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More Bioinformatics Jobs

Research Assistant Professor - Bioinformatics Computational Core...

Tampa, FL
2021/12/11.

USF Genomics Program Research Assistant Professor and Bioinformatics Computational Core Services Director... The University of South Florida Genomics Program is seeking to hire a non-tenure earning Assistant Professor to conduct research, teach, and serve as the Bioinformatics Computational Core Services Director. The USF Genomics Program is a consortium of active genomics research programs from different colleges and campuses at USF. The USF Genomics Program projects integrate modern genomic approaches to understand and help develop solutions for some of the major challenges affecting global health and especially the Florida community. USF Genomics research projects are naturally interdisciplinary with studies that cross many boundaries of traditional scientific fields, integrating bioscience approaches in experimental and environmental research with computation biology. The USF Genomics Program is administratively housed in the USF College of Public Health and is physically located in the USF Interdisciplinary Research Building (IDRB) on the USF Tampa campus. The IDRB is a state-of-the art research facility which houses programs from Public Health, Medicine, Chemistry, and Engineering. The major role of the Bioinformatics Computational Core Services Director will be to manage computational support services for the USF Genomics Program sequencing core projects. In addition, as a member of the faculty in the College of Public Health, the incumbent will be expected to cover a minimum of 25% of annual salary through consulting services or committed time on individual research grants. In addition, the incumbent will be expected to teach and mentor students and career professionals, staff, and faculty in computational methods applied to genomics research. The incumbent will be located in the IDRB along with the USF Genomics Program Director and many of its researchers. The University of South Florida is a high-impact global research university dedicated to student success. Over the past 10 years, no other public university in the country has risen faster in the U.S. News and World Report’s national university rankings than USF. Serving more than 50,000 students on campuses in Tampa, St. Petersburg and Sarasota-Manatee, USF is designated as a Preeminent State Research University by the Florida Board of Governors, placing it in the most elite category among the state’s 12 public universities. USF has earned widespread national recognition for its success graduating under-represented minority and limited-income students at rates equal to or higher than white and higher income students. USF is a member of the American Athletic Conference. Learn more at usf.edu. USF Health’s mission is to envision and implement the future of health. It is the partnership of the USF Health Morsani College of Medicine, the College of Nursing, the College of Public Health, the Taneja College of Pharmacy, the School of Physical Therapy and Rehabilitation Sciences, the Biomedical Sciences Graduate and Postdoctoral Programs and USF Health’s multispecialty physicians group. For more information, visit health.usf.edu. The USF College of Public Health was founded in 1984 as the first college of public health in the State of Florida and is ranked as the highest public health degree program in Florida and number 20 nationally by the 2021 U.S. News and World Report. The College of Public Health consists of 241 faculty from multiple disciplines with regular, adjunct and collaborative appointments serving the educational needs of more than 4,600 students in bachelor’s, master’s and doctoral degree programs. The College is a recognized leader in online education, social marketing, community health, maternal and child health and global infectious disease research. The College offers multiple concentrations that lead to BSHS, BSPH, MHA, MPH, MSPH, DrPH, and PhD degrees, as well as several dual degrees, graduate certificates and online programs. Learn more at publichealth.usf.edu. See directions below to access the USF Careers posting for position minimum and preferred qualifications. Closing Date: Positions will remain open until filled. Review of complete applications will begin February 11, 2022. Salary & Benefits: Nationally competitive salary with excellent benefits. To apply: Candidates must apply for each position separately in order to be considered for that position. Please visit www.usf.edu and access “Work at USF” and then click on Access Careers@USF and search for Job Opening ID 29494. Documents to be uploaded with each application include a letter of application addressing the advertised minimum and preferred qualifications for the position to which applying, a CV and a list of three references. Review of application will not begin until all required documents are uploaded into Careers. References will not be contacted without notifying applicants in advance. According to Florida law, search records, including applications and search committee meetings, are open to the public. USF is an Equal Opportunity, Affirmative Action, and Equal Access institution. Applicants who need disability accommodations in order to participate in the selection process should notify Sheri Shakes at (813) 974-6494 or TDD (813) 974-1758 at least five working days in advance of need

Staff Bioinformatics Scientist - CTT

Brisbane, CA
2021/12/11.

Headquartered in Brisbane, CA, CareDx, Inc. is a leading precision medicine solutions company focused on the discovery, development, and commercialization of clinically differentiated, high-value healthcare solutions for transplant patients and caregivers. CareDx offers products, testing services and digital healthcare solutions along the pre- and post-transplant patient journey. It is the... leading provider of genomics-based information for transplant patients. Staff Bioinformatics Scientist - Cell Transplant Therapy As a member of Bioinformatics & Data Sciences group you will drive algorithm development and analysis of genomic NGS data for cell transplant therapy (CTT), primarily in oncology patients. In this role you will develop, launch, and innovate CTT products, QC, deployment, and improvement. You should have an excellent working knowledge of statistical principles and analytical methodologies relevant to high-throughput DNA sequencing data analysis. Your contributions will be foundational to the company’s mission of improving the lives of cell transplant therapy patients, including patients treated by CAR-T. Responsibilities include but are not limited to: • Drive research efforts to build advanced models for next generation sequencing algorithms and products • Collaborate with assay development scientists on design and development of novel assays and troubleshooting of existing products • Design and execute analysis plans to generate insights from large volumes of experimental data for improving assays and bioinformatics pipelines • Develop tools and automated analysis pipelines for clinical grade diagnostic tests • Provide written documentation and specifications • Collaborate with bioinformatics scientists, statisticians, LIMS engineers, CLIA lab scientists, clinicians • Mentor junior bioinformatics staff Qualifications: • Ph.D degree in bioinformatics, computer science, computational biology, mathematics, or related field • 5+ years’ experience with analysis of genomic NGS data using industry standard bioinformatics tools • Proficiency in computational analysis of genomic data, statistical principles, and modeling with focus on DNA-Seq • Proficiency with a high-level scripting language (Python/R/Java), experience in database query • Proficiency with bioinformatics best practices (e.g., version control, unit testing, code documentation/validation) • Immunotherapy and oncology background a plus • Regulated software design control experience a plus • Experience leveraging AWS based services (e.g., EC2, S3) to speed analyses a plus • A self-driven approach with an ability and desire to communicate to a non-technical audience how complex systems work and can be applied to complex data problems • A solid scientific foundation and familiarity with current literature • Proven excellent team player Additional Details: Every individual at CareDx has a direct impact on our collective mission to improve the lives of organ transplant patients worldwide. We believe in taking great care of our people, so they take even greater care of our patients. Our competitive Total Rewards package includes: • Competitive base salary and incentive compensation • Health and welfare benefits including a gym reimbursement program • 401(k) savings plan match • Employee Stock Purchase Plan • Pre-tax commuter benefits • And more! In addition, we have a Living Donor Employee Recovery Policy that allows up to 30 days of paid leave annually to a full-time employee who makes the selfless act of donating an organ or bone marrow. With products that are making a difference in the lives of transplant patients today and a promising pipeline for the future, it’s an exciting time to be part of the CareDx team. Join us in partnering with transplant patients to transform our future together. CareDx is an Equal Opportunity Employer and participates in the E-Verify program. • We do not accept resumes from headhunters, placement agencies, or other suppliers that have not signed a formal agreement with us

Lead Bioinformatics Scientist

Westlake, MD
2021/12/11.

We are currently searching for a Lead Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the NCI/CCR/Genetics Branch-OMICS Facility. Primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it is on site in Bethesda, MD. Duties & Responsibilities... • Collaborate with Genetics Branch PIs, biologists, clinicians, PI team based computational staff, and OMICS facility staff to understand their experimental and technical goals and suggest statistical and bioinformatics solutions for biological and translational questions such as mechanisms of oncogenesis, drug target discovery, drug mechanism elucidation and patient stratification efforts • Design and implement state-of-the-art computational methods; use existing open-source algorithms and develop custom algorithms to answer key cancer genomics questions using data from short Illumina and long-read multiple technologies whole genomics sequencing, short-read- Illumina and long-read PACBio whole transcriptome sequencing, single cell RNAseq, single cell ATACseq, ChipSeq, HiC, HiChiP, spatial transcriptomics, mass spec proteomics, immunopeptidomics, and spatial proteomics including CyTOF Imaging Mass Spectrometry and microarray data sets • Develop and implement codes to analyze histological images, spatial transcriptomic or pro-teomic and other digital imaging data • Provides programming and troubleshooting support to the Federal Government in the dissemination of research data. • Ensuring that Github is maintained for all codes developed by incumbent • Performs computations on research data analysis. • Participate in the optimization of the data life cycle for each project including the use of local and central archival storage, and the submission of mature datasets to the appropriate public databases • Updating codes to current versions on a 6 monthly basis and making and documenting improvements to the current codes • Integrating somatic mutations, translocations, amplifications, deletions, proteomics and epigenetics data into databases for visualization • Incorporate newly generated omics data sets in large-scale databases to support data-mining including integration with publicly available omics databases • Develop and implement machine learning including artificial and convolutional neural networks and other sophisticated algorithms • Works with staff on scientific programming and experimental design. • Work with GB collaborators • Work with staff on scientific programming and experimental design Prepare summaries and reports; attend meetings; present results and findings to staff • Records observations and report results at weekly laboratory meetings. • Reading and presentation of current literature relevant to current ongoing efforts • Collect reports • Provides statistical support / analysis on research data. • Provides research / service goals in the context of the laboratory's overall mission. • Evaluates new types of experimental approaches to protocols based on knowledge of scientific literature, available facilities and research needs. • Create generalizable code bases to improve and support development of pipelines for the analysis, interpretation and visualization of next-generation sequencing data Develop interactive shareable code solution using technologies like Jupyter KnitR for collaborators and actively maintain them in a centralized version controlled repository in Github • Independently coordinates the training of personnel in the use of scientific software applications, statistical software applications and programmatic software applications # SOAR Requirements Skills • Experience in leading/supervision of staff • Experience in working with Next Generation Sequencing Data • Familiarity with Genomics • Next gen sequencing data analysis: Bulk RNA-Sequencing • Cloud-Based Computing • Strong communications skills, both oral and written • Excellent analytical, organizational and time management skills • Single Cell RNA-Sequencing • Microarray data analysis • Working in Linux/Sever/Cloud environment. Qualifications • PhD in Biology, Life Sciences or a related discipline. • Minimum of four (4) years of experience in bioinformatics or computational biology or programming. Due to our contractual requirements and federal orders, including an Executive Order from the White House and an emergency regulation from the Centers for Medicare & Medicaid Services (CMS), the position for which you are applying requires that you provide proof of your vaccination status. If you are unable to receive the COVID-19 vaccine for medical reasons or because of a sincerely held religious belief, you may request an exemption from the vaccination requirement which shall be reviewed after the submission of requested documentation. If an accommodation is granted, the conditions may include weekly testing and masking. All Guidehouse employees also agree to follow any additional health and safety mitigation policies that may be required in the workplace. Company Description Dovel Technologies and its Family of Companies (Medical Science & Computing and Ace Info Solutions) were acquired in October 2021. Guidehouse is a leading global provider of consulting services to the public sector and commercial markets, with broad capabilities in management, technology, and risk consulting. By combining our public and private sector expertise, we help clients address their most complex challenges and navigate significant regulatory pressures focusing on transformational change, business resiliency, and technology-driven innovation. Across a range of advisory, consulting, outsourcing, and digital services, we create scalable, innovative solutions that help our clients outwit complexity and position them for future growth and success. The company has more than 12,000 professionals in over 50 locations globally. Guidehouse is a Veritas Capital portfolio company, led by seasoned professionals with proven and diverse expertise in traditional and emerging technologies, markets, and agenda-setting issues driving national and global economies. Guidehouse is an Equal Employment Opportunity / Affirmative Action employer. All qualified applicants will receive consideration for employment without regard to race, color, national origin, ancestry, citizenship status, military status, protected veteran status, religion, creed, physical or mental disability, medical condition, marital status, sex, sexual orientation, gender, gender identity or expression, age, genetic information, or any other basis protected by law, ordinance, or regulation. Guidehouse will consider for employment qualified applicants with criminal histories in a manner consistent with the requirements of applicable law or ordinance, including the Fair Chance Ordinance of Los Angeles and San Francisco. If you have visited our website for information about employment opportunities or to apply for a position, and you require accommodation, please contact Guidehouse Recruiting at 1-571-633-1711 or via email at Guidehouse does not accept unsolicited resumes through or from search firms or staffing agencies. All unsolicited resumes will be considered the property of Guidehouse, and Guidehouse will not be obligated to pay a placement fee

Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Pleasanton, CA
2021/12/11.

Inscripta was founded in 2015 and recently launched the world's first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents, and software, offers a fully automated... workflow that enables multiplexed, trackable editing of cells at an unprecedented scale. Inscripta’s mission is to enable scientists to realize the full potential of biology. Due to rapid growth and recent commercialization, Inscripta has an opening for a Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist in the Bioengineering Software Design team located in Pleasanton, CA or San Diego, CA or Boulder, CO or in the Remote U.S.. Summary: The Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist is a full-time individual-contributor position, to which you would devote all your professional effort. You will be a member of an incredibly talented interdisciplinary team, and your primary responsibility will be devoted to creating and improving library designs and library design tools needed to support Product Development and Commercial teams’ development of cells comprised of thousands of precise genomic edits. Come work with us to build the tools that will power a new era of genome engineering! Responsibilities: • Create design library orders to support our R&D Product Development and Commercial teams. • Develop, deploy, and train others to use new library design tools that help our Product Development team iterate through the design-build-test-learn cycle more quickly. • Work closely with applications scientists to document & codify library design best practices and strategies that leverage Inscripta’s technology platform. • Develop backend software to support our design library pipeline. This responsibility includes architecture decisions, feature augmentation, refactoring, testing, and documentation of code as well as participation in scrum team activities. • Such other matters as may be determined by yourself and the Company. Requirements • A Bachelor’s degree in a technical or scientific area. An advanced degree is strongly preferred. • A minimum of 7-10 years of experience (or equivalent with advanced degree). • Firm understanding of molecular biology, metabolic engineering, biophysics, and biochemistry is strongly preferred. • A strong working knowledge of bioinformatics file types like VCF, GB, GFF3, BED, and SAM/BAM. • Familiarity with bioinformatics databases like EcoCyc, UniProt, NCBI, Pfam, Rfam, YGD, ENSEMBL, UCSC genome browser. • A strong working knowledge of Python in OO setting and familiarity with packages like biopython, pandas, numpy, and scikit-learn. • Experience managing user interfaces such as Shiny (from RStudio) or Dash (from plot.ly) is a plus. • Software development skills, including a working knowledge of version control systems, continuous integration processes, and Agile development techniques – experience with Scrum is preferred. • Enthusiasm for developing software as part of a team is a must. • Patience and tenacity regarding working in a startup culture with a complex code base is a must. • 1+ years of experience writing production code in a team setting is preferred. • Energetic and motivated self-starter with excellent analytical, problem solving, communication, and presentation skills. • Special consideration will be given to candidates with expertise in synthetic biology, metabolic engineering, and advanced genome editing tools and methodologies. • Special consideration will be given to candidates with an excellent track-record of publications and/or other scientific achievements. Inscripta offers a competitive base salary, bonus plan, benefits package, 401k match, and an attractive equity program to all team members. Join us and work with a cutting edge organization creating cutting edge technology. At Inscripta, we don’t just accept difference — we celebrate it, support it, and thrive on it for the benefit of our employees, our innovation, and our community. We are proud to be an equal opportunity workplace because the more inclusive we are as a company, the better our work will be. Inscripta is headquartered in Boulder, CO with offices in Pleasanton and San Diego, CA. This position can work out of either our Pleasanton, CA or San Diego, CA or Boulder, CO locations, or work remotely in the U.S

Bioinformatics Specialist - Tu Lab

Dallas, TX
2021/12/11.

HHMI is currently seeking a talented Bioinformatics Specialist for a full-time opportunity to join the lab of Dr. Benjamin Tu at the University of Texas Southwestern Medical Center in Dallas, TX.The Tu lab is investigating how fundamental cellular processes are coordinated with metabolism and the metabolic state of the cell. They use the budding yeast Saccharomyces cerevisiae for many of their... studies to discover fundamental regulatory principles, but are also expanding some of their findings to mammalian systems. Their research has begun to show that small molecule metabolites play very underappreciated roles in the regulation of cell growth and homeostasis. The influence and importance of the metabolic state on cell regulation are far too often overlooked; the lab aims to decipher these very mechanisms. For more information about the Tu lab, please visit https://www.utsouthwestern.edu/labs/tu/As the Bioinformatics Specialist, you will be an enthusiastic problem solver who loves science and is excited to support research projects within the lab by working with experimental biologists to do custom analyses. You will have the unique opportunity to work with a diverse group of team members within the Tu lab, collaborate with other labs on UT Southwestern’s campus, and have the ability to contribute their efforts to several different research projects. The lab also has flexibility to allow for a hybrid (on-site/remote) work schedule. Essential Duties: Perform analyses of RNA-seq, ChIP-seq, and genome/exome sequencing datasets. Perform analyses of proteomics datasets and protein conservation/alignments. Work closely with experimental biologists in the lab to do custom analyses. Write custom code for analyses as needed. Perform appropriate statistical analyses. Preparation of data figures and visualization tools. Qualifications:EducationA master’s degree in bioinformatics, computational biology, computer science, biostatistics, or a closely related area is required.Experience A minimum of 2 years of experience with RNA-seq and ChIP-seq data analysis in a laboratory environment is required. Experience and skill with at least one programming language (for example: Python, R, Java, C++, etc.) is required. Experience with data visualization is strongly preferred. Knowledge, Skills, and Abilities Ability to communicate technical information to an audience not versed in bioinformatics and/or programming. Strong interest and enthusiasm for contributing to the lab’s research. Strong written and verbal communication skills. Strong organizational, time management, and prioritization skills. Strong sense of self-motivation with an ability to work well both independently and as part of a team. Ability to work on multiple projects simultaneously. Ability to interact positively with all team members at all levels and from all backgrounds. Ability to work efficiently, meet deadlines, and be adaptable to changing priorities. Application Instructions:Please attach the following information (preferably as a single PDF document) as part of your application. Résumé/CV emphasizing prior experience Contact information for three professional references Physical Requirements: Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet). Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis. Please Note: This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act

Bioinformatics Analyst I/II/III

Bar Harbor, ME
2021/12/11.

Summary The Carter Lab is seeking a Bioinformatics Analyst to join our research in the genetics and genomics of Alzheimer’s disease. This position will focus on using bioinformatics and computational biology analyses to formulate network-level therapeutic hypotheses to drive the development of new treatments. This analysis is a critical component of our goal to integrate diverse data resources... screen candidate compounds, and translate findings into preclinical tests using precision mouse models of disease. This work will be performed as part of two NIA-funded projects, the Emory/Sage/SGC TREAT-AD center (treatad.org) and IU/Jax/Pitt MODEL-AD center (model-ad.org), that bring together researchers from more than a dozen institutions to develop new approaches to understanding and treating late-onset Alzheimer’s disease. These centers are components of a major open science initiative to understand and treat Alzheimer’s disease that includes the AMP-AD, ADNI, and ADSP research consortia. We are especially interested in candidates with systems biology expertise in model organisms who are seeking to apply their innovative ideas in a translational setting. The structure of TREAT-AD and MODEL-AD enable collaborative follow-up experimentation and refinement of computational hypotheses. We are dedicated to open science and establishing an inclusive culture to expand our vision of scientific progress. Responsibilities • Mining genome-scale data and interpreting results. • Performing statistical analysis, algorithm implementation, data visualization, and bioinformatics programming; packaging and interpreting results. • Developing novel computational strategies for big data integration. • Coordinating data analysis across multiple collaborating institutions. • Assisting in data dissemination. • Contributing to publications. • Level I Analyst duties include entry level statistical analysis, algorithm implementation, bioinformatics programming, running programs and packaging results. Evaluating data for quality assurance, and mining bioinformatics databases. Assisting development of requirements and testing for software/database systems. Tasks are complex, but the incumbent has support of immediate suppervisor or mentor for directional support during execution of work. • Level II Analyst duties include basic statistical analysis, algorithm implementation, bioinformatics programming, running programs and packaging and interpreting results. Conducting, analyzing, and interpreting quality assurance data. Mining bioinformatics databases and interpreting results. Developing requirements and test plans for software/database systems. Often receives tasks but requires attention from supervisor or mentor for additional directional support. • Level III duties include all the responsbilities of Level II Analyst but works more independently and provides more indepth analysis and interpretation of results. Level III Analysts act as mentor to junior level colleagues. They also presents materials at seminars and assists in research planning. Qualifications • Bioinformatics Analyst I: requires BS or MS degree in Bioinformatics or relevent biological sciences degree. Incumbents who have not achieved Masters degree may compensate for lack of a degree with at least five years of professional bioinformatics work experience. Works under close supervision. • Bioinformatics Analyst II requires MS or PhD degree in Bioinformatics or relevent biological sciences degree. Incumbents who have not achieved a Ph.D, may compensate with a Masters degree and at least five (5) years of professional work experience in bioinformatics. Works with limited supervision for tasks performed. • Bioinformatics Analyst III requires MS or PhD degree in Bioinformatics or relevent biological sciences degree. Incumbents who have not achieved the PhD level will have at least seven (7) years profession work experience in the bioinformatics domain. Incumbents with a PhD will have completed a bioinformatics postdoctoral fellowship and/or have a minimum of two years of professional work experience in the bioinformatics domain. • The ideal candidate will have experience in genetics and genomic analyses, with particular expertise in integrative analysis of transcriptomic, proteomic, metabolomic, and curated data. • Experience in Alzheimer’s disease research is preferred but not required. About JAX The Jackson Laboratory (JAX) is an independent, nonprofit biomedical research institution with more than 2,400 employees. Headquartered in Bar Harbor, Maine, it has a National Cancer Institute-designated Cancer Center in Augusta, Maine, a genomic medicine institute in Farmington, Connecticut, and facilities in Ellsworth, Maine, Sacramento, California, and Shanghai, China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health. JAX employees work in a collaborative, value-driven, and team-based environment where the focus is on advancing science and improving patients’ lives. Researchers apply genetics to increase the understanding of human disease and advance treatments and cures for cancer, neurological and immune disorders, diabetes, aging, and heart disease. JAX was voted among the top 15 “Best Places to Work in Academia” in the United States in a poll conducted by The Scientist magazine! EEO Statement The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws

Bioinformatics Research Scientist (Bioinformatician II-III)

Seattle, WA
2021/12/09.

Overview Combatting Immune Disease Through Systems Analysis. Come join our team and help fight immune diseases. We need individuals to apply cutting edge big data approaches to study of the human immune system. We believe that understanding how the immune system is broken in diseases like cancer and autoimmunity will lead to better patient care. We are looking for highly motivated and creative... individuals who enjoy working in a multidisciplinary team-oriented environment to use Systems Biology approaches to help discover new mechanisms, biomarkers, and therapies for immune diseases. Benaroya Research Institute at Virginia Mason (BRI) is an internationally recognized medical research institute committed to finding a cure for autoimmune and immune-mediated diseases, through a combination of basic and translational research programs. This means you can contribute to scientific advances that have a direct impact on people afflicted with these diseases, including type 1 diabetes, rheumatoid arthritis, multiple sclerosis, allergies, and asthma. BRI research leadership has identified Bioinformatics as a key enabling technology, so there is broad and strong support for the analysis, and visualization of research data. Responsibilities: The Bioinformatics Group in the Center for Systems Immunology is seeking Postdoctoral Fellows. These individuals will drive project teams performing RNA-seq profiling (single cell and bulk), and/or cytometric studies (flow and mass) of immune cells in autoimmune disease and cancer. The Bioinformatics Group is broadly engaged in basic and applied studies using complex systems theory, high throughput techniques as well as mathematical and computational tools to understand the functioning of the immune system in health and disease. The group works closely with informaticians and immunologists in many groups at BRI, resulting in a rich environment for quantitative, computational, and laboratory collaborations in immune disease research. Opportunities for training, conference attendance and publication are available. Qualifications: Ph.D. preferred in bioinformatics, biostatistics, or life science, with a strong understanding of biology and bioinformatics. Bioinformatician II: Ph.D: in bioinformatics, biostatistics, or other life science with a strong understanding of the principals of bioinformatics, and 3 or more years related experience; alternatively an M.S. in the above listed fields and 6 or more years experience. Bioinformatician III: Ph.D: in bioinformatics, biostatistics, or other life science with a strong understanding of the principals of bioinformatics, proven ability to develop new methodology when needed, and 6 or more years related experience; alternatively an M.S. in the above listed fields and 9 or more years experience. Knowledge of modern experimental biological science. Fundamental understanding of the application of statistics to scientific data. Experience with statistical tools (R, SAS, Matlab) and/or scripting or higher-level programming languages (Shell, Python, Perl, Java). Strong interpersonal, verbal, and written communication skills. Benaroya Research Institute at Virginia Mason (BRI) has a bold mission: Predict, prevent, reverse and cure immune system diseases, from autoimmune disease to cancer to COVID-19. We examine the immune system in both health and disease to understand how disorders start and how to rebalance the immune system back to health. Equipped with innovative tools and robust biorepositories, our team chips away at the biggest mysteries behind these conditions to work toward our vision of a healthy immune system for all. As an independent non-profit organization within Virginia Mason Franciscan Health, we collaborate with clinicians to accelerate the path from innovative lab discoveries to life-changing patient care. At BRI, each role is valued and an important contributor to the vision and mission. BRI is committed to a safe, caring and diverse workplace; as well as to taking action to further our commitments to foster inclusion, equity and belonging so employees feel comfortable bringing their full selves to work. Consider making a difference, join our team. Because together, we are Powering Possibility. Visit BenaroyaResearch.org or follow BRI’s Autoimmune Life Blog, Facebook, Instagram, LinkedIn or Twitter to learn more. Visit https://careers-benaroyaresearch.icims.com/jobs/1740/bioinformatics-research-scientist-%28bioinformatician-ii-iii%29/job to apply for this position. We strongly support and encourage applicants from diverse backgrounds including race, color, religion, sexual orientation, gender identity, national origin, citizenship, disability or protected veteran status

Principal Scientist, Bioinformatics

Boston, MA
2021/12/09.

Job Summary GentiBio is seeking a highly motivated bioinformatician to implement and manage diverse bioinformatic capabilities to support the discovery and preclinical development of cutting-edge regulatory T-cell therapies. This leadership role requires deep expertise in multi-omics dataset analysis, including but not limited to NGS. The successful candidate will also build and manage a small... wet lab delivering sequencing-ready libraries to streamline NGS workflows. This role offers exposure to an organizational and company build, leadership, and an ample opportunity to be a high-impact trailblazer in the emerging field of regulatory T-cell therapy. Job Responsibilities • Foster the culture of seeking and giving help, inclusion, authenticity, and fun • Lead the implementation and expansion of bioinformatic capabilities, including tools and databases to support discovery and preclinical work • Build a small lab and develop an integrated workflow from samples to sequencing-ready libraries • Implement state-of-art computational pipelines for NGS to analyze transcriptomic data, including TCR sequences • Identify and acquire relevant public and third-party 'omics datasets and perform integrative data analyses to generate insights leading to new testable therapeutic hypotheses • Work closely with discovery and platform teams to develop appropriate plans for data generation and analysis, as well as visualization tools to illustrate and communicate key findings • Represent the bioinformatic function in cross-functional program teams and develop and implement bioinformatic strategies to support project-level decision-making Qualifications and Education Requirements • PhD with 5+ years of industry experience in bioinformatics, computational biology, or other related fields • Demonstrated experience developing bioinformatic tools and pipelines to analyze NGS and multi-omics large scale datasets required, as evidenced by productive and successful programs and/or publications • Excellent programming capability using various coding languages (e.g., Python, R, Shell) • Experience with TCR-seq preferred • Experience and/or previous exposure to clinical translational research in a drug discovery organization (e.g., biomarkers discovery, patient stratification) preferred • Knowledge of bioinformatic analyses relevant to the regulation of cell and gene therapy products (e.g., gRNA design, GUIDE-Seq, HLA-Seq, Amp-Seq, or on/off-target) preferred • Experience working in the cloud environment (AWS) preferred • Experience working with deep learning or machine learning models preferred • Previous management experience preferred but not required • Exceptional teamwork and communication skills • Flexibility to pivot from plan A to plan B • Ability to synthesize complex information and focus on key deliverable

Scientist/Sr. Scientist, Bioinformatics

Cambridge, MA
2021/12/09.

By clicking the “Apply” button, I understand that my employment application process with Takeda will commence and that the information I provide in my application will be processed in line with Takeda’s Privacy Notice and Terms of Use. I further attest that all information I submit in my employment application is true to the best of my knowledge. Job Description... Are you looking for a patient-focused, innovation-driven company that will inspire you and empower you to shine? At Takeda, we are transforming the pharmaceutical industry through our R&D-driven market leadership and being a values-led company. To do this, we empower our people to realize their potential through life-changing work. Certified as a Global Top Employer, we offer stimulating careers, encourage innovation, and strive for excellence in everything we do. We foster an inclusive, collaborative workplace, in which our global teams are united by an unwavering commitment to deliver Better Health and a Brighter Future to people around the world. Here, you will be a vital contributor to our inspiring, bold mission. OBJECTIVES/PURPOSE: • Integrate and analyze pre-clinical and clinical, internal and public domain datasets, to generate and evaluate actionable hypotheses for drug combination, new disease indications, and mechanism of action purposes. • Apply state-of-the-art machine learning and deep learning methods for clinical biomarker identification and validation, on various types of data including molecular profiling data, imaging, unstructured text data, EHR data, RWE, and more. • Support translational and clinical bioinformatics needs for key oncology cell therapy clinical projects, including high-throughput data QC, processing, analysis and integration. • Drive collaborations with internal groups, external partners, including CROs and academia for data analysis and machine learning. ACCOUNTABILITIES: • Independently represent bioinformatics function on global project teams in support of oncology cell therapy clinical science and translational research projects. • Play a leadership role in the development and review of the study synopsis, protocol, biomarker analysis plan, clinical study report, ensuring accurate and valid deliverables. • Perform end-to-end data analyses, from hypotheses formulation, experimental design, writing analysis plans, data cleaning, executing analysis, and preparing reports and documentation. • Interact closely with biologists and clinicians to conduct analyses, data integration and data interpretation. • Identify, build, evaluate and use bioinformatic pipelines to process and QC omics data types including genomics, transcriptomics, single cell sequencing, spatial genomics, proteomics, metabolomics, immunophenotyping and other omics technologies. • Interpret preclinical and clinical datasets using appropriate computational and statistical methods. • Create visualizations, interpret high dimensional data and explain results to cross-functional teams. • Plan and coordinate computational biology activities internally and in partnership with external CROs and academic partners, including complex projects requiring collaboration with multiple members of the team and organizations. • Prepare and present comprehensive scientific reports to a full range of internal and external audiences. • Work collaboratively with data scientists and data engineering groups at DSI to enhance our computational infrastructure, user interface, query and visualization capabilities. • Writes study reports and presents data effectively in all settings and with participants of all levels of the organization. • Receives high level instructions on all work, determines methods for new assignments, works closely with manager, mentor junior staff • Determines methods for new assignments; perform literature search as needed to propose innovative solutions • Independently manages own workload • Conducts scientific presentations to internal audiences EDUCATION, BEHAVIOURAL COMPETENCIES AND SKILLS: • PhD degree in a scientific discipline, (with 5+ years experience for Sr. Scientist), or • MS with 5+ (10+ for Sr. Scientist) years experience, or • BS with 7+ (12+ for Sr. Scientist) years experience • Passion about science and technologies • Strong background with high dimensional data analysis derived from Next Generation Sequencing, including some of the following: RNASeq, DNASeq, epigenomics, single cell sequencing, and immune profiling data. • Strong scientific understanding of molecular biology and genomics, as well as disease biology such as cancer and immunology. • Knowledge of and experience with machine learning, deep learning, statistical inference and bioinformatic techniques. • Hands-on experience developing and implementing bioinformatic pipelines for data analysis of RNASeq, DNASeq, single cell datasets, and immunophenotyping data. • Solid knowledge of Unix/Linux, command line interfaces, and fluency in some common scripting and/or programming language (e.g., R, Python, Perl, Java, C / C++). • Familiarity with parallel computing, relational databases (e.g., SQL) and cloud computing or distributed computing (i.e. AWS, HPC). • Theoretical knowledge of bioinformatics, computational biology; keeps current with emerging trends in bioinformatics and computational biology. • Familiarity with popular public domain data sources and API. • Experience in designing and conducting computational biology activities to meet program objectives; able to provide input on timelines and resource needs as indicated. • Able to evaluate/develop computational methods based on project needs. • Excellent problem solving, communication, presentation, and interpersonal skills. • Independent, self-starting and supportive of team-based research and able to work effectively in a matrix organization. • Ability to work in a team and influence team to make data driven decisions • Ability to search literature and come up with innovative solution to difficult problems • Background in cell/gene therapy, oncology or immunology is a plus Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law. WHAT TAKEDA CAN OFFER YOU: • 401(k) with company match and Annual Retirement Contribution Plan • Tuition reimbursement Company match of charitable contributions • Health & Wellness programs including onsite flu shots and health screenings • Generous time off for vacation and the option to purchase additional vacation days • Community Outreach Programs • Empowering Our People to Shine • Discover more at takedajobs.com No Phone Calls or Recruiters Please. Absent an approved religious or medical reason, all US office-based and lab-based Takeda employees who work fully on-site or in a hybrid model (as determined by Takeda) must be fully vaccinated to work at a Takeda site or to engage with Takeda colleagues or anyone else on behalf of Takeda. US field-based employees must be fully vaccinated as a condition of employment, absent an approved religious or medical reason. US employees who work at a Takeda manufacturing facility, and those who work at a BioLife center or BioLife lab, may be subject to different guidelines. If you are contacted by a Takeda recruiter about your job application, we encourage you to seek more information on the applicable guidelines for the Business Unit/Function to which you have applied. #LI-KD1 This job posting excludes CO applicants. EEO Statement Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law. Locations Cambridge, MA Worker Type Employee Worker Sub-Type Regular Time Type Full time

Bioinformatics Scientist - Translational

Stamford, CT
2021/12/09.

Sema4 is a patient-centered health intelligence company founded on the idea that more information, deeper analysis, and increased engagement will improve the diagnosis, treatment, and prevention of disease. Sema4 is dedicated to transforming healthcare by building dynamic models of human health and defining optimal, individualized health trajectories, starting in the areas of reproductive health... and oncology. Centrellis™, our innovative health intelligence platform, is enabling us to generate a more complete understanding of disease and wellness and to provide science-driven solutions to the most pressing medical needs. Sema4 believes that patients should be treated as partners, and that data should be shared for the benefit of all. Sema4 is seeking a talented, self-motivated Bioinformatics Scientist to lead cutting-edge basic and translational bioinformatics research as a member of the R&D Bioinformatics department, as well as contribute to clinical product development. You will collaborate with physician-scientists and innovative technology development labs to shed new light on disease mechanisms in various neoplasms by integrating data from novel genomic and transcriptomic assays. You will be part of an interdisciplinary team that develops wet lab assays, computational methods, pipelines, and databases to interpret large-scale human genome and transcriptome data and translate that understanding to clinical utility. You will publish the innovative results of your work to show the world how Sema4 differentiates in science and technology. RESPONSIBILITIES • Lead or support bioinformatics projects to translate NGS results, as well as public and internal genomic, phenotype, and clinical/EMR datasets, to novel discoveries on a path to clinical utility. • Design, develop, and test components of clinical NGS pipelines for oncology tests, including but not limited to liquid biopsy, single cell tests. • Analyze and integrate heterogeneous NGS data (somatic and germline SNVs, indel variants, copy-number alterations, structural variants, gene fusion / splicing variants, RNA abundance, RNA editing and modification) from diverse next-generation sequencing assays (Illumina, Ion Torrent, Pacific Biosciences; targeted panels, whole-exome sequencing, whole-genome sequencing, RNA-Seq; bulk and single-cell) and microarrays. • Work with wet labs to plan and design experiments to generate such data. • Contribute to development of infrastructure for integrating data from multiple NGS technologies, as well as variant annotation and interpretation. • Publish and present novel findings in academic journals and conferences. QUALIFICATIONS • PhD in Bioinformatics, Biomedical Informatics, Computational Biology, Genomics, or a related discipline requiring strong computational and analytical skills supplemented with biology background • Hands-on experience working with NGS tools with high proficiency, including for sequence analysis and expression analysis (such as co-expression network and Bayesian inference analysis) • Strong expertise on big data analysis skills, particularly on machine learning. • Strong coding proficiency in R, Python and SQL programming languages in a Linux environment. • Well-versed in the art of effective communication on interdisciplinary teams (scientists, programmers, and clinicians), especially graphical communication about high-complexity datasets to scientific audiences from different backgrounds. • High self-motivation, great ability to work in both multiple-task and independent fashions. • Good understanding of molecular, cell, and developmental biology, especially where relevant to cancer genomics, oncology, or endocrine neoplasms, and especially molecular cloning and NGS library preparation methodologies. • Developing code using distributed version control tools (especially Git) and software issue tracking/management systems (especially Jira). • Experience working with cloud computing infrastructures will be a plus, especially on Amazon AWS. • Minimum 2 years relevant post-graduate experience

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