intractable problems in the biomedical sciences in cancer and AIDS, drug development and first-in-human clinical trials, applications of nanotechnology in medicine, and rapid response to emerging threats of infectious diseases. Accountability, Compassion, Collaboration, Dedication, Integrity and Versatility; it's the FNL way. PROGRAM DESCRIPTION The Cancer Genomics Research Laboratory (CGR) investigates the contribution of germline and somatic genetic variation to cancer susceptibility and outcomes in support of the NCI's Division of Cancer Epidemiology and Genetics (DCEG), the world’s most comprehensive cancer epidemiology research group. CGR is located at the NCI-Shady Grove campus in Rockville, MD and operated by Leidos Biomedical Research, Inc. We care deeply about discovering the genetic and environmental determinants of cancer, and new approaches to cancer prevention, through our contributions to the molecular, genetic, and epidemiologic research of the 70+ principal investigators (PIs) in DCEG. Working in concert with epidemiologists, biostatisticians and basic research scientists in DCEG’s intramural research program, CGR provides the capacity to conduct genome-wide discovery studies and targeted regional approaches to identify the heritable determinants of various forms of cancer. Within CGR, the Molecular and Digital Pathology Laboratory (MDPL) is dedicated to the support of genetic and epidemiologic studies for DCEG investigators through tissue profiling and image analysis. This includes the design and analysis of high throughput molecular epidemiologic studies using various types of “omics” technologies such as AI-based histomics, proteomics (immunohistochemistry, multiplex immunofluorescence, digital spatial profiling), and somatic genomic analyses. We are seeking a highly motivated bioinformatics analyst to provide dedicated statistical support and AI model development to support large-scale epidemiological research on cancer etiology and progression through integrative analyses of risk factors and image analysis to inform prevention and clinical strategies. KEY ROLES/RESPONSIBILITIES • Coordinate with existing laboratory, project management and analytical staff to track study progress from conception (developing analytical plans and study protocols) through completion (preparation of summary reports for presentation and publication). • Execute statistical and AI efforts of epidemiologic, pathological and clinical image-based data. • Accurately maintain thorough documentation and version control of data management activities (data cleaning, harmonization, and statistical analysis). • Document all analyses and pipelines used in support of reproducible and FAIR research. • Meet expected schedules and performance expectations in a fast-paced research laboratory environment. • Support a culture of continuous improvement and accountability; contribute to troubleshooting of issues associated with assay processing. BASIC QUALIFICATIONS To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below: • Possession of a Bachelor’s degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in genetics, genomics, bioinformatics, biostatistics, computer science, computational biology or another related field or four (4) years relevant experience in lieu of degree. Foreign degrees must be evaluated for U.S equivalency. • In addition to educational requirements, a minimum of five (5) years of progressively responsible related analytical or bioinformatics pipeline development experience. • Strong analytical skills and experience with statistical software applications used in public health research, such as Stata and/or R, Python, C++ (please indicate relevant software applications and degree of proficiency). • Demonstrable shell scripting skills (e.g., bash, awk, sed). • Experience working in a Linux environment (especially a HPC environment or cloud). • Experience with AI model development and validation. • Experience with risk estimation and/or prediction models using AI. • Experience with image analysis software such as Halo, QuPath, Visiopharm, Definiens, etc. (please indicate relevant software applications and level of proficiency). • Experience in the application of artificial intelligence (machine learning or deep learning) to pathology and clinical image analysis. • Careful attention to detail. • Collaborative, team-oriented approach to solving problems and achieving goals. • Strong organization skills, ability to multitask and manage time effectively. • Excellent communication skills (verbal and written). • Ability to obtain and maintain a security clearance. PREFERRED QUALIFICATIONS Candidates with these desired skills will be given preferential consideration: • Master’s degree in epidemiology, public health, data science, biostatistics, or a related field. • Familiarity with eLN and/or LIMS systems for sample and workflow tracking. • Proficiency with core statistical and bioinformatics methods (linear regression, logistic regression, eQTL analysis, LDscore regression, credible set and colocalization analysis, etc.). • Knowledge of DevOps tools and technologies, such as Docker/Singularity, GitHub for code management. • Team-oriented with demonstrated ability to self-educate in current bioinformatics techniques and resources. • Ability to multi-task in a fast-paced environment, organize and execute multiple projects in parallel both independently and as part of working groups. Commitment to Non-Discrimination All qualified applicants will receive consideration for employment without regard to sex, race, ethnicity, color, age, national origin, citizenship, religion, physical or mental disability, medical condition, genetic information, pregnancy, family structure, marital status, ancestry, domestic partner status, sexual orientation, gender identity or expression, veteran or military status, or any other basis prohibited by law. Leidos will also consider for employment qualified applicants with criminal histories consistent with relevant laws. Pay and Benefits Pay and benefits are fundamental to any career decision. That's why we craft compensation packages that reflect the importance of the work we do for our customers. Employment benefits include competitive compensation, Health and Wellness programs, Income Protection, Paid Leave and Retirement. More details are available here 109,600.00 - 188,250.00 The posted pay range for this job is a general guideline and not a guarantee of compensation or salary. Additional factors considered in extending an offer include, but are not limited to, responsibilities of the job, education, experience, knowledge, skills, and abilities as well as internal equity, and alignment with market data. The salary range posted is a full-time equivalent salary and will vary depending on scheduled hours for part time positions.

The Lead-Bioinformatics Research Scientist takes a lead role in data analysis, data visualization, statistical analysis, experimental design, database development, mathematical modeling, and novel method development. Working independently, provides bioinformatics analysis for investigators and communicates analytical process and results. A Lead Bioinformatic Research Scientist position is available in the lab of Dr. Jian Xu at Department of Pathology and Center of Excellence for Leukemia Studies (CELS) at St. Jude Children’s Research Hospital to study the genomic and/or metabolic mechanisms controlling stem cell development and blood cancers. Our lab uses cutting-edge genomics, metabolomics and bioinformatics approaches in a multi-disciplinary and collaborative team setting. Our recent studies include the development of the CRISPR CAPTURE approach (Cell 170:1028), the analysis of rewired BCAA metabolism (Cancer Discovery 9:1228), the role of pathogenic non-coding variants (Cancer Discovery 10:724), retrotransposon silencing (Nature Genetics 53:672), therapy resistance in hematologic malignancies (Cancer Discovery 13:170), and metabolic rewiring in erythropoiesis (Science 386:eadh9215). The main responsibilities will be developing and implementing bioinformatic methodologies for integrative genomic and metabolomic studies of childhood cancers; overseeing operations related to genomic and metabolomic data processing and analysis within the Advanced Technology & Genomics (ATG) core, including software pipelines for short-read and long-read-based genome sequencing, single-cell genomics, high throughput metabolomic profiling, and stable isotope tracing; managing databases; and providing bioinformatic support and services to other lab members and St. Jude researchers. Candidates must hold a MS or PhD degree with a strong background and expertise in genomics, computational biology, metabolism research, and/or cancer biology. The ideal candidate will exhibit independence, flexibility and creativity with a record of scientific productivity. Previous experience in single-cell genomics, computational biology, and/or hematology-oncology is strongly preferred. Interested individuals should upload a CV, a short summary of research interest and experience, and a list of three references. Job Responsibilities: • Lead data analysis and deliver high-quality results by formulating advanced and/or new analytical approaches with the available data/ to address challenging data analysis questions. • Deliver data files, and document the analytical process. Participate in manuscript preparation at project's conclusion. • Establish and document protocols or best practices for common research tasks. • Recommend ideas to automate or improve existing analysis methods and implement the improvement. • Evaluate and test new methods and technologies. Develop reusable code and pipeline. Participate in redistribution and education of novel methods to research community when required. • Lead and participate in the department's developmental projects and interdepartmental team projects. Act as a project manager when required. • Perform other duties as assigned to meet the goals and objectives of the department and institution. • Maintains regular and predictable attendance. Minimum Education and/or Training: • Bachelor's degree in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry) or related field. • Master's degree or PhD preferred. Minimum Experience: • Minimum Requirement: Bachelor's degree with 10+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry). • Experience Exception: Master's degree with 8+ years of relevant post-degree experience (OR) PhD with 5+ years of relevant post-degree experience. • Substantial experience in at least one programming or scripting language and at least one statistical package, with R preferred. Compensation In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $125,840 - $238,160 per year for the role of Lead-Bioinformatics Research Scientist. Explore our exceptional benefits! St. Jude is an Equal Opportunity Employer No Search Firms St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.

The Epigenetics Group, a part of the Center for Applied Bioinformatics (CAB) at St. Jude Children's Research Hospital, is seeking a highly motivated and creative Bioinformatics Research Scientist or Lead Bioinformatics Analyst. This position involves developing and applying innovative analytical approaches to uncover the mechanisms driving pediatric cancers and other human diseases. By contributing to a wide range of projects and assisting researchers across St. Jude, you will make a meaningful impact on science and, ultimately, on the care and survival of pediatric cancer patients. In addition to performing diverse analytical tasks, we encourage team members to engage in pipeline development, explore novel trends in the field, stay updated on the latest methods, and even create new methodologies—provided these efforts align with our ultimate goal: “Finding cures. Saving children.™”. Our work often leads to high-profile publications, offering significant opportunities for career growth and scientific contributions. What We Offer: CAB provides a highly interactive and collaborative environment with opportunities to work alongside experts in transcriptomics, genomics, and genetics, as well as across basic and clinical research departments. Resources include but are not limited to: Access to St. Jude's high-performance computing clusters and cloud computing environments.Cutting-edge sequencing platforms, such as long-read sequencing technologies, single-cell DNA/RNA sequencing, and spatial transcriptomics. Innovative visualization tools and highly automated analytical pipelines powered by GPU technology. Mentorship from experienced scientists in data analysis and management, with an expertise in delivering high-quality results for competitive projects. Opportunities to participate in and present at scientific conferences, enhancing your expertise and expanding your network. CAB members have opportunities to contribute to high-impact research, co-author prominent publications, and file patents for novel biomarker discoveries or innovative methods in clinical diagnosis and treatment. Job Responsibilities: • Independently perform basic and advanced level statistical analysis, algorithm implementation, programming from a variety of biotechnology platforms, and oversee quality check. • Design and prepare materials and courses for training on various bioinformatics software and databases, computing, data mining, and analysis. • Act as a liaison between end-users, software developers, system designers, and different departments. • Establish protocols or best practices for common research tasks and SOP, evaluate products and solutions to make recommendations, and integrate solutions. • Lead the development, implementation, installation, and maintenance of databases; coordinate data collection, database implementation, and usage and any hardware and software related to database collection. • Develop programs to assist in the analysis of data within the databases. • Assist in planning, coordinating, and organizing projects across departments and delegate tasks based on priority, expertise, and capacity. • Perform other duties as assigned to meet the goals and objectives of the department and institution. • Maintains regular and predictable attendance. Minimum Education and/or Training: • Bachelor's degree in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry) or related field. • Master's degree or PhD preferred. Minimum Experience: • Minimum Requirement: Bachelor's degree with 6+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry). • Experience Exception: Master's degree with 4+ years of relevant post-degree experience (OR) PhD with no experience. • Experience in at least one programming or scripting language and at least one statistical package, with R preferred. Qualifications: Ideal candidates will have: • Experience building, maintaining and optimizing analysis pipelines or installing tools for high-throughput next-generation sequencing data analysis (e.g., ChIP-Seq, ATAC-Seq, RNA-Seq, Hi-C, HiChIP, or Capture-C) in Linux/Unix environments. • A solid understanding of basic epigenetic gene regulation mechanisms, like histone modifications, chromatin accessibility, DNA methylation or the 3D genome. • Very good programming skills in Bash scripting language and Python (preferred) or R programming languages. • Experience with version control systems such as Git. • Strong communication and project managements skills. • Experience with deep learning and Nextflow is a plus. This is an exceptional opportunity to gain experience in diverse areas of bioinformatics, contribute to cutting-edge research, and play a vital role in advancing St. Jude’s mission. Responsibilities • Specific responsibilities may include NGS data quality control, multi-omics integrative analyses, data visualization, and the development and evaluation of analytic tools. Excellent communication skills are essential. You will collaborate closely with various St. Jude Principal Investigators and their research teams to provide standardized or customized analyses, utilizing St. Jude's high-performance computing clusters and cloud computing environments. Additional Requirements: • Proficiency in programming (e.g., Python, R, C/C++, Perl, or other programming/scripting languages) in Linux/Unix environments is required. • Proven ability to work effectively with a wide range of users. • Demonstrated experience in analyzing and interpreting epigenetics data. • Proven experience conducting independent data analyses and managing projects is required. • Experience providing end-user support and training is required. Compensation In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $86,320 - $154,960 per year for the role of Bioinformatics Research Scientist- Epigenetics Group. Explore our exceptional benefits! St. Jude is an Equal Opportunity Employer No Search Firms St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.