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Stanford University is seeking a Bioinformatics Engineer to manage and analyze large amounts of information, typically technical or scientific in nature, independently with minimal supervision. About the Department of Pathology... Comprised of extraordinary faculty and staff, our mission is to improve the ability to diagnose, treat and understand the origin and manifestation of human disease, and to care for those who have or are at risk to develop disease. We accomplish this through our clinical services (in all fields of anatomic and clinical pathology, including molecular and genomic pathology, histocompatibility testing and transfusion medicine) and be research (which includes basic, translational and clinical research into the origins and manifestations of disease, including efforts to improve disease prediction and prevention as part of the goal of achieving precision medicine and health), and also by educating future leaders in pathology and related fields. Everything we do is to achieve the goals of providing the highest quality of clinical services to the patients for whom we passionately care, to advance our ability to understand, diagnose, monitor and ultimately to cure disease or to prevent or delay its occurrence, and to provide outstanding education and career development opportunities to those who share these goals. For more information about the department visit http://pathology.stanford.edu/ As an organization that receives federal funding, Stanford University has a COVID-19 vaccination requirement that will apply to all university employees, including those working remotely in the United States and applicable subcontractors. To learn more about COVID policies and guidelines for Stanford University Staff, please visit https://cardinalatwork.stanford.edu/working-stanford/covid-19/interim-policies/covid-19-surveillance-testing-policy. About GREGoR Stanford Site : GREGoR Stanford Site (GSS), is one of 6 sites in the National Institutes of Health (NIH)'s Genomics Research to Elucidate the Genetics of Rare disease (GREGoR) Consortium. The GSS (https://gregor.stanford.edu/) mission is to provide a platform for functional genomics research and validation to improve diagnosis in Mendelian disease through integrated analysis of multi-omics data. GSS is led by co-PIs Dr. Stephen Montgomery (Department of Pathology), Dr. Matthew Wheeler (Division of Cardiovascular Medicine) and Dr. Jon Bernstein (Division of Medical Genetics). At GSS, research participants who remain undiagnosed after exome sequencing will undergo short read and long read genome sequencing, transcriptome sequencing, methylation assays, metabolomics and/or lipidomics assays. State-of-the art computational algorithms and new methods will be applied and developed to prioritize the variants and genes. The data will be analyzed in a secure and scalable manner using a HIPAA compliant cloud platform like AnVIL and Google Cloud Platform (GCP). Novel causal variants and genes will be validated through state-of-the-art targeted approaches including massively parallel reporter assays, induced-pluripotent stem cell assays and CRISPR engineered cellular and mouse models. About the Position: We are seeking a highly talented and motivated Bioinformatics Engineer to support our GSS pipeline and data analysis team. Your role will focus on the development of pipelines and tools for comprehensive analysis of large amounts of molecular data generated by the GSS, with special emphasis on genomics, transcriptomics, and metabolomics datasets. You will also establish and support cloud infrastructure for storage and computation of the multi-omics data. Your ability to understand biological experiments, strong experience in the analysis of large-scale biological datasets, proficiency with programming languages and experience in high-performance computing environments or cloud will be a key resource in enabling high-quality data to flow through our systems to enable diagnosis and discovery of new disease-gene associations. A complete application will include CV (including GitHub account) and cover letter. Duties include: • Development of pipelines and tools for the comprehensive analysis of large amounts of multi-omics data being generated by the GSS. • Establish and maintain the cloud infrastructure for GSS on AnVIL and GCP. • Interact with GREGoR team members as well as external tool developers to implement new tools, algorithms, and updates. • Develop intuitive reports for molecular pipelines for tracking progress and quality metrics. • Track reports for problems with pipeline analysis and underlying data. • Extract relevant data from a variety of sources, including RESTful API services, databases and medical records. • Serve as a resource for bioinformatics inquiries from the clinical team members to access data or results from local cluster/cloud/external provider. • Work with stakeholders across the consortium to best understand data structures to model metadata schemas. • Mentorship to Junior Analysts with regards to primary analysis • Document and report as needed to fulfill grant and regulatory obligations. • - Other duties may also be assigned Due to the nature of the work, this position will be fully onsite. Desired Qualifications: • Graduate degree (Ph.D or M.S) that emphasizes bio/medical informatics, engineering, computer science and statistics are preferred. • Relevant work experience preferred, two or more years. • Domain expertise in analysis and running pipelines and bioinformatic tools for at least one of the following 'omes: genomics, transcriptomics, metabolomics, atac-seq, proteomics. • Proficiency in Python and/or R and Linux bash scripting. • Experience with pipeline languages like WDL or snakemake or nextflow. • Proven track record of data and infrastructure management in a HPC (High Performance Computing) cluster or cloud computing like Google Cloud Platform or AWS. • Experience with container systems such as setting up virtual machines and docker instances. • Experience and knowledge of code management such as github. • Experience in systems biology approaches for data integration is a plus • Experience in developing tools and statistical methods for large-scale data analysis is a plus. • Biological domain knowledge (rare disease) is a plus. • Experience on bioinformatics and/or software development team-based projects. • Willingness to work in a highly collaborative environment. Experience as part of large NIH consortiums is a plus. • Ability to quickly adapt and learn the latest tools and skills. • Strong communication skills (e.g., put together reports and presentations). • Ability to work independently (e.g., find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results). Education & Experience (REQUIRED): Bachelor's degree and three years of relevant experience or combination of education and relevant experience. Experience in a quantitative discipline such as economics, finance, statistics or engineering. Knowledge, Skills and Abilities (REQUIRED): • Substantial experience with MS Office and analytical programs. • Excellent writing and analytical skills. • Ability to prioritize workload. Physical Requirements*: • Sitting in place at computer for long periods of time with extensive keyboarding/dexterity. • Occasionally use a telephone. • Rarely writing by hand. • - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job. The expected pay range for this position is $100,000 to $113,000 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location and external market pay for comparable jobs. Additional Information • Schedule: Full-time • Job Code: 4752 • Employee Status: Fixed-Term • Grade: I • Requisition ID: 98520 • Work Arrangement : On Site
Bioinformatics Programmer I - 122294
Payroll Title: BIOINFORMATICS PROGR 1 Department: MEDICINE/Cardiology Hiring Pay Scale... $25.67 - $33.00 / Hour Worksite: Campus Appointment Type: Career Appointment Percent: 100% Union: Uncovered Total Openings: 1 Work Schedule: Days, 8 hrs/day, Mon - Fri #122294 Bioinformatics Programmer I Filing Deadline: Fri 4/7/2023 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply. For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy UCSD Layoff from Career Appointment: Apply by 03/28/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 04/07/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will remain open until a successful candidate has been identified. DESCRIPTION The Department of Medicine (DOM) is the largest department within the UCSD School of Medicine and is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego School of Medicine. The department employs approximately 500 salaried faculty, 168 academic appointees, 331 residents, fellow and postdocs and 479 staff personnel. Computational biologist. Resolves routine programming problems, applying established data processing algorithms to novel data. Works on issues and projects of limited scope. Follows standard programming procedures to analyze situations and data from which answers can be readily obtained. Maintains repositories of published code and answers outside user requests. Aids in the publications of research results, but will not be responsible for algorithm development. Proficiency in python, R, UNIX, and git version control systems required. AWS experience a plus, Understanding of major biological data types (genomic SNPs, single-cell RNA-seq expression, protein-protein interaction networks, ATAC-seq, Chip-seq) is required. Will design and develop bioinformatic programs to process genomics data. Responsible for lab computer and software maintenance and coordination with other computer facilities. Will independently perform cell culture experiments with human ES cells to investigate mesoderm and cardiovascular formation. Under direct supervision, applies professional bioinformatics concepts and computational procedures to complete small projects or portions of projects. Works on assignments of limited scope and complexity. Follows standard programming procedures to analyze situations and data from which answers can be readily obtained. MINIMUM QUALIFICATIONS • Four (4) years of related experience, education/training, OR a Bachelor's degree in biological science, computational / programming, or related area and /or equivalent experience/training. • Basic knowledge of bioinformatics methods and data structures. • Demonstrated experience collecting, processing, and analyzing genomics data. • Proven knowledge of applications programming and web development. • Experience with functional programming, the R class system (both S3 and new classes), the R packaging system, R methods and generic functions. Knowledge of Apache server on Linux, scripting and familiarity with Internet protocols. • Knowledge of modern biology and applicable field of research. Theoretical knowledge in molecular, cellular, or developmental biology. • Effective interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization. • Strong ability to communicate technical information in a clear and concise manner. • Basic knowledge of application and data security concepts. PREFERRED QUALIFICATIONS • Proficiency in python, UNIX, and git version control systems. • Knowledge relating to the design development, modification and implementation of software including object-oriented programming concepts. • Understanding of major biological data types (genomic SNPs, RNA-seq expression, protein-protein interaction networks.). SPECIAL CONDITIONS • Employment is subject to a criminal background check. Pay Transparency Act Annual Full Pay Range: $53,600 - $111,600 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $25.67 - $53.45 Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable). Apply Now Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral). If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable. UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information. UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening
PacBio (NASDAQ: PACB) is a premier life science technology company that is designing, developing, and manufacturing advanced sequencing solutions to enable the promise of genomics to better human health... The Computational Biology team supports the company mission by developing easy-to-use informatics solutions that deliver the best clinical and research genomes, transcriptomes and methylomes. Our team works closely with customers and the scientific community to continually identify and solve the most impactful genomics problems. Through collaborations, conference presentations and peer-reviewed publications, we represent the externally visible scientific face of PacBio. We are seeking a computational biologist who has passion for making ideas a reality by exploring the unknown, implementing proven and novel techniques to solve hard problems, and working collaboratively with internal and external scientists. Required qualifications • A Ph.D. or M.S. in a computational field or equivalent years of related work experience. • Strong problem-solving and analytical skills. • Experience analyzing DNA/RNA sequencing data, or proteomics data • Demonstrated ability to develop novel algorithms and write scientific software. • A published author in a peer reviewed journal. • Clear written and verbal communication. Preferred qualifications • Strong programming skills in Python, Rust, or C++. • Experience writing software collaboratively using version control. • Willingness to disseminate work at scientific conferences, in person. • Experience with data visualization. • Ability to work collaboratively in cross-functional teams. All listed tasks and responsibilities are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional tasks and responsibilities. #LI-Hybrid Salary Range: $110,500.00 - $149,500.00 Please be aware that, as a condition of employment, proof of COVID vaccination is required for all U.S.-based employees (subject to limited exceptions). To ensure the health and safety of all PacBio employees and our prospective candidates, we have instituted a virtual interview experience. To all Staffing and Recruiting Agencies: Our Careers Site is only for individuals seeking a job at PacBio. Staffing and recruiting agencies and individuals being represented by an agency are not authorized to use this site or to submit profiles, applications or resumes, and any such submissions will be considered unsolicited. PacBio does not accept unsolicited resumes or applications from agencies. Please do not forward resumes to our jobs alias, PacBio employees or any other company location. PacBio is not responsible for any fees related to unsolicited resumes/applications. All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status, or on the basis of disability, gender identity, and sexual orientation. If you are an individual with a disability and require a reasonable accommodation to complete any part of the application process, or are limited in the ability or unable to access or use this online application process and need an alternative method for applying, you may contact us at 650-521-8000, or http://email@example.com for assistance. Visit our following pages for more information on: • FAQs • Benefits • Culture • Equal Opportunity Employment
Bioinformatics Scientist, Center for Genomics & Bioinformatics
Description UCLA Technology Center for Genomics & Bioinformatics (UCLA TCGB) seeks a talented and highly motivated Bioinformatics Scientist to carry out genomic data analysis and serve as a lead in our bioinformatics group. Primary duties include: • Program and execute bioinformatics pipelines for genomic research applications. • Oversee the proper functioning of the NGS bioinformatics pipeline... • Develop custom script to streamline data analysis process; perform statistical and other data analyses for next-generation sequencing (Miseq, Hiseq2500, HiSeq3000, Novaseq6000, single cell sequencing with 10X genomics, Oxford nanopore, Parse Biosciences single cell, 10X Visium spatial gene expression and Nanostring GeoMx digital spatial profiling). • Performs NGS demultiplexing, data analysis and data delivery, including RNAseq, WGS, WES, Chiseq, methyseq, miRNAseq, single cell sequencing and spatial RNAseq data analysis. • Consult with customers to plan for upcoming experiments, focusing on data requirement and analysis design. Salary Range: $66,300.00 - $131,100.00/year
Molecular Genetic Bioinformatician
Job Summary: To develop, optimize, and implement NGS pipelines for clinical diagnostic tests. These include proficiency in one or several commonly used computer languages in the bioinformatics field (such as python, Unix, R, C++). To facilitate writing algorithms as they needed, ability to design and create, or adapt and modify software that are suited to process and analyze the sequencing data... considering the current regulatory requirements as they pertain to an NGS pipeline validation and maintenance (i.e., version control) and various publicly available or vendor developed tools as they pertain to NGS data visualization and data processing.Essential Responsibilities: • Provides general bioinformatics analysis support for NGS projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers. • Summarizes data analyses results in the form suitable as the basis for the first draft of written reports and makes preliminary interpretations of the data. • Assists in development, testing, and maintenance of modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms such as Illumina, Thermo-Fisher, and Pacific Biosciences. • Manages data including loading and querying data from database systems, downloading data from public repositories, and transforming data to the necessary formats. • Helps to identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology. • The primary focus will be on bioinformatics data analysis, software development and systems administration. • Evaluation and selection of commercial or open-source software required in assisting the proteomics database analysis may be required • Provides general bioinformatics analysis support and assist in development, testing and maintenance of software pipelines such as NGA or mass spectrometry data, network analysis, and visualization tools and browsers. • Coordinating with fellow programmers, scientists and technicians for providing support programming for analysis of genomic and proteomic data sequencing in various therapeutic areas and providing quality control instructions in programming • Development of scripts to move data from one analysis module to another, typically as part of the management of large data sets (loading, transformation, report generation, quality checks, etc.). • Aiding in software training for the scientists and technicians, maintaining the in-house tools and databases and supporting the bioinformatics team with their on-going efforts. • Ensures compliance/ regulatory and accreditation agencies rules and regulations. • Implements effective risk control process. • Researches/resolves problems/issues. • Oversees and coordinates startup, implementation and maintenance activities resulting from new bioinformatics services or transfer of services. • Participates in department, inter-department, inter-facility and inter-regional projects which help the Regional Laboratory achieve its goal of providing quality service and client support in a cost effective manner. • Other duties as necessary
Biomedical Specialist - Bioinformatics & Functional Genomics Core
The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group established in 2016, with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. Led by director, Simon Gayther, PhD, the primary goals of the CBFG are to establish a research nexus that integrates... leading-edge developments in computational sciences, next-generation genomics and epigenomics, and to use functional biology to improve our understanding of disease etiology applied to personalized health. To learn more, please visit Bioinformatics & Functional Genomics | Cedars-Sinai. Are you ready to be a part of breakthrough research? The CBFG Biomedical Specialist performs DNA/RNA isolation from different sources including cells, tissue, FFPE curls and scrapes, and blood, as well as understands and performs the full NGS workflow, including DNA/RNA quant and QC analysis, manual library preparation, library quant and QC analysis, sequencing on the Illumina platform, and sequencing metrics analysis. The Biomedical Specialist will maintain accurate and up-to-date electronic documentation using an electronic lab notebook, project management software, and laboratory information management system, and manually prep libraries of bulk cell, single cell, and spatial omics, including transcriptomics (RNA-Seq), genomics (WGS/WES), epigenomics (WGBS, ATAC-Seq), and metagenomics (16S/ITS amplicon sequencing, shotgun). Primary Duties and Responsibilities: • Train, guide, and supervise a team of junior associates. • Train and supervise junior associates on Next-Generation Sequencing experiments, procedures, and day-to-day service request fulfillment and lab operations. • Effectively communicate needs and requirements to junior associates as required for the management of service requests and day-to-day lab operations. • Manage junior associate performance, mentor and coach, and seek opportunities to help them grow and become their best. • Assign service requests to junior associates and ensure their proper execution and successful completion. • Ensure the availability of all required resources for the execution of service requests. • Liaise with investigators regarding service requests. • Participate in the planning, execution, and troubleshooting of service requests. • Provide research and input on new technologies and assays for testing to possibly develop and implement new service offerings. • Execute or manage the execution of projects testing new technologies, assays, or kits. • Analyze, summarize, and present findings at monthly R&D meetings. • Assist with the implementation of new technologies, assays, or kits into new service offerings by writing and reviewing standard operating procedures, service guidelines, and staff training guides, and training junior associates. • Receive, store, and document samples. • Attend meetings and seminars/webinars as assigned. Education: • Bachelor's degree in molecular biology, biochemistry or a related science/engineering field is required. Experience & Skills: • Two (2) years of experience are required. • Ability to take on new challenges while independently executing new or unusual and complex technical procedures and protocols. • Operate state-of-the art instruments, including Illumina and Pacific Biosciences sequencers, single cell instruments, automated liquid handlers, tissue dissociators, flow cytometers, cell sorters, ultrasonicators, and fragment analyzers. • Interact with professionalism with teammates, peers, researchers, investigators, and support staff of diverse backgrounds and educational levels. • Critical analysis, problem-solving, troubleshooting, multitasking, time management, following through tasks with details, working independently with minimal supervision. • Respond to rapidly changing priorities and exceptionally diverse demands through constant interruptions in a fast-paced laboratory environment. • Work cooperatively with other personnel as part of a team to accomplish daily and weekly goals. Working Title: Biomedical Specialist - Bioinformatics & Functional Genomics Core Department: BMS - Bioinfo & Func Genomics Business Entity: Cedars-Sinai Medical Center Job Category: Biomanufacturing Job Specialty: Biomanufacturing Position Type: Full-time Shift Length: 8 hour shift Shift Type: Day Base Pay:$71,300.00 - $110,400.00
The University of Southern California (USC), founded in 1880, is located in the heart of downtown Los Angeles and is the largest private employer in the City of Los Angeles. USC is consistently ranked among the nation’s most prestigious universities, and the USC Leonard Davis School of Gerontology features one of the world’s best degree and research programs in gerontology. The USC Leonard Davis... School has an international reputation as a hub of aging research and with additional strong programs throughout the university leads the way in defining and advancing the field of gerontology. An exciting opportunity has been created for an enterprising Bioinformatician to join the USC-Buck Nathan Shock Center (NSC) Genomic Translation Across Species Core (GTASC) within the Leonard Davis School of Gerontology’s Bioinformatics Core at the University of Southern California (USC). The mission of the Gerontology Bioinformatics Core (GBC) is to facilitate the development of data analytic procedures to enable the translation of big data into research findings. The Bioinformatics Core has growth opportunities with funded research projects that integrate multiple disciplines, including aging biology, geroscience, lifespan, and developmental psychology, genetics, demography, and public health. In particular, we have a strong focus on using genomic data derived from diverse human cohorts to validate findings in model organisms to better understand the architecture of complex traits related to aging-related diseases and longevity. For more information about the GBC (https://gero.usc.edu/bioinformatics-core/) or the Davis School of Gerontology (https://gero.usc.edu), click on the included links Responsible for creating and running analytical pipelines to answer research questions on funded projects. Serves as an integral part of the research team. Works closely with faculty and research leads to develop and implement coding approaches. Educates and cross-trains graduate students, staff, or post-docs in external collaborating groups. Makes independent decisions on analysis approaches, free from immediate direction, within scope of responsibilities. The GTASC focuses on testing hypotheses in humans that were generated from research conducted in model organisms to aid in identifying processes that influence health and lifespan. We do this using genomic data (genetic, epigenetic, gene expression) collected as part of large population-based studies. The bioinformatician would be responsible for creating and running analytical pipelines to answer research questions that are instrumental in accelerating the pace of translational genomics relevant to human aging. The bioinformatician will be an integral part of the research team and work closely with the core leaders to develop, implement, and document these pipelines. Demonstrated knowledge of programming and/or scripting languages (i.e., R, SAS, python) is required for this position. The ideal candidate will be a person who has demonstrated skills in genomics data analysis (e.g., GWAS, EWAS, TWAS, etc.), using high-performance computing clusters, managing large data files, documenting methods used for bioinformatic analyses, applying statistical methods for work with high dimensional data. High attention to detail, good organization, and communication skills are essential. The successful candidate will perform quality control, data management, and analysis of data using biosocial, behavioral, health, environmental, and genetic/epigenomic measures; assist with annotation of findings; prepare data for reports and manuscripts, and grant applications; stay abreast of new technology and analytic techniques; and present research activities within the group and with collaborators. The bioinformatician will have the authority to make independent decisions on matters of significance, free from immediate direction, within the scope of their responsibilities. Flexible working environment. Posting will remain open until a suitable candidate is identified. Key Accountabilities • Evaluate and assess epigenome- and genome-wide data in large population studies of older adults (e.g. Health and Retirement Study, English Longitudinal Study of Ageing). Independently analyze and interpret data analyses from quality control to regression models. This includes developing/implementing quality control protocols, generating epigenetic or genetic measures (epigenetic age, polygenic scores, etc), and conducting analyses (e.g. EWAS, GWAS, SKAT, etc). Annotate findings. • Consult with collaborators to clarify, improve and evaluate research projects. Manage data acquisition, storage, and sharing tasks, such as data use agreements and interfacing with data repositories (e.g. dbGaP, NIAGADS, and GEO). • Perform regular maintenance of datasets including merging refreshment files, restructuring and recoding variables, and checking for errors (while providing feedback to analysts during this process). Create and maintain clear and organized workflow documentation for internal and external review. Chronicle data management and analysis steps and annotate program files to ensure full transparency and reproducibility as part of a public analysis pipeline (interface with Github, etc.) to accompany manuscripts. • Perform code review for other analysts as part of the team, including working with other team members to fix errors and discuss differences in scientific opinion. Assist in the supervision of students/staff/postdocs, including guiding and managing tasks. Conduct literature reviews on aging, genomic, and bioinformatic topics. Write data, analysis, and results sections for working papers, reports, grants, and manuscripts. Collaborate in the development of data presentations for conferences and workshops. The GBC fosters a work environment that is inclusive as well as diverse, where ideas and perspectives are valued. We are building a team where individuals can thrive, contribute to cutting-edge research related to health with aging, and collaboratively elevate translational science. We welcome applicants from all backgrounds and do not discriminate based on race, color, religion, sex, sexual orientation, gender identity or expression, national origin, age, disability, veteran status, marital status, or an individual’s status in any group or class protected by applicable federal, state, or local law. Required Qualifications • Master’s degree in a recognized field of science or learning which is directly related to the duties of the position, including, but not limited to, biostatistics, quantitative social science, molecular genetics, statistical genetics, translational genomics, or bioinformatics. • Two or more years of experience in at least two domains characteristic of the bioinformatics, including at least one biological/biomedical science and one quantitative/informatics/computing science, with an aptitude for others. • Experience analyzing large and complex biological and/or -omics datasets using reproducible analysis approaches (e.g. analysis pipelines). • Data management and statistical modeling programming experience in R or other –omic analysis software using command line programming such as Linux/Unix. • Highly motivated to learn and implement novel quality control and analyses techniques for genomic data. • Ability to multi-task in order to facilitate several research projects at different stages of completion. • Experience with record-keeping for documentation of analyses and analysis pipelines. • Good communication on technical and non-technical aspects of data analysis, tasks, and timelines. • Must be able to work independently and as part of a research team. • Familiarity with statistical genetic and social science research methods. Preferred Qualifications • Familiarity with statistical genetic and social science research methods. • Experience with genomic analysis of large health or social science studies. • Programming experience with R Markdown, Python, and R shiny apps. • Experience with standard bioinformatics software tools and packages e.g. Bioconductor. • Experience analyzing large and complex biological and/or -omics datasets using reproducible analysis approaches (e.g. analysis pipelines). Work Locations This position will be on-site at the University of Southern California, Leonard Davis School of Gerontology, with flexible scheduling and remote opportunities made available within our overall school policies. If relocation is required, we will allow for reasonable time and flexibility to make necessary arrangements. Additional Information The University of Southern California offers a competitive benefits package including medical, dental, vision, life insurance, accidental death, and dismemberment insurance, and short and long term disability insurance. The annual base salary range for this position is $80,000-$96,000. When extending an offer of employment, the University of Southern California considers factors such as (but not limited to) the scope and responsibilities of the position, the candidate’s work experience, education/training, key skills, internal peer equity, federal, state and local laws, contractual stipulations, grant funding, as well as external market and organizational considerations. REQUIRED DOCUMENTS: In order for your application to be considered, a cover letter and resume must be attached. Minimum Education: Master's degree Minimum Experience: 2 years Minimum Skills: Experience analyzing large and complex biological/-omics datasets using reproducible analysis approaches (e.g., analysis pipelines). Demonstrated knowledge of programming/scripting languages (e.g., R, SAS, python). Programming experience in data management and statistical modeling (e.g., R or other –omic analysis software, using command line programming). Demonstrated skills in genomics data analysis (e.g., GWAS, EWAS, TWAS, etc.); experience using high performance computing clusters, managing large data files, documenting methods used for analytical procedures, and applying statistical methods for working with repeated measures data (e.g., from large-scale, population-based datasets). Highly motivated to learn and implement novel quality control and analyses techniques. Ability to multi-task. Experience with analysis pipeline record-keeping. Strong organizational and communication skills. High level of attention-to-detail. Ability to work independently and as part of a research team. Familiarity with statistical genetic and social science research methods. Preferred Skills: Experience with genomic analysis of large health or social science studies. Programming experience with R Markdown, Python, and R shiny apps. Experience with standard bioinformatics software tools and packages (e.g., Bioconductor). Experience analyzing large and complex biological/-omics datasets using reproducible analysis approaches (e.g., analysis pipelines
Bioinformatics Scientist - Computational Biology
Spatial Genomics is an early-stage company pioneering new frontiers in genomics. We are passionate and committed to developing revolutionary platform technologies for diverse applications of spatial genomic analysis of human and other biology. Join us in our mission to make Spatial Genomics broadly accessible and enable new discoveries in basic research and healthcare. Description... We are seeking exceptional candidates to spearhead analysis of spatial microscopy image data, single-cell data, and develop algorithms for quantitative image and sequence analysis. As a bioinformatics scientist, you will develop pipelines for data extraction and analysis from biological images. You will also aid in data interpretation to draw novel biological conclusions. This position will require working within a cross-functional product development team alongside members of R&D, Manufacturing, Marketing/Product-management, Operations, and your bioinformatics & software engineering colleagues. Spatial Genomics is a young and rapidly growing startup company in the life sciences industry. The successful applicant will ideally have experience thriving in a dynamic and rapidly evolving organization, working proactively and independently across multiple canonical job functions to execute on priorities with limited resources, support, and high expectations. Major Responsibilities • Collaborate on the development of new tools/algorithms for analysis of genomics data • Construct single cell analysis pipelines • Develop methods for data visualization and interpretation • Assist with data extraction from spatial images • Review and test methods reported in the literature • Document code and processes • Assist others in the use of software packages and pipelines • Be a strong contributor to achieving the overall product development objectives • Other duties as assigned Qualifications Required • PhD in Bioinformatics, Physical or Life Sciences, Computer Science, or related field • Experience in microscopy image analysis, single-cell data analysis, algorithm development for quantitative image and sequence analysis • Good coding ability, working knowledge of Python • Working knowledge of statistics and linear algebra • Interest in the life sciences and enthusiasm for collaborating with life science researchers • Ability to learn and apply new tools and technologies to solving technical/scientific problems • Interest in the life sciences and enthusiasm for collaborating with life science researchers Preferred • Experience with multi-omic analyses, possibly including ISH, Immunofluorescence, IHC, RNA and DNA sequencing • Experience working in software development or in genomics research • Working knowledge of git and Github • Experience with digital pathology applications or cloud-based analysis tools/platforms are a plus Spatial Genomics, Inc. is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation or any other characteristic protected by law
Bioinformatics Programmer - 121793
Payroll Title: BIOINFORMATICS PROGR 2 Department: CELLULAR & MOLECULAR MEDICINE Hiring Pay Scale... $75,850 - $92,000 / Year Worksite: La Jolla Appointment Type: Career Appointment Percent: 100% Union: Uncovered Total Openings: 1 Work Schedule: Days, 8 hrs/day, Monday - Friday #121793 Bioinformatics Programmer Extended Deadline: Fri 4/7/2023 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply. For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy UCSD Layoff from Career Appointment: Apply by 03/01/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 03/10/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. DESCRIPTION The mission of the collaborative effort between the Bintu lab and the UCSD Center for Epigenomics is to develop a quantitative and molecular framework to study the function and regulation of the human genome, with the ultimate goal to understand the molecular basis of neurodegenerative diseases. The epigenome plays a central role in regulating the functional output of the genome during development. Changes in the epigenome that result from exposure to stress, pathogenic conditions, and aging can determine the patterns of gene expression and predispose an individual to diseases. Epigenome research promises to significantly improve our understanding of the factors that drive human development and disease. The Bintu lab and the UCSD Center for Epigenomics works with researchers on the UCSD campus and beyond to foster the application of epigenomic concepts and technologies to clinical, translational, and basic research. Under the co-mentoring of Assistant Professor Bogdan Bintu and the Associate Director of Spatial Genomics Quan Zhu, the incumbent will help in running, customizing, and optimizing data analyses pipelines for spatial transcriptomics/genomics experiments. The incumbent will help to evaluate data quality and gain biological insights, as well as assist to prepare results for oral presentation, scientific publications, and grant applications. Furthermore, the incumbent will be trained in maintaining the advanced Fluorescence In Situ Hybridization (FISH)-based imaging technologies to conduct high throughput, spatially resolved single cell analysis of transcriptomics and chromatin structure. CT - Uses professional bioinformatics concepts. Applies computational procedures to resolve a variety of analysis and research issues. Works on assignments of moderate scope where analysis of data requires a review of a variety of factors. Assists in additional analyses as needed to achieve research objectives. MINIMUM QUALIFICATIONS • Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training. • Two (2+) or more years of relevant experience. • Working knowledge of bioinformatics methods and data structures. • Thorough knowledge of applications programming and web development. • Working knowledge of databases. • Working project management skills. Excellent organizational, problem solving, and analytical skills, and attention to detail. • Working knowledge of modern biology and applicable field of research. • Effective interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization. • Ability to communicate technical information in a clear and concise manner. • Thorough knowledge of application and data security concepts. • Working knowledge in genomics, biostatistics, molecular biology, and/or genetics. • Ability to work in a dynamic "startup" atmosphere. • Knowledge of analyzing next generation sequencing data. Experience with single cell genomics data like single cell RNA-seq, single cell ATAC-seq or single cell DNA methylation data is a plus. • Prior experience in statistics and programming languages such as Python, Perl, and R. Proficiency with relational databases and programming languages used in the development of web-based MIS systems is a plus plus (e.g. SQL Server, HTML). SPECIAL CONDITIONS • Job offer is contingent upon satisfactory clearance based on Background Check results. • Occasional holidays, weekends, evenings, nights, and on-call may be required. Pay Transparency Act Annual Full Pay Range: $59,700 - $124,300 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $28.59 - $59.53 Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable). Apply Now Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral). If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable. UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information. UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening
Research Bioinformatician II - Knott Lab - Center for...
The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II! The Knott laboratory is searching for a computational scientist with strong software engineering skills. We prefer this person have a background in single cell RNA sequencing or image analysis, or have experience studying the... spatial distribution of objects and their influence over one another. This research bioinformatician will lead the analysis of novel single cell sequencing and spatial data for a multidisciplinary team that is studying how cancer cells metastasize to distant organs away from the primary tumor site. To learn more, please visit: Knott Research Lab | Cedars-Sinai. The Research Bioinformatician II (RBII) performs general bioinformatics analysis and software support for projects involving in omics, and interacts with investigators to identify research problems, find appropriate software tools and recognize national biological databases and online resources for omic data. The RBII will also work with bioinformatics faculties to determine future bioinformatics needs, and helps to develop tools and pipelines as necessary to keep pace with rapid advances in sequencing technology. The RBII will demonstrate continuous self-improvement, make effective contributions to the section, and adhere to CSHS compliance plan, code of conduct, and hospital and departmental policies and procedures. Primary Job Duties & Responsibilities: • Provides general bioinformatics analysis support for omic projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers. • Summarizes data analyzes results in the form suitable as the basis for the first draft of written reports, and makes preliminary interpretations of the data. • Develop, test, and maintain modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences • Manages data including loading and querying data from database systems, downloading omic data from public repositories • Familiar with medical and biological terminologies, bioinformatics resources, and national biological databases, Ready to provide solutions for investigator’s problems through data mining and extraction • Identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology • Assists or collaborates in the preparation of grant proposals, publications, and presentations involving omic data • Educate others about bioinformatics through mentoring and teaching colleagues, investigators, fellows, and graduate students. Education: • Master of Science Degree in Computer Science, Electric Engineering, Computational biology, or Bioinformatics, or Master of Science/ Engineering in relevant fields (e.g. Biology with strong quantitative training, biostatistics with a concentration in bioinformatics) is required. • Doctorate in Computer Science or a related computational field is preferred. Experience & Skills: • Three (3) years in a research environment. • Background and work knowledge in algorithms, scientific computing, and machine learning or statistics. • Previous experience with C/C++, Java, Perl, python, and the Unix (Linux) environment. • Experiences in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets both in exploratory and pipelined fashions. Working Title: Research Bioinformatician II - Knott Lab - Center for Bioinformatics and Functional Genomics Department: BMS - Bioinfo & Func Genomics Business Entity: Cedars-Sinai Medical Center Job Category: Academic/Research Job Specialty: Bioinformatics Position Type: Full-time Shift Length: 8 hour shift Shift Type: Day Base Pay:$78,400.00 - $133,100.00