Bioinformatics Jobs

Overview The Scientist, Bioinformatics, will be conducting data analysis for Next Generation Sequencing (NGS) experiments to develop and characterize tumor-infiltrating lymphocytes. The successful candidate will also collaborate with wet lab scientists to design the NGS experiments and interpret the results... Essential Functions and Responsibilities • Conduct Bioinformatics analyses of bulk and single-cell RNA and TCR sequencing data related to the study of preclinical and clinical TIL products. • Aid biological and immunological interpretation of sequencing data; summarize and present results with clear conclusions. • Guide wet lab scientists on the design of next-generation sequencing experiments. • Develop and implement data analysis pipelines for Next Generation Sequencing and other genomics applications, from raw instrument output to interpretable and publishable results. These include but are not limited to sequence alignment, variant calling differential expression analysis, and single-cell clustering. • Contribute to publications at international conferences and in peer-reviewed journals. • Maintain expertise in state-of-the-art NGS applications and Bioinformatics methods. • Expected to be available and communicative during scheduled work hours. • Must adhere to Iovance Biotherapeutics’ core values, policies, procedures, and business ethics. • Perform miscellaneous duties as assigned. Required Education, Skills, and Knowledge • Ph.D. degree in Bioinformatics, Biology, Immunology, Bioengineering or relevant fields with 0-3 years of experience. • Fluent in Shell, R, and Python programming. Experience working on a Linux server either locally or on the cloud. • Extensive hands-on experience in analyzing next-generation sequencing data on applications including but not limited to single-cell DNA, RNA, and TCR sequencing, whole transcriptome and whole exome sequencing, targeted DNA and RNA sequencing, etc. • Excellent problem-solving and collaboration skills. Preferred Education, Skills, and Knowledge • Knowledge in Immunology, especially T cell biology, and cancer biology. The physical demands described here represent those that an employee must meet to perform the essential functions of this job successfully. Reasonable accommodations may be made upon request to enable individuals to perform essential functions. Please contact Human Resources to request an accommodation. #LI-remote

The research intern will be training and collaborating with Dr. Su's Lab within the Department of Bioinformatics and Computational Biology. The research intern will be exposed to a variety of projects that are conducted in Dr. Su's Lab, ranging from projects on performing alignment for NGS data such as RNA-Seq, DNA-Seq, ChIP-Seq, and ATAC-Seq data; implementation of R scripts to perform... clustering analysis for scRNA-Seq data; or writing scientific manuscripts for publications. LEARNING OBJECTIVES Learn how to use high-performance computing cluster for bioinformatics data analysis. Specifically, write HPC job submission scripts for different bioinformatics data analyses, and perform alignment for NGS data such as RNA-Seq, DNA-Seq, ChIP-Seq, and ATAC-Seq data by using HPC cluster. Implement R scripts to perform clustering analysis for scRNA-Seq data. Improve scientific writing skills. Improve verbal communication skills. ELIGIBILITY REQUIREMENTS Bachelor degree in Computer or related field. ADDITIONAL APPLICATION INFORMATION This is an unpaid research opportunity

Grade - UE06 £31,396 to £36,024 per annum (A revised salary range for this grade of £32,982 to £38,025 is planned to take effect from Spring 2024) College of Medicine and Veterinary Medicine - Deanery of Biomedical Sciences... Full Time - 35 Hours Per Week Contract type - Fixed Term - 24 months The Opportunity : The Mason / Chan group is recruiting a research associate for a project focussed on identifying the molecular mechanisms underlying pathological phenotypes in PAX6 haploinsufficiency patients. The group uses stem cell models, including organoids, to study embryonic human brain development and Autism Spectrum Disorders. You will contribute to this project via supporting and conducting bioinformatic analyses of data including single-cell transcriptomic data. In addition, the candidate will work closely with members of the lab on related informatics projects. Aside from this main project, there will be opportunities for collaboration within CDBS as well as across Edinburgh Neuroscience. You are encouraged to apply if you have expertise in bioinformatics. It is also desirable for you to have interest in, and some knowledge of neurodevelopmental biology and neuroscience but not essential. This post is available for 24 months full-time (35 hours per week), however, we are open to considering part-time or flexible working patterns. We are also open to considering requests for hybrid working (on a non-contractual basis) that combines a mix of remote and regular on-campus working. Your skills and attributes for success : • Experience in single-cell transcriptomics analysis • Background in neurodevelopmental biology • Proficiency in R and Python • Excellent oral and written communication skills Last updated : 2024-03-02

Summary The KLemon Lab at Baylor College of Medicine is hiring a bioinformatics analyst l. Our long-term goal is to identify bacterial strains and compounds that will be leads for new approaches to prevent and treat infections due to nasal bacterial pathobionts and respiratory viruses. To achieve this, we are elucidating the molecular mechanisms of interspecies interactions in the human nasal... microbiome. The bioinformatics analyst I will perform bioinformatic analysis on human nasal microbiota data and human nasal organoids. A complete application includes a CV, examples of your work on GitHub, the names and email addresses for three references and a cover letter. Job Duties Work closely with the Bioinformatics Manager to: • Research, assess, and test third-party bioinformatic workflows and software. • Establish, test, and improve bioinformatic workflows. • Establish a custom database to storage and process data generated from Human Nasal Organoid wet-lab experiments. • Use computational analyses and biological interpretation of results to review existing data and propose improvements. • Ensure proper documentation, accuracy and storage of all data generated using bioinformatic tools. Assist microbiologists in lab to learn documentation skills and to perform basic bioinformatic analyses using workflows. • Maintain computational resources in the lab, which includes taking the lead on troubleshooting any hardware, software, or platform issues and interfacing with BCM IT and outside software/hardware vendors. • Take the lead both on producing data that generates new hypotheses and on testing hypotheses using bioinformatic analyses with a focus on bacterial phylogenomics, pangenomics, and metapangenomics to generate data for publication. Then, as needed, assist with key experiments to test hypotheses generated. • Write publication quality methods and results for both main and supplemental figures and tables that result from bioinformatic data analysis. This includes appropriate citations, which requires reading both the bioinformatic and microbiological literature related to the project. Prepare publication-quality final figures of bioinformatic data, along with figure legends. • Participate in weekly lab meetings, subgroup meetings, and meetings with PI. Minimum Qualifications • Bachelor's degree in Genetics, Biology, Bioinformatics, Biostatistics, Computational Biology, Computer Science, or a related field. • No experience required. Preferred Qualifications • Master’s degree in a field listed above or a related field. • Three years of research experience using bioinformatics for microbiome or bacterial or bacterial-host research can substitute for preferred education experience. Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer. 18501

Job Purpose: Use common bioinformatics and data science methods to analyze and communicate Trace Genomics data. Design and implement improvements to the Trace Genomics bioinformatics pipeline. Use data from our metagenomics pipeline to advance the scientific understanding and application of soil biology. Work with a team to apply bioinformatics methods to soil metagenomes, help design and analyze... experiments to understand the soil microbiome, and relate findings to the data in our metagenomics database. Develop methods to ensure data compatibility across lab and pipeline improvements. Ensure reference databases are up to date, accurate and efficient. Serve as a lead resource to communicate bioinformatics-related information to teams across the company. Duties and Responsibilities • Develop and test bioinformatics methods (proportional to bioinformatics experience) • Contribute to bioinformatics infrastructure (proportional to programming experience) • Curate and maintain taxonomic and functional gene databases • Develop algorithms and applications for inferring biological knowledge from metagenomic data • Keep up to date with the latest developments in algorithms for analysis of metagenomics data and its applications in the field of agriculture/soil sciences • Perform custom analytics to investigate pipeline performance, develop new data products, or satisfy customer requests • Provide cross-functional assistance with soil science and WGS teams in experimental designs and data analysis • Collaborate with scientists and agronomists to develop new high-quality data products that solve agricultural problems • Train and inform team members on the proper application and interpretation of metagenomic data • Be the voice of expertise for metagenomic and bioinformatic tools at Trace Genomics Qualifications • Ph.D. or equivalent experience in microbiology or bioinformatics • Expertise in the analysis and interpretation of metagenome data • Working knowledge of Python (preferred) or R to read code, write functions, create plots • Experience packaging and documenting code for re-use by other team members or for deployment in production • Experience creating custom reference datasets from large publicly available resources (NCBI, uniprot, etc) • Strong skills in statistical reasoning and data visualization • Ability to communicate science to experts and non-experts • Ability to collaborate with others effectively • 2+ years work experience in non-academic research preferred • Expertise in bioinformatics, specifically microbial genomics or metagenomics preferred • Experience using tools for data analysis in Python (e.g. numpy, pandas, matplotlib, scikit-learn) or R • Familiarity with cloud computing services like AWS (preferred) or equivalent • Some/basic knowledge of relational databases Please note, there is no relocation allowance or visa sponsorship available for this position

A company is looking for a Leader for a Bioinformatics Hub Key Responsibilities... Develop and implement hub vision in collaboration with research leadership and functional bioinformatics leaders Recruit, manage and grow the bioinformatics hub team Manage data processing pipelines and quality Required Qualifications and Background: Master's or PhD in Bioinformatics, Biostatistics, Computational Biology, or similar area of study Minimum of 6-8 years of experience in computational biology, bioinformatics, and/or computer science Previous experience leading a team is preferred Pharma/Biotech experience also considered a plus Previous experience with enterprise omics visualization/query/meta-analysis capabilitiesEstimated Salary: $20 to $28 per hour based on qualifications

The Department of Internal Medicine, Division of Infectious Diseases, is seeking a new faculty member at the Assistant Professor level. Applicants must have an M.D. degree or equivalent, from an approved LCME medical school and satisfactory completion of an Internal Medicine residency program as well as both an Infectious Diseases fellowship program and a Bioinformatics fellowship program from an... ACGME accredited program. Candidate must be eligible for Texas medical licensure and be board certified in Internal Medicine and board certified/eligible in Infectious Diseases. Appointment rank will be commensurate with academic accomplishments and experience. Consideration may be given to applicants seeking less than a full-time schedule. The successful candidate could provide clinical analytic or genomic analyses support, develop bioinformatics pipelines, and innovative bioinformatics approaches for the analysis of EMR data, design support or sequencing data, as well as interact with collaborators to develop grant applications, to write text for article submissions and to create journal-quality graphics and figures. Candidates will also provide patient care at the Moody HIV/OPAT Clinic at Parkland Health and Hospital System (PHHS), or the West Campus Clinic at UT Southwestern and provide inpatient care at both Clements University Hospital and Parkland Hospital. Other duties will include sharing ward attending duties in both Internal Medicine and Infectious Diseases and the teaching and training of medical students, house staff, and residents. This position is security-sensitive and subject to Texas Education Code 51.215, which authorizes UT Southwestern to obtain criminal history record information. UT Southwestern Medical Center is committed to an educational and working environment that provides equal opportunity to all members of the University community. As an equal opportunity employer, UT Southwestern prohibits unlawful discrimination, including discrimination on the basis of race, color, religion, national origin, sex, sexual orientation, gender identity, gender expression, age, disability, genetic information, citizenship status, or veteran status

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. Data-driven computational approaches are a critical driver across all therapeutic areas at Lilly. At Lilly Research Labs (LRL), we are expanding our efforts in bioinformatics, creating a centralized bioinformatics hub that works with bioinformatics groups across different therapeutic areas and functions to provide centralized scientific resources, enable state-of-the art infrastructure and tools, and bring new technologies to Lilly. We are... searching for a talented and experienced scientist to join the Lilly Omics Hub that operates in an interdisciplinary manner within a tightly integrated research community at Lilly. The successful candidate will have a flexible, learning mindset to design customer-aligned solutions; they will work in a highly dynamic team, creating workflows to process and analyze high-dimensional data. This will include development of self-service analytics tools to enable and facilitate the real-time analysis of scientific data within our research community. This position will work closely with internal and external partners to find new ways to accelerate bioinformatics efforts across LRL and will represent LRL bioinformatics to internal and external partners. Minimum Qualifications • Bachelor’s/Master’s/PhD in computer science, bioinformatics, or equivalent experience • 2+ years of software development experience, including experience in computer science, bioinformatics or other applied science • Documented track record delivering and deploying large-scale informatics production solutions in the cloud using AWS/Azure and Docker • Experience implementing bioinformatics pipelines using scalable cloud solutions Familiarity with Nextflow is a plus • A strong knack for creating visually appealing UX/UI, and ability to abide by clear design rules • Understanding of NGS technology, and downstream -omics data analysis (RNAseq, ATACseq, ChIPseq, etc) • Familiarity with designing, maintaining and implementing relational databases. Experience with NoSQL databases a plus • Proficiency in working within a Linux/Unix environment Additional Information: • Location is flexible, within the US • Lilly currently anticipates that the base salary for this position could range from between $80,000 to $240,000 and will depend, in part, on the successful candidate’s qualifications for the role, including education and experience. Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).  Of course, the compensation described above is subject to change and could be higher or lower than the range described above.  Further, Lilly reserves the right to amend, modify , or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees. Eli Lilly and Company, Lilly USA, LLC and our wholly owned subsidiaries (collectively “Lilly”) are committed to help individuals with disabilities to participate in the workforce and ensure equal opportunity to compete for jobs. If you require an accommodation to submit a resume for positions at Lilly, please email Lilly Human Resources ( LillyRecruitingCompliance@lists.lilly.com ) for further assistance. Please note This email address is intended for use only to request an accommodation as part of the application process. Any other correspondence will not receive a response. Lilly is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status. Our employee resource groups (ERGs) offer strong support networks for their members and help our company develop talented individuals for future leadership roles. Our current groups include: Africa, Middle East, Central Asia Network, African American Network, Chinese Culture Network, Early Career Professionals, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinos at Lilly, PRIDE (LGBTQ + Allies), Veterans Leadership Network, Women’s Network, Working and Living with Disabilities. Learn more about all of our groups. #WeAreLilly

Postdoctoral and Associate Research Scientist positions in Bioinformatics, Multi-Omics Data Science and Computational Proteogenomics for Immunotherapy and Cancer Vaccine Research. Postdoctoral and Associate Research Scientist Positions in Etienne Caron Lab at Department of Immunobiology, Yale School of Medicine. The Caron Lab seeks exceptional Postdoctoral and Associate Research Scientist... candidates with a passion for innovation in immunotherapy and cancer vaccine research using computational proteogenomics and immunopeptidomics approaches. The overarching goal of the Caron Lab is to develop and apply mass spectrometry-based immunopeptidomics and systems immunology approaches to understand the generation, composition and dynamics of both the self and nonself immunopeptidome, as well as its interaction with T cells, with the goal of innovating treatments and preventive strategies for a broad range of immune-related diseases. Responsabilities: • Develop and apply computational pipelines and innovative bioinformatics approaches for the discovery of novel tumor-specific antigens, PTMs, and both canonical and non-canonical actionable T cell epitopes from large immunopeptidomics datasets, • Collaborate with other researchers (academic and industry), • Train other lab members, • Publish high impact factor publications, • Present at conferences, locally, nationally and internationally, • Actively contribute to the lab's activities, including preparation of manuscripts and research grants. Qualifications: • Ph.D. in bioinformatics, systems immunology or related field, • Demonstrated expertise in the integration and analysis of large multi-omics datasets (WGS, RNAseq, ribo-seq, proteomics, immunopeptidomics), • Knowledge in T cell biology and neoantigen prediction algorithms, • Demonstrated expertise in the development of computational pipelines and databases, • Strong communication skills in English (spoken and written), • Demonstrated excellence in time management and teamwork. Opportunities and Benefits: The selected candidates will have the opportunity to gain expertise in mass spectrometry, systems immunology, spatial immunopeptidomics, T-cell epitope discovery, immunology, and vaccine design. The selected candidates will also have the opportunity to become active players within several Yale Centers, including the Yale Center for Immuno-Oncology (YCIO), Center for Infection and Immunity (CII), and Center for Systems and Engineering and Immunology (CSEI). Strong support will be given to pursue independent directions. Compensation and benefits will be according to Yale policies. About the Caron Lab: Dr. Caron is an Assistant Professor at Yale University. Over the last five years, the Caron Lab has published 14 immunopeptidomics manuscripts including 10 as corresponding papers in Journal of Experimental Medicine, Cell Systems, Cancer Discovery, and other high-profile journals. Dr. Caron is co-founder and former chair (2015-2020) of the Human Immunopeptidome Project. He has a total citation of >4400 times to date and is the recipient of multiple Awards and Recognitions. Please see https://medicine.yale.edu/profile/etienne-caron/ for more information. If interested, please send your CV and motivation letter to etienne.caron@yale.edu. Yale University is an Affirmative Action/Equal Opportunity Employer. Yale values diversity among its students, staff, and faculty and strongly welcomes applications from women, persons with disabilities, protected Veterans, and underrepresented minorities

• Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and... comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals. • We seek an enthusiastic and highly motivated bioinformatics associate to join our cancer genomics research group. This individual will join oncologists, computational biologists and research scientists on our effort aimed at studying the relationships between cancer causing genomic alterations and clinical outcome. This position will provide ample opportunities for professional development and the acquisition of cutting-edge skills in basic and translational cancer genomics research, research planning and strategy, and data analysis and interpretation. • This individual will analyze cancer genomic data generated at Dana Farber using software tools within our team and by generating their own statistical analysis code. This individual will collaborate with oncologists, computational biologists and research scientist to study alterations in patients’ somatic genomes in order to assist in finding new cancer treatments and cures. • Works in teams with oncologists, research scientist and molecular biologists to define and execute computational approaches. • Performs computational analysis of next generation sequencing data, somatic copy number alterations, expression profiling, and biological pathways using in house algorithms. • Generates own code to conduct various other statistical analyses including those to discover relationships between cancer alterations and clinical correlates. • Presents data at project team meetings. • Assists in drafting of scientific manuscripts. • This employee will be located at both the Dana-Farber Longwood Medical Area campus and at the Broad Institute in Cambridge. At Dana-Farber Cancer Institute, we work every day to create an innovative, caring, and inclusive environment where every patient, family, and staff member feels they belong. As relentless as we are in our mission to reduce the burden of cancer for all, we are equally committed to diversifying our faculty and staff. Cancer knows no boundaries and when it comes to hiring the most dedicated and diverse professionals, neither do we. If working in this kind of organization inspires you, we encourage you to apply. • Required: B.S./B.A. in the life sciences, physical sciences, or computational sciences. Some coding knowledge of either R, Matlab, and/or python. The ability to work in teams, excellent communication and data presentation skills. • Preferred: Background in molecular genetic data. Understanding of statistical methods and working in cloud computing and UNIX environments. • We will consider May 2024 graduates. Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law. EEOC Poster