Bioinformatics Jobs

Pay Range $118,800.00-$196,200.00 Company Overview The people of Memorial Sloan Kettering Cancer Center (MSK) are united by a singular mission: ending cancer for life. Our specialized care teams provide personalized, compassionate, expert care to patients of all ages. Informed by basic research done at our Sloan Kettering Institute, scientists across MSK collaborate to conduct innovative translational and clinical research that is driving a revolution in our understanding of cancer as a disease and improving the ability to prevent, diagnose, and treat it. MSK is dedicated to training the next generation of scientists and clinicians, who go on to pursue our mission at MSK and around the globe. Please review important announcements about vaccination requirements and our upcoming EHR implementation by clicking here. Important Note for MSK Employees: Your Career Hub profile is submitted to the hiring team as your internal resume. Please be sure your profile is fully complete with your skills, relevant experience and education (if required). Click here to learn more. Please note, this link is only accessible for MSK employees. Job Description Exciting Opportunity at MSK: Join our team as a Bioinformatics Software Engineer for the Computational Oncology team at the Olayan Center for Cancer Vaccines . This role is integral to MSK's immuno-oncology transformation, where you will collaborate with software and data engineers, computational biologists, clinicians, and molecular biologists. In this position, you will analyze, visualize, and interpret genomic data to inform treatment decisions and facilitate patient enrollment in clinical trials for therapeutic cancer vaccines. Utilizing ultra-sensitive DNA sequencing technologies, you will help detect genetic alterations in patient tumor samples, which are crucial for guiding vaccine design and development. As a Bioinformatics Software Engineer, you will implement software development best practices in a collaborative, team-oriented environment, contributing to software design, implementation, testing, and documentation. Key Responsibilities: * Implement best practices in software development, including code versioning, testing, and deployment.* Participate in technical discussions, including code reviews and build/release management.* Collaborate with data architects to design and develop software and data architecture.* Gather and evaluate user requirements in partnership with product managers and engineers.* Design, develop, and support innovative multi-tiered full-stack software systems for research.* Create and maintain robust, available, and reliable APIs.* Contribute to containerization efforts and develop effective CI/CD pipelines. Key Qualifications: * Masters in computer science or a related field with 2+ years of experience, or a PhD (preferred).* Experience in full stack development with technologies such as Python/Java, Flask/Spring/Django, MySQL/MongoDB, and ReactJS/AngularJS/Node.js.* Experience with automated testing suites and CI/CD tools like GitLab and Jenkins. Core Skills: * Knowledge of messaging systems like Apache Kafka, RabbitMQ, or ZeroMQ is a plus.* Understanding of Common Workflow Language (CWL) is beneficial.* Experience with scalable system architecture in cloud or on-premises environments (e.g., Kubernetes) is a plus.* Familiarity with containerization using Docker and UI Design is a plus.* Resilience and creativity in overcoming challenges. Additional Information: * Location: 323 East 61 Street (Macklowe)* Schedule: Hybrid 4 days onsite #LI-Hybrid Pay Range $118,800.00-$196,200.00 Please click to learn more about MSK's compensation philosophy. Closing MSK is an equal opportunity and affirmative action employer committed to diversity and inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration without regard to race, color, gender, gender identity or expression, sexual orientation, national origin, age, religion, creed, disability, veteran status or any other factor which cannot lawfully be used as a basis for an employment decision. Federal law requires employers to provide reasonable accommodation to qualified individuals with disabilities. Please tell us if you require a reasonable accommodation to apply for a job or to perform your job. Examples of reasonable accommodation include making a change to the application process or work procedures, providing documents in an alternate format, using a sign language interpreter, or using specialized equipment.

The Fund for Public Health in New York City (FPHNYC) is a 501(c)3 non-profit organization that is dedicated to the advancement of the health and well-being of all New Yorkers. To this end, in partnership with the New York City Department of Health and Mental Hygiene (DOHMH), FPHNYC incubates innovative public health initiatives implemented by DOHMH to advance community health throughout the city. It facilitates partnerships, often new and unconventional, between the government and the private sector to develop, test, and launch new initiatives. These collaborations speed the execution of demonstration projects, effect expansion of successful pilot programs, and support rapid implementation to meet the public health needs of individuals, families, and communities across New York City. Program Overview The Public Health Laboratory (PHL) mission is to ensure the health of all New York City (NYC) residents by providing quality laboratory testing services that address the needs of the NYC DOHMH and its community partners as they respond to clinical and environmental public health concerns. Position Overview This position will serve as a Bioinformatics analyst & coordinator at the PHL and be involved with sequencing and data management activities within the bureau. Responsibilities • Support onboarding pipelines & data management for current and emerging pathogens such as Tuberculosis, Carbapenem-resistant organisms, and other pathogens. This requires strong skills in BASH shell scripting and R. Python and SQL are good to have skills. • Manage the packaging and publishing of genomic sequences to public repositories such as NCBI and GISAID. • Lead and/or support the data unit in maintaining meta-data datasets for genomic sequences. • Coordinate the implementation and enhancements of high throughput sequencing and bioinformatics projects. • Participate in analytical activities as needed to support outbreak investigations and routine surveillance. • Perform research to identify and implement new analytical tools and visualization methods. • Assist with progress reports to ensure projects run smoothly. • Liaise between units and sections at PHL to identify, prioritize, and finalize goals for pathogen sequencing. • Lead efforts to improve sustainable data management and tracking across multiple units and bureaus. • Communicate effectively with lab technologists and analysts as well as internal and external partners. • Evaluate data, prepare reports, maintain records, and assist in the coordination of research efforts of the Agency. • Maintain and participate in a quality control and assurance program as required by job functions and title assignments in the laboratory. • Recognize, troubleshoot, and initiate corrective action for problems in a timely manner. • Participate in writing original manuscripts for publication based on data analyses. QUALIFICATIONS • Master’s degree in Biological science or Bioinformatics. • Knowledge of biology, high throughput sequencing, and bioinformatics are highly desired. • Strong verbal and written communication skills. Ability to work well within a management team environment. • Excellent project management skills and familiarity with project management tools. • Excellent interpersonal communication skills. SALARY • Salary range is $90,000 to $95,000 WORK SCHEDULE 9:00 am – 5:00 pm Monday through Friday In-office Benefits At a Glance FPHNYC offers a comprehensive benefits package • Generous Paid Time Off (PTO) policy • Medical, dental, and life insurance with low or no employee contribution • A retirement savings plan with generous employer contribution • Flexible spending medical and commuter benefits plan • Meaningful work at an organization striving to advance health equity and social justice RESIDENCY REQUIREMENT You must live in New York City Tri-state area (NY, NJ, CT) in order to be considered for a position at FPHNYC. TO APPLY To apply, upload Resume, including how your experience relates to this position. Applicants who best match the position needs will be contacted. The Fund for Public Health in New York City is an Equal Opportunity Employer and encourages a diverse pool of candidates to apply. Apply Now

Organization Overview Cancer remains a daunting problem despite decades of active research into its molecular causes. Such studies have predominantly focused on the earliest stages of cancer progression,such as the formation of a cancer or genes involved in the growth of the primary tumor. In humans afflicted by cancer,the primary tumor is typically surgically resected or eliminated by radiation. Vast numbers of patients,nonetheless,die of cancer as a result of metastasis or the spread of cancer cells from the primary tumor site to distal organs. This process is,in fact,the overwhelming cause of death from cancer,and its occurrence changes a patient's prognosis to incurable. Despite its vast clinical significance and inherently fascinating underlying biology,the metastatic program is poorly understood both at the molecular level and at the cellular/tissue micro-environment levels. Our laboratory employs a multi-disciplinary approach involving molecular,biochemical,computational,imaging,and clinical association methods to characterize the critical regulatory pathways that mediate the steps of this process. By implanting human cancer cells obtained from patients with breast or colon cancer into recipient mice,we study and interfere with the various stages of metastasis. By comparing human cancer cells that are highly metastatic to those that fail to metastasize,we have uncovered a set of small RNA molecules (microRNAs) that suppress metastasis. Our future work is aimed at gaining a better understanding of the mechanisms by which these microRNAs block metastasis. Our hope is that a better understanding of this process will enhance our therapeutic arsenal against it. Overview As a Bioinformatics Assistant II, you will be trained in the analysis and interpretation of next-generation sequencing (NGS) data, originating from mouse experiments of cancer metastasis as well as patients, under the guidance of postdoctoral scientists and bioinformaticians. Responsibilities Responsibilities include: • Learn and assist in analyzing sequencing data using established pipelines • Learn and perform appropriate QC measures • Learn and develop/benchmark new tools for sequencing data analysis • Assist and collaborate with internal and external researchers in interpretation of sequencing data • Other responsibilities, as assigned Qualifications Requirements: • Bachelor's degree is required; Master's degree or equivalent experience preferred • Team-oriented • Excellent written and verbal communication skills • Collaboration skills and an eagerness to learn • A working understanding of code and script Preferred: • Exposure to NGS data analysis preferred • Training in statistics or machine learning is a plus. The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above. The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Compensation Range: Min USD $55,000.00/Yr. Compensation Range: Max USD $65,000.00/Yr.

Overview: The Bioinformatics Pipeline Engineer will work as part of the New York Center for Rare Diseases (NYCRD) at Montefiore-Einstein. They will work closely with the Variant Interpretation Scientist to develop, implement, maintain and upgrade the software needed to analyse genomic data, using computationally efficient and secure pipelines within a local high-performance computing or remote cloud architecture. While current short-read sequencing technology will be part of their responsibility, they will focus innovation on long-read sequencing data, and on the incorporation of Human Phenotype Ontology (HPO) terms in the diagnostic process. Towards the latter goal, they will maintain and further develop our GenomeDiver software and interface, and work with the team from the Center for Health Data Innovations (CHDI) at Montefiore-Einstein on the ingestion of HPO terms mined using Natural Language Processing from patient notes in the electronic health record system. The goal will be to discover the genetic cause of the patient’s rare disease, working in an innovation environment with internal and external colleagues committed to improving rare disease diagnostics and promoting equity in diagnostics in individuals of all genetic ancestries. The position requires being on-site but with flexibility to build a hybrid model once the NYCRD infrastructure is developed. Requirements • Bachelor's degree required (advanced degree such as an Master's Degree or a doctoral MD or PhD degree strongly advantageous) • At least 3 years of relevant experience required • Python or R basic competency • SQL basic competency • Scala/Java experience advantageous • Javascript and Web Development experience a positive • Experience in building, maintaining, and troubleshooting analytical workflows for massively-parallel sequencing data in high-performance computing and cloud environments. Department: Pediatrics Bargaining Unit: Non Union Campus: CHAM Employment Status: Regular Full-Time Address: 1300 Morris Park Avenue, Bronx Shift: Day Scheduled Hours: 8:30 AM-5 PM Req ID: 222002 Salary Range/Pay Rate: $93,750.00 - $125,000.00 For positions that have only a rate listed, the displayed rate is the hiring rate but could be subject to change based on shift differential, experience, education or other relevant factors. To learn more about the “Montefiore Difference” – who we are at Montefiore and all that we have to offer our associates, please click here. Diversity, equity and inclusion are core values of Montefiore. We are committed to recruiting and creating an environment in which associates feel empowered to thrive and be their authentic selves through our inclusive culture. We welcome your interest and invite you to join us. Montefiore is an equal employment opportunity employer. Montefiore will recruit, hire, train, transfer, promote, layoff and discharge associates in all job classifications without regard to their race, color, religion, creed, national origin, alienage or citizenship status, age, gender, actual or presumed disability, history of disability, sexual orientation, gender identity, gender expression, genetic predisposition or carrier status, pregnancy, military status, marital status, or partnership status, or any other characteristic protected by law. N/A

• Job Type: Officer of Administration • Regular/Temporary: Regular • Hours Per Week: 35 • Salary Range: $85,000 - $95,000 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 We are seeking a highly motivated bioinformatician to join our innovative research team at the Center for Precision Medicine and Genomics (CPMG). Our mission is to revolutionize healthcare through the integration of personalized medicine into clinical practice. We collaborate closely with clinicians, research scientists, and genetic counselors to drive groundbreaking research and translate genomic discoveries into improved patient outcomes. The ideal candidate will be a skilled bioinformatician with a passion for leveraging genomic data to address complex biomedical challenges. You will contribute to a dynamic, interdisciplinary environment and collaborate with researchers from Columbia University and beyond on a variety of national and international projects. This position offers the opportunity to make a significant impact on the field of precision medicine. Responsibilities • Bioinformatics Analysis (40%): Provide comprehensive bioinformatics support for genomic data analysis, including sequence analysis, pipeline optimization, and data management. Utilize both cloud-based and on-premise computational resources (e.g., exome, genome, RNAseq). Collaborate with team members to ensure efficient data access, analysis, and interpretation. • Communication and Dissemination (20%): Effectively communicate complex bioinformatics findings to both technical and non-technical audiences through presentations, reports, and publications. Collaborate with researchers from diverse backgrounds to translate bioinformatics insights into actionable knowledge. • Workflow Development (20%): Design, develop, and optimize bioinformatics workflows and pipelines to efficiently process and analyze large-scale genomic datasets. Explore innovative approaches to data visualization, exploration, and mining. • Mentorship and Collaboration (20%): Mentor junior team members, including students and post-docs, in bioinformatics techniques and research methodologies. Collaborate with researchers across disciplines to drive successful research projects and grant applications. • Perform additional related duties and responsibilities as needed. Minimum Qualifications • Bachelor's degree in computer science, bioinformatics, or a related field with at least four years of relevant experience. • Master's or Doctoral degree in related field would substitute for experience. • Proficiency in programming languages such as R, Python, and Bash. • Strong communication and interpersonal skills. Preferred Qualifications • Master’s or PhD degree in computer science, bioinformatics, or a related field with at least two years of relevant experience. • Expertise in workflow management tools (e.g., CWL, Nextflow, WDL) and cloud computing platforms (AWS, GCP, Azure). • Advanced knowledge of statistical and machine learning techniques. Other Requirements • Successful completion of applicable compliance and systems training requirements. Equal Opportunity Employer / Disability / Veteran Columbia University is committed to the hiring of qualified local residents.

Description Per hourly rate: $32 / hour Department: GGS Physical work location: Remote work Web link to Lab: https://labs.icahn.mssm.edu/dolab/ Web link to Department: https://icahn.mssm.edu/research/genomics The associate bioinformatician will lead projects related to machine learning, data mining and analysis of electronic health record-linked biobanks for disease prediction and genetic discovery for common, complex diseases and rare diseases. The candidate will also be expected to assist other members of the lab with data analysis and lending bioinformatics expertise, and to attend project and group lab meetings. Responsibilities 1. Designs and implements bioinformatics tools and processes. 2. Identifies and resolves technical issues and proposes upgrades to current software. 3. Develop projects and work independently on a variety of bioinformatics analysis projects. 4. Manages databases, conducts statistical and genomic analysis, and participates in the preparation of manuscripts and presentations. 5. May be involved in sequence and structural analysis, data mining, or statistical modeling. 6. May collaborate with wet-bench biologists and work independently to analyze data derived from several types of projects using microarrays and high-throughput sequencing. 7. May conducts analysis of microarray and high-throughput sequencing data, genome sequence analysis, experimental design and statistical analysis. 8. Other related duties as assigned. Qualifications • B.S. in Biological Sciences, Bioinformatics, Computer Sciences, Statistics or related discipline. M.S. in related field preferred. • Minimum 1 year of experience in research environment, 2-3 years preferred Non-Bargaining Unit, 024 - Personalized Medicine Inst - ISM, Icahn School of Medicine Employer Description Strength Through Diversity The Mount Sinai Health System believes that diversity, equity, and inclusion are key drivers for excellence. We share a common devotion to delivering exceptional patient care. When you join us, you become a part of Mount Sinai’s unrivaled record of achievement, education, and advancement as we revolutionize medicine together. We invite you to participate actively as a part of the Mount Sinai Health System team by: • Using a lens of equity in all aspects of patient care delivery, education, and research to promote policies and practices to allow opportunities for all to thrive and reach their potential. • Serving as a role model confronting racist, sexist, or other inappropriate actions by speaking up, challenging exclusionary organizational practices, and standing side-by-side in support of colleagues who experience discrimination. • Inspiring and fostering an environment of anti-racist behaviors among and between departments and co-workers. At Mount Sinai, our leaders strive to learn, empower others, and embrace change to further advance equity and improve the well-being of staff, patients, and the organization. We expect our leaders to embrace anti-racism, create a collaborative and respectful environment, and constructively disrupt the status quo to improve the system and enhance care for our patients. We work hard to create an inclusive, welcoming and nurturing work environment where all feel they are valued, belong and are able to advance professionally. Explore more about this opportunity and how you can help us write a new 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 43,000 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 approximately 7,400 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 and top 20 in Cardiology/Heart Surgery, 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. 14 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. The Mount Sinai Health System is an equal opportunity employer. We comply with applicable Federal civil rights laws and does not discriminate, exclude, or treat people differently on the basis of race, color, national origin, age, religion, disability, sex, sexual orientation, gender identity, or gender expression. We are passionately committed to addressing racism and its effects on our faculty, staff, students, trainees, patients, visitors, and the communities we serve. Our goal is for Mount Sinai to become an anti-racist health care and learning institution that intentionally addresses structural racism.” EOE Minorities/Women/Disabled/Veterans Compensation The Mount Sinai Health System (MSHS) provides a salary range to comply with the New York City Law on Salary Transparency in Job Advertisements. The salary range for the role is $59999.94 - $64999.91 Annually. Actual salaries depend on a variety of factors, including experience, education, and hospital need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.

Organization Overview Our Vertebrate Genome Laboratory conducts research and services for individual and large vertebrate genome projects such as the Vertebrate Genomes Project (VGP/G10K) that aims to sequence high-quality genomes for all 66,000 vertebrate species on the planet. https://vertebrategenomesproject.org/. Overview We seek a highly motivated individual with a strong background in Computer Science and Genomics to join the Bioinformatics team of the Vertebrate Genome Laboratory (www.vertebrategenomelab.org) at the Rockefeller University. This person will generate reference genomes of eukaryotic species as part of the Vertebrate Genomes Project (VGP, www.vertebrategenomesproject.org) and the Earth Biogenome Project (EBP, https://www.earthbiogenome.org/). In particular, the individual is expected to help achieve the following goals: • Work closely with the VGL data production and bioinformatics teams, and the broader international scientific community of the VGP, to actively generate draft high-quality genomes. • Help make the current pipeline, which is already heavily streamlined, fully automated, such that the sequencing data is automatically processed into draft assemblies along with QC, ready for manual curation. • Consistently improve the pipeline for genome assembly quality and efficiency, based on feedback from genome curators, incorporating novel data types, and adding or help in designing novel tools. Our current workflow involves: 1) in-house generation of a variety of long- (PacBio, Nanopore) and short- (Hi-C, Element, Illumina) read data; 2) in-house generation of reference-grade draft genome assemblies; 3) manual curation of the draft assemblies; 4) submission of the final, curated assemblies to the public archives. The individual will be integrated in step 2, and will be responsible to run, maintain, further develop, and improve the VGL genome assembly pipeline currently implemented in Galaxy (Lariviere et al. 2024 Nature Biotechnology DOI: 10.1038/s41587-023-02100-3). Responsibilities Responsibilities include: • Genome assembly • Genome assembly pipeline maintenance Qualifications The ideal candidate will have a sound knowledge of genomics, ideally with insights into genome assembly, genome curation and genome analysis. Required: • Master's degree required, Ph.D. preferred • Educational emphasis in computer science or computational biology • Strong programming skills, includin knowledge of computational data-analysis workflows (e.g. CWL) • Familiarity with Unix and HPC environments • The ability to work both independently and as part of a team Preferred: • Previous experience with Galaxy workflows is a plus • The ability to organize, prioritize and plan a diverse range of work to meet deadlines • An investigative and solution-orient mindset • Good communication skills • Skilled in working effectively within large national and international scientific consortia The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above. The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Compensation Range: Min USD $64,400.00/Yr. Compensation Range: Max USD $80,000.00/Yr.

Job Description At Compugen, we are transforming immuno-oncology through the power of predictive drug discovery. Our multidisciplinary team blends expertise across biology, data science, and bioinformatics to drive innovative therapeutic development. We are expanding our bioinformatics and data engineering team within the Computational Discovery unit and are seeking a Bioinformatics Scientist to enhance our UnigenTM cloud-based platform and push the boundaries of AI/ML-driven data analysis. The Bioinformatics Scientist will play a key role in identifying and validating novel immuno-oncology drug targets and biomarkers using advanced computational techniques. Join us at the cutting edge of cancer research innovation. • Conduct End-to-End processing, analysis, and interpretation of large-scale single-cell RNA-Seq and other multi-omics datasets, driving the discovery of novel immuno-oncology drug targets • Contribute to establishment and maintenance of single-cell and additional bioinformatics processing pipelines • Implement and develop innovative tools for integrating and visualizing complex multi-omics datasets, to uncover actionable insights using AI/ML-enhanced techniques • Advance analytics support for in-vitro and in-vivo validation of drug targets, mechanism-of-action (MOA) analysis, patients’ stratification and biomarkers discovery • Work closely and routinely with computational scientists, biologists and immunologists • Present, visualize and communicate the analytics results and scientific insights to internal and external collaborators Job Requirements • Ph.D. or M.Sc. in Bioinformatics / Computational Biology & Data Sciences • Strong programming and data science skills (Python preferred) • Hands-on experience in data analysis workflows of RNA-Seq and single-cell RNA-Seq • Ability to propose and carry out independently computational biology research projects • Demonstrated impact via the development of novel innovative algorithms/analyses and the adoption of available open source or licensed solutions • A team player in a multidisciplinary environment • Outstanding interpersonal, verbal and written communication skills • Strong collaborative skills, professionalism and commitment Advantages • Experience in cancer or immunology studies, pathways analysis and biological interpretation • Background in AI/ML, statistics, and big-data analysis to advance computational discoveries • Spatial transcriptomics, image analysis expertise • Experience with multi-modal data analysis combining imaging, genomics, and clinical datasets • Experience in agile software development and databases • Cloud-based data science experience (AWS Preferred)

BIOINFORMATICS SPECIALIST (ASSOCIATE or FULL Rank) - ULLIAN LAB The Department of Ophthalmology at the University of California, San Francisco (UCSF) is looking to hire a full-time Associate or Full Specialist to focus on bioinformatics and data analysis for various research projects. We are seeking a highly motivated and dedicated professional who can thrive in a collaborative, multidisciplinary environment that involves working with multiple laboratories with diverse interests. Our vision researchers are based in Rock Hall, Cardiovascular Research Building, Sandler Neurosciences Center, and Wayne and Gladys Valley Center for Vision on the UCSF Mission Bay Campus. The Bioinformatics Specialist (Associate or Full) will work with Vision researchers to provide comprehensive bioinformatics support to users of the Department of Ophthalmology’s NIH-funded Vision Core Grant. Key responsibilities will include the following: • provide expertise in the design, execution, data management, and analysis of a variety of genomics projects from start to finish including but not limited to, typical sequencing techniques, such as single-cell/bulk RNA-seq, ATAC-seq, spatial transcriptomics (MERFISH/Visium), proteomics, metabolomics, and other omics data across modalities. • develop bioinformatics tools used for whole genome sequencing, targeted sequencing, RNA sequencing, and single cell sequencing to analyze sequence data and provide bioinformatics and data science support to various research projects in understanding mammalian eye diseases. • design and implement state-of-the-art analysis pipelines using best software engineering practices, including benchmarking, quantitative assessment, adaptation, and parameter optimization of emerging bioinformatic pipelines and algorithms. The successful candidate will join a dynamic community of investigators and can participate in a range of collaborative projects in the field of vision neuroscience. The Specialist will develop and cultivate relationships with research groups through one-on-one and group meetings. Additionally, responsibilities will involve oral presentations and preparing high-quality publication level graphs and figure panels, and written work for meetings and publications. The position offers excellent career development opportunities such as co-authorship of manuscripts, participation in meetings and conferences, and networking opportunities both within and beyond the UCSF campus with other vision scientists if the candidate is motivated, a self-starter and eager to take advantage of the opportunities. Required qualifications • Specialists appointed at the Associate rank must possess a master's degree (or equivalent degree) or five to ten years of experience in the relevant specialization. • Specialists appointed at the full rank must possess a PhD/postdoctoral level training in bioinformatics and a strong research background in vision neuroscience with a biological, theoretical and practical application of a body of highly specialized knowledge in the human, primate and non-human primate visual system. • Experience and track record in leading the construction and comparison of single cell retinal atlas of marmoset, and/or other non-human primate, human, as well as probing postnatal development mechanisms of the fovea. • The candidate must have organizational and collaborative skills. • Must be adaptable, reliable, and willing to learn. • Excellent communication, organizational and time management skills are essential. • Applicants' materials must list current and/or pending qualifications upon submission. • Applicant must have all requirements met by time of hire. Preferred qualifications • Background knowledge of genomics, genetics, molecular biology, data science, and statistical modeling. • Proficiency with R, Unix, Bash, Python. SLURM for on HPC. Version control such as Github. • Single-cell omics analysis pipelines and tools such as Seurat, Signac, Monocle, Harmony, Liger, FastMNN, Limma, RNA-velocity, SCENIC(plus), Scanpy, GSVA, GO-PCA, Clustering Trees, Encode-ATAC-seq, NicheNet, CellPhoneDB, CellChat, Infercnv, Metascape etc. • Knowledge with whole genome sequencing (WGS) and typical NGC analysis pipelines and tools such as Fastqc, samtools, bwa, bedtools, freebayes, GATK, SOILoCo, Lep-Map3, HAWK, AFLAP. • Experience in statistical modeling for neural recordings, imaging and behavioral data. • Experience with data science projects encountered in vision and ophthalmology research, such as large electronic health records, epidemiology datasets, neural recordings, imaging, and behavioral data. • Ability to coordinate and mentor people with non-bioinformatics background. • Ability to prioritize and multi-task is necessary. Please apply online at https://aprecruit.ucsf.edu/JPF05312. Document requirements Curriculum Vitae (CV) Reference requirements 2 required (contact information only) Screening of applicants will begin immediately and will continue as needed throughout the recruitment period. Salary and Rank will be commensurate with the applicant’s experience and training. See Table 24B for the salary range for this position. A reasonable estimate for this position is $73,000 - $188,200. Please direct any questions to Erik.Ullian@ucsf.edu.

Pay: Salary starting at $80,000 annually Shift: M-F, standard working hours Location: El Monte, CA- 100% onsite Overview As a Bioinformatics Scientist, you will collaborate in cross-functional teams to design, implement, and continually improve advanced computational pipelines for high-throughput analysis of multiple types of NGS data. You will refine methodologies for data analysis, processing, visualization, and storage. You will strive to maximize efficiency, quality, reliability and customer usability and satisfaction. Responsibilities • Research and Development Investigate and compare available algorithms, methods, and data sources. • Make recommendations for pipeline component improvements or new pipelines. • Write SOPs for new or updated pipeline components or new pipelines. • Write specifications for implementation by software developers. Oversee pipeline development and integration. • Production and Customer Support Investigate and resolve analysis and pipeline production issues. • Review client projects for compatibility with current pipelines, make recommendations, and implement customizations as needed. • Oversee sequencing service projects, ensuring timely processing, quality results, and client satisfaction. • Support software and LIMS developers in automation efforts. • Perform specialized analyses as needed for specific projects. • Keep up-to-date with current best practices and emerging methods. • Treat data with a high level of integrity and ethics. • Data Maintenance Investigate available annotation and reference data sources. • Validate and deploy/update selected data sources. • Write reports detailing validation/update methodology and results. • Write SOPs for updating existing or new data sources. • Validation Develop appropriate procedures for testing and validation of new or updated pipelines or pipeline components. • Document and maintain data used for testing and validation. • Write validation reports detailing validation methodology and results. Requirements: • Ph.D. degree from an accredited institution in Bioinformatics, Biostatistics, or related field. Preferred Requirements: • Experience analyzing multiple types of next-generation sequencing (NGS) data and facility with statistics for big data analysis and multi-omics data integration • Strong hands-on skills in bioinformatics databases, bioinformatics tools, and relevant programming languages. • Experience in team software development and integration projects. As part of our promise to talent, Kelly supports those who work with us through a variety of benefits, perks, and work-related resources. Kelly offers eligible employees voluntary benefit plans including medical, dental, vision, telemedicine, term life, whole life, accident insurance, critical illness, a legal plan, and short-term disability. As a Kelly employee, you will have access to a retirement savings plan, service bonus and holiday pay plans (earn up to eight paid holidays per benefit year), and a transit spending account. In addition, employees are entitled to earn paid sick leave under the applicable state or local plan. Click here for more information on benefits and perks that may be available to you as a member of the Kelly Talent Community. Why Kelly® Science & Clinical? Kelly Science & Clinical is your connection to premier scientific and clinical companies looking to hire industry experts just like you. Our team creates expert talent solutions to solve the world’s most critical challenges. Every day, we match science professionals with dream jobs that fit their skills, interests, and career goals—it’s the way we think job searching should be. Nearly 100 percent of our science recruiters have a professional background and education in science, so we know a thing or two about the science market and how to get your expertise noticed. About Kelly Work changes everything. And at Kelly, we’re obsessed with where it can take you. To us, it’s about more than simply accepting your next job opportunity. It’s the fuel that powers every next step of your life. It’s the ripple effect that changes and improves everything for your family, your community, and the world. Which is why, here at Kelly, we are dedicated to providing you with limitless opportunities to enrich your life—just ask the 300,000 people we employ each year. Kelly Services is proud to be an Equal Employment Opportunity and Affirmative Action employer. We welcome, value, and embrace diversity at all levels and are committed to building a team that is inclusive of a variety of backgrounds, communities, perspectives, and abilities. At Kelly, we believe that the more inclusive we are, the better services we can provide. Requests for accommodation related to our application process can be directed to Kelly’s Human Resource Knowledge Center. Kelly complies with the requirements of California’s state and local Fair Chance laws. A conviction does not automatically bar individuals from employment. Kelly participates in E-Verify and will provide the federal government with your Form I-9 information to confirm that you are authorized to work in the U.S.