Bioinformatics Jobs

This position is located in the USDA, ARS, Northeast Area, Beltsville Agricultural Research Center, Animal Parasitic Disease Lab in Beltsville, MD. In this position, you will serve as an expert resource in bioinformatics, computational biology, machine learning, AI, simulation, or statistics in the development of novel quantitative solutions for standardizing, harmonizing, analyzing, interpreting, and communicating all forms of research data needed to address complex problems in agriculture.

Bioinformatics Analyst III $55 - $58/hr medical benefits available at a cost... 6 month initial contract Fully remote Orion Group and our largest US client are teaming up for an exciting contract opportunity! We are seeking Bioinformatics Analysts with extensive experience with upstream processing of 'omics data (QC, normalization, exploratory data analysis), as well as downstream processing of bulk, single-cell, and/or spatial transcriptomic data. Candidates with experience integrating multi-modal data (e.g., scRNAseq + scATACseq, spatial RNAseq + spatial proteomics) are especially encouraged to apply. Daily Responsibilities will include: • Analysis of proteomics or other data modalities depending upon project needs. • Working within High-performance computing systems. • Shell scripting in a Linux environment, and have strong facility with R and/or Python, including relevant bioinformatics packages (e.g., Seurat, edgeR/limma). • The successful candidate will use a variety of 'omics data to test and refine biological hypotheses in coordination with wet-lab and computational colleagues. • Upstream processing of 'omics data (QC, normalization, exploratory data analysis). • Downstream processing of bulk, single-cell, and/or spatial transcriptomic data (e.g., cell type annotation, differential gene expression analysis, gene set enrichment analysis, results visualization). Qualifications to be successful in this role: • PhD in Bioinformatics, Genetics, Molecular and Cellular Biology, or related field or MS with at least 6 years of experience. • single-cell and/or spatial transcriptome QC and analysis (e.g., with Seurat or Scanpy) • bulk RNAseq data processing and analysis • facility with R and/or Python for data exploration and statistical analysis • experience with high-performance computing (HPC) and job submission systems Our role in supporting diversity and inclusion As an international workforce business, we are committed to sourcing personnel that reflects the diversity and values of our client base but also that of Orion Group. We welcome the wide range of experiences and viewpoints that potential workers bring to our business and our clients, including those based on nationality, gender, culture, educational and professional backgrounds, race, ethnicity, sexual orientation, gender identity and expression, disability, and age differences, job classification and religion. In our inclusive workplace, regardless of your employment status as staff or contract, everyone is assured the right of equitable, fair and respectful treatment

Black Canyon Consulting (BCC) is searching for a Bioinformatics Data Scientist/Analyst to support our work for the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), an institute of the National Institutes of Health. This opportunity is full time and onsite at the NIH-NCBI in Bethesda, MD and/or remote work. The National Center for Biotechnology... Information (NCBI) is part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). NCBI is the world’s premier biomedical center hosting over six million daily users that seek research, clinical, genetic, and other information that directly impacts biomedical research and public health. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). NCBI is one of the top 400 most visited sites and its wide range of applications serve more users and more data than any other US Government Agency. NCBI provides free access to petabytes of biomedical and genomic information, and scientists all over the world use our products, including PubMed, ClinicalTrials.gov, GenBank, RefSeq, and ClinVar. Job Description We are looking for an outstanding candidate to help process and analyze data in NLM-NCBI’s RefSeq Virus group. The candidate will be responsible for: • Collecting, processing, and analyzing biological datasets to support public virus resources • Developing methodologies and tools for the identification and classification of viral sequences based upon genomic and protein sequence content • Improving sequence data quality and annotation based on bioinformatic analysis, appropriate scientific literature, and through direct communication with scientists • Outreach to research scientists, data scientists, and clinicians • Interacting and collaborating with a diverse group of scientists, bioinformaticians and software developers within and outside the NIH to meet the needs of clinical and basic researchers and public health professionals. Qualifications: The ideal candidate must have a doctoral degree and postdoctoral experience. We are looking for an individual with: • A track record of research or work in viral genomics and bioinformatics • Familiarity with virus taxonomy, comparative genomics, and evolutionary processes • Experience in bioinformatics of DNA and RNA sequence analysis and the development of robust workflows for automated data processing • Proficiency in at least one scripting language (e.g., Python) • Experience with SQL • Ability to work with common structured documents (XML, JSON, CSV) • Familiarity with NCBI resources and tools • Experience in interpreting complex biological problems, critically analyzing the scientific literature, and demonstrating a thorough understanding of the strengths and weaknesses of high-throughput experimental datasets • Excellent verbal and written communication skills, organizational skills, and problem-solving skills • A proven ability to successfully engage in multi-disciplinary collaborative research

This Position is Fully Grant Funded School of Medicine... Established in 1930, Duke University School of Medicine is the youngest of the nation's top medical schools. Ranked sixth among medical schools in the nation, the School takes pride in being an inclusive community of outstanding learners, investigators, clinicians, and staff where interdisciplinary collaboration is embraced and great ideas accelerate translation of fundamental scientific discoveries to improve human health locally and around the globe. Composed of more than 2,600 faculty physicians and researchers, nearly 2,000 students, and more than 6,200 staff, the Duke University School of Medicine along with the Duke University School of Nursing, and Duke University Health System comprise Duke Health, a world-class academic medical center. The Health System encompasses Duke University Hospital, Duke Regional Hospital, Duke Raleigh Hospital, Duke Health Integrated Practice, Duke Primary Care, Duke Home Care and Hospice, Duke Health and Wellness, and multiple affiliations. Bioinformatician II Summary We are looking for a talented and motivated individual to work with teams of Researchers and Scientists providing bioinformatics expertise, consulting, application development, and support as part of the Duke Predictive Modeling Center (PMC), an NHGRI-funded center with the Impact of Genomic Variation on Function (IGVF) Consortium. Work performed • Contribute to the design, development, adaptation, implementation, and testing of neural networks that are used for predictive modeling of genomic data. Work involved with require increased independence of identifying and implementing solutions with some leadership and supervisory activities. (30%) • Train predictive models using machine learning approaches and technologies. This might include not only writing new code but repackaging and documenting existing scripts to make them reusable and easy to maintain. Work will include training increasingly complex models and will require navigating dynamic computing environments. (25%) • Collaborate and consult with researchers individually or in small groups to analyze problems, recommend technology-based solutions, and design computational strategies for a wide range of biological research. Initiate interdisciplinary collaborations with other centers or departments within the Duke PMC and in collaboration with other research teams with the IGVF consortium. (20%) • Recommend new methods, strategies, and improvements to incorporate into existing models. Try latest tools and analysis methods for new non-conventional genomic data (e.g. CRISPR screens), evaluating their fit and gradually incorporating them into existing analysis pipelines. (15%) • Provide training on bioinformatics-related concepts, applications, and tools to researchers across the PMC and relevant teams within the IGVF. Design and participate in hands-on workshops to teach scientists how to use predictive models and associated neural networks so that these resources are accessible to other groups. (10%) Skills • Experience working with high throughput sequencing datasets (e.g. RNA-seq, ChIP-seq, ATAC-seq, etc.). • Strong and demonstrable programming skills in Python, Tensorflow, and/or R. • Experience with independently identifying solutions and ability to investigate and learn new approaches necessary to adapt existing or new models. • Experience with collaborative development environments, including management of shared repositories (github). • Good communication skills; run and deliver results in a clear and precise way. • Familiarity with High Performance Computing clusters (e.g. SLURM, PBS), including computing environments constructed with CPUs and GPUs. • Familiarity with workflow languages (e.g. CWL, WDL). Education Work requires a M.S. in Bioinformatics or the biological sciences with demonstrable computational skills or a M.S. in computer science with a strong interest in biology/genomics. PhD preferred. Experience Strong expertise with programming required. Minimum Qualifications Education Work requires a M.S. in Bioinformatics or the biological sciences with demonstrable computational skills or a M.S. in computer science with a strong interest in biology/genomics. PhD preferred. Experience Work requires at least 2 years of experience in bioinformatics. OR AN EQUIVALENT COMBINATION OF RELEVANT EDUCATION AND/OR EXPERIENCE Experience with web-based bioinformatics tools, public domain biological databases and software tools for sequence, domain and structural analysis. Extensive familiarity with and development of computational tools in biology that use genomic data to generate biological hypotheses. Experience with a procedural language, proficient in Java, Perl, 'C', web design, DNA genome informatics, proteomics informatics, statistics, and computer science. Experience with relational databases and SQL helpful. Duke is an Affirmative Action/Equal Opportunity Employer committed to providing employment opportunity without regard to an individual's age, color, disability, gender, gender expression, gender identity, genetic information, national origin, race, religion, sex, sexual orientation, or veteran status. Duke aspires to create a community built on collaboration, innovation, creativity, and belonging. Our collective success depends on the robust exchange of ideas—an exchange that is best when the rich diversity of our perspectives, backgrounds, and experiences flourishes. To achieve this exchange, it is essential that all members of the community feel secure and welcome, that the contributions of all individuals are respected, and that all voices are heard. All members of our community have a responsibility to uphold these values. Essential Physical Job Functions: Certain jobs at Duke University and Duke University Health System may include essentialjob functions that require specific physical and/or mental abilities. Additional information and provision for requests for reasonable accommodation will be provided by each hiring department

The Lead Bioinformatics Research Scientist (Clinical Genomics) performs NGS data analysis for pediatric somatic and germline clinical tests, and provides guidance to less experienced team members. Case findings are presented bi-weekly in a group setting before clinical reports are issued by the on-duty molecular pathologist. Clinical genomics testing relies on a strong partnership between the... Departments of Molecular Pathology and Computational Biology; as a primary user of the clinical pipeline, the Lead Bioinformatic Research Scientist works at the intersection of pipeline development and reporting, providing feedback and facilitating improvement requests/user testing in support of ongoing improvement efforts. Job Responsibilities: • Perform validity review and interpretation of genetic sequence variation identified through diagnostic clinical genetic testing; prepare and present findings • Establish/maintain/improve protocols and best practices of clinical tasks • Support activities of the molecular pathology lab relevant to new test and technology development and updates • Lead and participate in the department's developmental projects and interdepartmental team projects; acts as a project manager when required • Mentor junior variant scientists regarding variant calling/interpretation • Recognize and report system performance problems • Follow written standard operating procedures (SOPs), and maintain proficiency and competency standards required for lab accreditation • Perform other duties as assigned to meet the goals and objectives of the department and institution 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, biological sciences, chemistry, bioinformatics, or statistics/computer science (with a background in biological sciences) • Experience Exception: Master's degree with 8+ years of relevant post-degree experience (OR) PhD with 5+ years of relevant post-degree experience • For lead bioinformatics scientists, substantial experience in at least one programming or scripting language and at least one statistical package is preferred. Alternative titles (for example, Clinical Variant Scientist) may otherwise be deemed appropriate. 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! Diversity, Equity and Inclusion St. Jude Children’s Research Hospital has a diverse, global patient population and workforce, built on the principles of diversity, equity and inclusion. Our founder Danny Thomas envisioned a hospital that would treat children of the world—regardless of race, religion or a family’s ability to pay. Learn more about our history and commitment. Today, we continue the mission to advance cures and means of prevention for pediatric catastrophic diseases through research and treatment. As we accelerate this progress globally, we believe our legacy of diversity, equity and inclusion is foundational to success. With the commitment of leaders at all levels of the organization, we strive to ensure the St. Jude culture, leadership approaches and talent processes are equitable and culturally responsive. View our Diversity, Equity and Inclusion Report to learn about the hospital’s roots in diversity, equity and inclusion, where we are today and our aspirations for an even better future. 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

Position Overview: We are seeking a talented and experienced Bioinformatics Scientist to join our interdisciplinary team. As a Bioinformatics Scientist, you will play a crucial role in analyzing complex biological data, developing computational algorithms, and interpreting results to advance our understanding of biological systems and support research and development efforts. Roles and... Responsibilities: • Data Analysis and Interpretation: • Utilize bioinformatics tools and computational algorithms to analyze large-scale biological datasets, including genomics, transcriptomics, proteomics, and metabolomics data. • Perform statistical analysis, data mining, and visualization to extract meaningful insights and identify patterns or correlations. • Algorithm Development and Optimization: • Develop and implement computational algorithms, machine learning models, and data analysis pipelines for biological data analysis. • Optimize algorithms for efficiency, accuracy, and scalability to handle large volumes of biological data. • Biological Database Management: • Manage and curate biological databases, ensuring data integrity, accuracy, and accessibility. • Design and maintain database schemas, query optimization, and integration with other bioinformatics tools and resources. • Collaboration and Communication: • Collaborate with biologists, geneticists, clinicians, and other researchers to understand research goals and translate biological questions into bioinformatics analyses. • Communicate findings, results, and technical concepts effectively to interdisciplinary teams and stakeholders. • Bioinformatics Tool Development: • Contribute to the development and improvement of bioinformatics software tools, pipelines, and databases. • Stay updated with advancements in bioinformatics tools, algorithms, and methodologies to enhance research capabilities. • Quality Assurance and Validation: • Implement quality control measures and validation protocols to ensure accuracy, reproducibility, and reliability of bioinformatics analyses. • Document methodologies, protocols, and computational workflows for transparency and reproducibility. • Research and Innovation: • Participate in research projects, publish findings in scientific journals, and present at conferences to contribute to the field of bioinformatics and computational biology. • Explore novel approaches and technologies to address biological research challenges and drive innovation in bioinformatics. Skills and Qualifications: • Proven experience (X+ years) as a Bioinformatics Scientist, Computational Biologist, or similar role in analyzing biological data using bioinformatics tools and techniques. • Strong proficiency in programming languages such as Python, R, Perl, or Java, with experience in bioinformatics software and databases (e.g., NCBI databases, Ensembl, UCSC Genome Browser). • Expertise in statistical analysis, machine learning, data mining, and visualization techniques applied to biological datasets. • Knowledge of genomics, transcriptomics, proteomics, and other -omics data analysis methods and technologies. • Familiarity with bioinformatics tools and algorithms for sequence analysis, protein structure prediction, and pathway analysis. • Excellent problem-solving skills and ability to apply computational methods to biological research questions. • Effective communication and collaboration skills, with the ability to work in multidisciplinary teams and communicate technical concepts to non-technical stakeholders. Education: • PhD or Master's degree in Bioinformatics, Computational Biology, Biostatistics, Computer Science, or a related field; equivalent industry experience may be considered. Additional Attributes: • Passion for bioinformatics, computational biology, and advancing scientific research through data-driven approaches. • Ability to thrive in a fast-paced research environment and manage multiple projects effectively. • Commitment to continuous learning and staying updated with the latest bioinformatics tools, technologies, and methodologies. This job description outlines the essential responsibilities and qualifications expected of a Bioinformatics Scientist, emphasizing expertise in biological data analysis, algorithm development, database management, collaboration, and research. Adjustments can be made based on specific company needs, industry focus, and organizational structure

We have an exciting opportunity for a candidate who is interested in working at the forefront of the gene editing (CRISPR knock-out, base editing) and gene modulation (CRISPRa, CRISPRi, RNAi) fields. As a Bioinformatics Scientist 1, you will have the opportunity to apply your bioinformatics background, programming skills, and data analytical knowledge to make key contributions in support of a... wide variety of Revvity products and services including screening services, base editing research, whole genome CRISPR/RNAi reagents, and diagnostics reference standards. In this role, you will work closely with scientists, software engineers, product managers, and other bioinformaticians to support and drive cutting edge research products and services. If you are a strong team player, can learn quickly, and love working on challenging problems, then this is the right role for you! Key Responsibilities • Work as part of an Agile development team with the support of fellow bioinformatics scientists to develop, test, document, and support bioinformatics tools (primarily Python with some C# and R) • Support the Agile development process by adding information to work items and providing feedback on new code through pull requests • Curate, analyze, and interpret complex data sets • Collaborate with scientists, product managers, and software engineers to understand and address the complex emerging needs of our scientists and customers • Prepare and occasionally present high quality client facing data packages and reports to internal/external clients Nothing in this job description restricts management’s right to assign or reassign duties and responsibilities of this job at any time. Basic Qualifications: • Bachelor's degree in bioinformatics, computational biology, statistics, physics, computer science or a life/natural sciences discipline • 2 years of experience in bioinformatics using standard tools and common data sources • 1+ year of Python development experience including creating and querying databases (e.g. PostgreSQL) OR • Master's degree in bioinformatics, computational biology, statistics, physics, computer science or a life/natural sciences discipline • 1+ year of Python development experience including creating and querying databases (e.g. PostgreSQL) Preferred Qualifications: • Bioinformatics experience • Experience analyzing and interpreting complex scientific data • Knowledge of version control (e.g. Git) • Fluent in Python and experience in other languages (e.g. R, C#) • Team player - enjoys collaborating with others to achieve shared goals and objectives • Excellent interpersonal and communication skills, both written and verbal • Problem-focused and able to drive tasks to completion • Experience working as part of an Agile development team • Experience with unit testing • Familiarity with cloud development and resources (Azure, AWS); Linux & HPC experience a plus • Some experience handling or processing Next Generation Sequencing (NGS) data Compensation Range: The base salary for this full-time position is $91,500-95,000. The base pay actually offered to the successful candidate will take into account internal equity, work location, and additional factors, including job-related skills, experience, and relevant education or training. Your recruiter can share more about the specific salary range for your preferred location during the hiring process. Please note that base pay is only one part of our total compensation package and is determined within a range. This range allows for the successful candidate to have an opportunity to progress within the position and develop at our company. This base pay range does not take into account bonuses, equity, or other benefits which may be applicable and are dependent on the level and position offered. What do we offer? We provide competitive and comprehensive benefits to our employees. Below are some highlights of our benefits: · Medical, Dental, and Vision Insurance Options · Life and Disability Insurance · Paid Time-Off · Parental Benefits · 401k with Company Match · Employee Stock Purchase Plan Learn more about Revvity’s benefits by visiting our Why Revvity page. #LI-CH1

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

Senior Bioinformatics Engineer SPARK, launched by the Simons Foundation in 2016, is the largest... study of autism ever undertaken. It is open to all individuals living in the U.S. with a professional diagnosis of autism and their family members. The initiative aims to improve the lives of people with autism by identifying the causes of autism and informing more effective therapies, treatments, services, and supports. Participants share medical and behavioral information through online surveys. They can also choose to provide saliva samples for DNA analysis. This data is made available to researchers worldwide to explore the genetic underpinnings of autism, identify potential subtypes, and power downstream research. SPARK also engages the autism community by offering participants access to the latest research findings and potential opportunities to participate in additional studies. POSITION SUMMARY The Bioinformatics team at the Simons Foundation is seeking a full-time senior bioinformatics engineer. The position will play an integral role in returning genetic results to thousands of SPARK participants, including ASD and secondary health-related variants, as well as work with petabytes of genomics data and develop workflows for a variety of informatics needs across SFARI. The ideal candidate will have experience developing bioinformatics pipelines, coding using software development best practices, and performing reproducible genetic analyses. The candidate will be responsible for bioinformatics analysis of the SPARK return of genetic results process, including tracking samples from sequencing to return, developing and running analysis workflows, and working with the SPARK return of results (RoR) team on the review and selection of returnable variants. The candidate will also be responsible for packaging SFARI cohort genetic datasets for release in SFARI Base as new sequencing data is received and as other dataset updates are needed. The senior bioinformatics engineer will report to the Deputy Director of Bioinformatics and will work alongside a growing team, including a software engineer, a data manager, and a data analyst on the Bioinformatics team, as well as with Informatics' engineering team, the SDBR (SFARI Data and Biospecimen Repository) team, and various SFARI cohort teams (SPARK, Searchlight, ABN, etc.). This is a full-time position based at the Simons Foundation offices in New York City. Essential Functions & Responsibilities Return of Genetic Results • Manage the bioinformatics portion of the return of genetic results process, including delivery of sequencing data, variant analysis, and clinical validation orders • Track data deliveries of samples sent for sequencing • Run quality control pipeline to confirm RoR eligibility • Run variant filtering and annotation pipelines for SNVs/Indels & CNVs • Coordinate lab confirmation orders for predicted pathogenic variants • Analyze and summarize statistics for sequencing batches • Respond to questions from SPARK or lab related to variant predictions/orders Maintenance and Development of Bioinformatics Pipelines • Implement new features in existing pipelines, as needed • Design, develop, and test new bioinformatics pipelines, implementing end-to-end workflows that integrate existing tools, to support the needs and goals of SFARI and Informatics Data Releases • Package SFARI cohort genomics datasets for release by performing quality control, integrating data from various sources/versions, and documenting datasets details and methods descriptions • Answer questions about genomics datasets for data in SFARI Base MINIMUM QUALIFICATIONS Education • Ph.D. in bioinformatics, computational biology, or related field Required Skills & Experience • At least 4+ years of relevant work experience • Strong Python skills and software development best practices • Experience with sequencing data (whole exome or whole genome) and related tools • Experience performing reproducible data analysis • Experience working in an HPC environment • Experience with git/github • Effective oral and written communicator • Ability to thrive in collaborative environments Helpful skills • Project management experience • Experience analyzing large research datasets (>10,000 individuals) • Familiarity with core genetics concepts • Solid understanding of statistical analysis • Experience generating interactive data visualizations or dashboards • Desire to continually learn and stay up-to-date with best practices and the latest methods REQUIRED APPLICATION MATERIALS • Resume / CV • Cover Letter • Example code or repositories (e.g., github) COMPENSATION AND BENEFITS • The full-time annual compensation range for this position is $150,000 – $175,000, depending on experience. • In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package. THE SIMONS FOUNDATION'S DIVERSITY COMMITMENT Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law. To apply, visit: https://simonsfoundation.wd1.myworkdayjobs.com/en-US/simonsfoundationcareers/job/Senior-Bioinformatics-Engineer_R0001635 jeid-5fbd00174d38e348bc0c77a94004db94

**The ideal candidate will have experience developing and implementing computational pipelines and software tools for NGS data** MISSION STATEMENT... The mission of The University of Texas M. D. Anderson Cancer Center is to eliminate cancer in Texas, the nation, and the world through outstanding programs that integrate patient care, research and prevention, and through education for undergraduate and graduate students, trainees, professionals, employees and the public. SUMMARY The primary purpose of NGS Bioinformatics Developer is to develop, implement, and maintain computational pipelines and software tools for the analysis of Next Generation Sequencing (NGS) data for clinical molecular diagnostics laboratory. This would include working closely with a multidisciplinary team of molecular diagnostics scientists, bioinformaticians, pathologists, and software developers to support various genomics testing applications. This role requires strong expertise in bioinformatics algorithms and data analysis techniques, and the ability to adapt to evolving technologies and clinical applications. JOB SPECIFIC COMPETENCIES Develop bioinformatics pipelines. Develop and optimize bioinformatics pipelines for clinical molecular diagnostics laboratory. This would include processing and analyzing next generation sequencing (NGS) and other genomic data, including tasks such as quality control, alignment, variant calling, and annotation. This involves staying up-to-date with the latest tools and methods in the field and integrating them into existing pipelines to ensure accurate and efficient analysis. Design and implement bioinformatic algorithms. Design and implement algorithms and statistical methods for the interpretation of genomic data, including identification of genetic variants, differential expression analysis, and pathway analysis. This requires a deep understanding of both bioinformatics theory and practical applications to derive meaningful insights from complex genomic datasets. Develop RNA-seq pipelines for transcriptomic analyses. Develop specialized RNA-seq pipelines tailored for transcriptomic analysis, including preprocessing steps such as adapter trimming, read alignment to reference genomes or transcriptomes, quantification of gene and isoform expression levels, and differential expression analysis. This involves integrating specialized tools such as HISAT2, STAR, Salmon, or Kallisto into comprehensive workflows optimized for specific experimental designs and biological questions. Implement bioinformatics pipelines for various NGS applications such as whole genome sequencing (WGS), exome sequencing (WES), targeted sequencing, single-cell sequencing, liquid biopsy analysis, and minimal residual disease (MRD) detection. This includes adapting existing pipelines and developing new methodologies to address the specific requirements and challenges associated with each application. Gather input from stakeholders. Collaborate with molecular diagnostics professionals to understand project requirements, propose solutions, and provide technical support for data analysis and interpretation. This involves actively engaging with project teams to translate biological questions into computational workflows and troubleshooting issues that arise during data analysis. Integrate existing bioinformatics tools and databases into custom workflows to address specific clinical application needs and improve analysis efficiency. This includes evaluating the suitability of available tools and databases for particular analyses and developing scripts or wrappers to automate data processing tasks and facilitate reproducibility. Maintain documentation and version control for developed software and pipelines, ensuring reproducibility and transparency of analyses. This includes writing comprehensive documentation for code and pipelines, managing code repositories using version control systems such as Git, and adhering to best practices for software development and data management. Stay informed about new developments in bioinformatics tools, algorithms, and genomic databases, and evaluate their potential applicability to ongoing projects. This involves actively monitoring scientific literature, attending conferences, and participating in online forums and community discussions to identify emerging trends and technologies relevant to genomics research. Participate in team meetings, seminars, and training sessions to share knowledge and best practices in bioinformatics analysis. This includes presenting updates on ongoing projects, leading discussions on relevant topics in bioinformatics, and providing training to team members on new tools and methods. Provide support and training to other team members, including laboratory staff, precision oncology scientists, bioinformaticians, pathologists and clinical oncologists, on the use of bioinformatics tools and data analysis techniques. This involves offering guidance on experimental design, data preprocessing, and interpretation of results, as well as troubleshooting issues and answering technical questions to facilitate productive collaborations across disciplines Bachelor's degree in Biomedical Engineering, Electrical Engineering, Computer Engineering, Physics, Applied Mathematics, Science, Engineering, Computer Science, Statistics, Computational Biology, or related field. Three years experience in scientific software development/analysis. With Master's degree, one years experience required. With PhD, no experience required. It is the policy of The University of Texas MD Anderson Cancer Center to provide equal employment opportunity without regard to race, color, religion, age, national origin, sex, gender, sexual orientation, gender identity/expression, disability, protected veteran status, genetic information, or any other basis protected by institutional policy or by federal, state or local laws unless such distinction is required by law. http://www.mdanderson.org/about-us/legal-and-policy/legal-statements/eeo-affirmative-action.html Additional Information • Requisition ID: 168670 • Employment Status: Full-Time • Employee Status: Regular • Work Week: Day/Evening • Minimum Salary: US Dollar (USD) 91,000 • Midpoint Salary: US Dollar (USD) 113,500 • Maximum Salary : US Dollar (USD) 136,000 • FLSA: exempt and not eligible for overtime pay • Fund Type: Soft • Work Location: Onsite • Pivotal Position: Yes • Referral Bonus Available?: Yes • Relocation Assistance Available?: Yes • Science Jobs: No #LI-Onsite