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    BACKGROUND

    The Korem Lab (koremlab.science) aims to obtain a mechanistic and actionable understanding of the microbiome's role in human health and disease, using rigorous bioinformatics, statistical analysis and machine learning. As part of the Program for Mathematical Genomics and the Departments of Systems Biology and Ob/Gyn, we operate in an engaging and multi-disciplinary environment consisting of computational biologists, applied mathematicians, statisticians, physicists, and physicians. The lab operates at the intersection between computational biology and medicine, developing analytic approaches and algorithms and computational methods that aim to integrate multi-omic and clinical data to study health and disease.

    RESPONSIBILITIES

    We are seeking a postdoctoral researcher who is looking to work in a creative and collaborative environment on new analytic approaches for inferring the activity and dynamics of the human microbiome and other microbial communities. A strong background in statistics and causal inference is highly preferred.

    REQUIREMENTS

    • Ph.D. in any quantitative science (statistics, computer science, physics, or similar fields) or in life sciences with a strong computational background. You will acquire any missing domain or biological knowledge with us.
    • A strong background in statistics and causal inference is highly preferred.
    • Excellent communication and organizational skills.

    TERMS

    Full time.

    LOCATION

    New York, NY

    COMPENSATION

    Annual salary with robust employment package including: Medical, Dental, Vision, Retirement plans, Employment Assistance Program, and generous PTO policy.

    HOW TO APPLY

    Please apply here: apply.interfolio.com/99261. Or send the following to pr2470[at]cumc.columbia.edu:
    • Cover letter
    • CV
    • Names and contact information for 2-3 references.
    For inquiries, please contact tal.korem[at]columbia.edu.

    DEADLINE

    Applications are open until the position is filled.

    POLICY

    Columbia University is an affirmative action/equal opportunity employer and encourages applications from women and underrepresented minorities.

    Lawrence Berkeley National Lab's (LBNL, www.lbl.gov) Joint Genome Institute Division (jgi.doe.gov) has an opening for a Software Developer to join the team.

    RESPONSIBILITIES

    In this exciting role, you will lead the design and development of software in support of synthetic biology projects. Acting as a key contributor, will utilize in-depth and advanced knowledge in bioengineering, genomics, and computational biology to develop computational tools and approaches for the design, assembly, and sequence QC of synthetic DNA constructs and combinatorial libraries, and may coordinate activities of other personnel. Duties and responsibilities include working closely with the DNA Synthesis Platform to build and implement computational tools enabling streamlined deployment of cutting-edge molecular approaches at scale, with an approximately 80/20 split between tool development and team lead. Will provide feedback to end users on both technical and biological interpretation of the data. Will collaborate with various JGI groups on data analysis and facilitate transfer of knowledge of technologies and applications to JGI staff as needed. You will report to the DNA Synthesis Platform Lead.

    What You Will Do:
    Software developer:
    • Lead and/or participate in the development of computational approaches to aid in the design, assembly and analysis of DNA constructs, oligonucleotide pools and synthetic libraries.
    • Work closely with the platform group to provide interpretation of downstream data output and iteratively improve design software accordingly.
    • Maintain an accurate and detailed documentation of tools developed.
    • Ensure that developed tools have biologist-appropriate user interfaces and functionality.
    • Present technical and analytical status updates in weekly meetings.
    • Contribute to scientific research papers, reports and presentations.
    • Follow standard practices for executing version control, testing, and release.
    • Implement data-specific user interfaces and data retrieval reports.
    • Assist users to resolve tool malfunction or data entry errors.
    • Survey and provide feedback on existing and new third-party software that can be incorporated into our workflows.
    • Provide updates of progress in regular meetings.
    • Promote a culture that reflects JGI core values of work/life balance, respect, teamwork, collaboration, diversity & inclusion, team-building, employee development, communication, and first-rate science.
    Team lead of the DNA Synthesis Bioinformatics group:
    • Strategize for and develop future informatic applications.
    • May coordinate activities of other team members.
    • May manage collaborative projects with other teams.

    REQUIREMENTS

    What is Required:
    • A minimum of 8 years of experience programming in Python, Java or R in a UNIX environment with a Bachelor's degree; or 6 years and a Master's degree.
    • Experience successfully managing and leading a team of software developers in a research science setting.
    • Extensive experience leading all stages of independent scientific software development projects through publication in peer reviewed journals and presentation at scientific meetings.
    • Knowledge of synthetic biology/bioengineering/computational biology/genome science.
    • Proficiency with scripted programming languages (Python preferable) in a Unix environment.
    • Proficiency with object-orientated languages (JAVA preferable).
    • Experience with web application frameworks (Tomcat/Django/Flask).
    • Experience with relational database design, query language, and administration (SQL, Postgres, MySQL).
    • Experience with HPC environments.
    • Experience with containers (Docker).
    • Experience with web development and related technologies (Javascript, ORMs, REST APIs).
    • Familiarity with full stack software development and deployment.
    • Analytical skills sufficient to troubleshoot discrepancies in data results and make improvement recommendations.
    • Strong organizational and record-keeping skills.
    • Experience with and adherence to software development best practices (version control, code review).
    • Effective oral and written communication skills as well as interpersonal skills.
    • Ability to work independently and as a team member in a diverse team environment.
    • Ability to handle multiple tasks in parallel while working on a large number of projects.
    • Effective problem-solving, decision-making, organizational and analytical skills.
    Desired Qualifications:
    • Ph.D. degree in computational biology, bioinformatics, synthetic biology, or a similar field.
    • Experience performing computational analysis of complex biological datasets, focused on biological design.
    • Familiarity with commercial laboratory software (e.g. Benchling, LabKey etc).
    • Experience in writing software for analysis of DNA sequence or experimental data.
    • Proficiency in utilizing assembled genomes, various alignment tools, visualization tools, and other genome interrogation and analysis software.
    • Familiarity with statistical tools and interpretation of data.
    • Proficiency with compiled programming languages (C/C++, Java or others) in a Unix environment.
    • Experienced with Data Exchange Standards in synthetic biology such as SBOL.
    • Experience with workflow managers (Cromwell preferable).

    TERMS

    • This is a full-time career appointment, exempt (monthly paid) from overtime pay.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

    LOCATION

    Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]14869 and follow the on-line instructions to complete the application process.

    POLICY

    Equal Employment Opportunity:
    Based on University of California Policy – SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit covid.lbl.gov for more information.

    Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, diversity.lbl.gov/ideaberkeleylab/) and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

    Equal Opportunity and IDEA Information Links:
    Know your rights, click here (www.dol.gov/ofcc[...]t.htm) for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision (www.dol.gov/ofcc[...].html) under 41 CFR 60-1.4.

    BACKGROUND

    Multiple Postdoctoral Research Associate positions are available in the Division of Epidemiology, Department of Medicine at Vanderbilt University Medical Center (VUMC). Our current research concentrates on population-based molecular, genetic and genomic epidemiologic studies for the exploration of novel candidate biomarkers and susceptibility genes for cancer prevention and precision medicine. To achieve the goals, We will apply and develop bioinformatics tools and build statistical models to process large multiomics data, including whole genome sequencing, whole exome sequencing, RNA-seq, array-based genotype, epigenetics, proteomics, and metabolomics data. The chosen candidate will lead independent research projects in the fields of genetics, epigenetics, functional genomics, and bioinformatics & biostatistics. The candidate should also expect to participate in multiple collaborative projects in cancer-related genetic epidemiology studies. Please find more information about our research from Dr. Xingyi Guo's lab website: www.guoxlab.org.

    RESPONSIBILITIES

    Under the guidance from Dr. Xingyi Guo, the candidate is expected to work on a wide range of bioinformatics, cancer genetics and functional genomics projects. He/she should have a PhD in bioinformatics, computational biology, biostatistics, epidemiology, genetics/genomics or related fields. The candidate should have experience in processing high-throughput genomic and genetic data with biostatistics knowledge. Experience with script languages such as Perl, Python or R. and experience with the Linux/Unix environment are required.

    TERMS

    The position is for two years with the possibility of further extension.

    COMPENSATION

    Salary is commensurate with the NIH pay scale. The postdoc positions will be provided with benefits following the VUMC standards.

    HOW TO APPLY

    To apply, please send a cover letter, CV, summary of past work, and the names and email addresses of three references to Dr. Xingyi Guo at xingyi.guo[at]vumc.org.

    DEADLINE

    The deadline for applications is July 30, 2022.

    ABOUT US

    Our lab is affiliated with Vanderbilt University Medical Center, Division of Epidemiology, Department of Medicine, and Department of Biomedical Informatics. The Division of Epidemiology is committed to conducting research to enhance and expand our understanding of the distribution and determinants of disease, to promoting collaboration aimed at the translation of research into cost-effective strategies of disease prevention and health care delivery, and to training independent investigators in epidemiological research and disease prevention. We have a broad interest in the research of cancer etiology, prevention and precision medicine through developing bioinformatic and statistical approaches and integrating multi-omics data, with a major goal of identifying genetic susceptibility factors for human cancers. Our research projects will primarily build upon valuable clinical and molecular resources based at the VUMC, e.g., the BioVU, a large hospital-based DNA biobank, population-based genome-wide association studies (GWAS) and functional genomics data.

    i) We are applying and developing bioinformatics tools and pipelines to process large multi-omics data, including whole genome sequencing (WGS), whole exome sequencing (WES), RNA-seq, array-based genotype, epigenetics and proteomics data, as well as metabolomics data. We have established computing platforms via our local university computing resource (Advanced Computing Center for Research & Education, ACCRE) and Amazon Web Services (AWS) to handle population-based sequencing and high-dimensional omics data for identifying risk genetic variants (i.e. coding and structure variants) and somatic mutations in human cancers.

    ii) We are highly interested in developing computational epigenetics (i.e. ChIP-seq and ATAC-seq) and statistical approaches to improve discovery of susceptibility non-coding variants (i.e. regulatory variants) and genes from current study designs of genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS).

    iii) We are building statistical models to explore the inter-relationship of somatic alterations in tumor tissues (i.e. tumor mutational burden/mutational signatures/tumor-infiltrating lymphocytes (TILs)) with genetic susceptibility and carcinogens environmental exposures in human cancers.

    iv) In order to understand the underlying molecular mechanisms of carcinogenesis, we are conducting cell and molecular biology studies, including in vitro functional assays and ChIP-seq to investigate transcription factor regulation mechanisms and biological functions of genes in cell proliferation, invasion, and clonogenesis.

    POLICY

    VUMC wishes to reflect the diversity of society and welcomes applications from all qualified candidates, regardless of backgrounds and individual characteristics.

    BACKGROUND

    The Department of Pathobiology at the University of Guelph invites applications for a tenure-track position at the Assistant or Associate Professor level.

    The Department of Pathobiology at the University of Guelph invites applications and nominations for a Canada Research Chair Tier II in Animal Disease Bioinformatics. The appointment will be tenure-track at the rank of Assistant or Associate Professor. Tier 2 Chairs are awarded for a five-year term and can be renewed once. For more details, visit the CRC program. This position will form part of a One Health cluster of researchers at the University of Guelph) working in an interdisciplinary manner at the interface of animal, human, and environmental health.

    The Department of Pathobiology has recognized strengths in immunology, microbiology, veterinary infectious diseases, and mammalian and comparative pathology. The Department, together with the Animal Health Laboratory, has a new state-of-the-art 13,000 square meter building housing well-equipped modern research and diagnostic laboratories. The College has a large veterinary teaching hospital (Health Sciences Centre), the Animal Cancer Centre and the Centre for Public Health and Zoonoses. In addition, researchers have access to nearby research stations suitable for conducting studies in a variety of domestic animals and on-campus housing for laboratory animals.

    To see the full online posting please go to: www.uoguelph.ca/facu[...]shtml

    RESPONSIBILITIES

    The Chair is expected to establish a strong independent, collaborative and multi-disciplinary research program in the area of Animal Disease Bioinformatics. The program should aim to find solutions, using big data analytic approaches, for control of disease and improving health and welfare in agricultural and/or companion animals. The Chair is expected to work collaboratively with Pathobiology and OVC faculty to promote and implement high throughput technologies and bioinformatics.

    While this is a research-intensive appointment, the successful candidate is expected to contribute to the undergraduate and graduate education in the Department of Pathobiology, and to development a new graduate program in Bioinformatics.

    "Food from Thought" is a current initiative at the University of Guelph. The goal of this initiative is to exponentially increase our ability to leverage big data for the benefit of food production and biodiversity at global, landscape and micro scales of research and innovation through strong multidisciplinary research. The successful candidate will work synergistically with members of the Food from Thought initiative.

    REQUIREMENTS

    Exceptional emerging scholars, with the potential to become world leaders in a field related to Animal Disease Bioinformatics, are invited to apply. The successful candidate will have a PhD and post-doctoral training in a discipline related to animal health and disease research. Expertise and experience in applications of big data (including but not limited to transcriptomics, genomics, proteomics, epigenomics and metabolomics) to delineate disease processes in animals, especially those caused by infectious agents, is expected. Holding a Doctor of Veterinary Medicine or another health professional degree will be an asset.

    Regular full-time tenure-track faculty position at the level of Assistant or Associate Professor

    LOCATION

    Guelph, Ontario Canada

    COMPENSATION

    Negotiable

    HOW TO APPLY

    Assessment of applications will begin on December 14, 2021 and will continue until the position is filled. Interested applicants should submit the following materials (preferably as a single PDF file): (1) a cover letter; (2) a curriculum vitae; 3) a Quality of Nominee statement (max 1 page) and Description of Proposed Research Program (max 6 pages, not including 100 word Executive Summary) as per CRC guidelines(detailed instructions here); (4) a one page summary of how your proposed research program differs from that of the labs you are or have trained in (5) names and contact information of three references. Applications should be sent to the attention of:

    Brandon Lillie
    Associate Professor and Chair
    Pathobiology
    Ontario Veterinary College
    University of Guelph
    Guelph, ON N1G 2W1

    Email: blillie[at]uoguelph.ca

    DEADLINE

    Until a suitable candidate is found, however review of applications will begin December 14th, 2021.

    ABOUT US

    The University of Guelph is the third largest employer in Guelph, a city of approximately 130,000 people, located about an hour drive west of Toronto, Ontario. University of Guelph is a top-ranked comprehensive university in Canada with an enrolment of about 30,000 undergraduate and graduate students across over 40 academic units. The University is known for its commitment to student learning, innovative research, and collaboration with world-class partners. It is a unique place, with transformative research and teaching and a distinctive campus culture. People who learn and work here are shaped and inspired by a shared purpose: To Improve Life. Reflecting that shared purpose in every experience connected to our university positions us to create positive change, here and around the world. Our University community shares a profound sense of social responsibility, a drive for international development, and an obligation to address global issues.

    POLICY

    At the University of Guelph, fostering a culture of inclusion is an institutional imperative. The University of Guelph is committed to an Employment Equity Program that includes special measures to address the underrepresentation of individuals from four designated groups (women, persons with disabilities, Indigenous peoples, and members of visible minorities/racialized groups) within its allocation of Canada Research Chairs. The university especially seeks and prioritizes applications from qualified applicants from these four groups. We encourage applicants to self-identify within their cover letter in their application and through the confidential Applicant Tracking Questionnaire. To be considered a priority applicant, self-identification data must be provided. Learn more about the University's Equity, Diversity, and Inclusion Action Plan for the CRC Program. Canadians and permanent residents will be given priority.

    The University recognizes that applicants may have had obligations outside of work that have negatively impacted their record of achievements (e.g., parental, elder care, and/or medical). You are not required to disclose these obligations in the hiring process. If you choose to do so, the University will ensure that these obligations do not negatively impact the assessment of your qualifications for the position.

    The University of Guelph resides on the ancestral lands of the Attawandaron people and the treaty lands and territory of the Mississaugas of the Credit and we offer our respect to our Anishinaabe, Haudenosaunee and Métis neighbours as we strive to strengthen our relationships with them.

    If you require a medical accommodation during the recruitment or selection process, please contact Occupational Health and Wellness at 519-824-4120 x52674.

    BACKGROUND

    The Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna is looking for a highly motivated bioinformatician who wants to contribute to the booming fields of precision medicine and genomic methods in biomedical research. The successful candidate will join a group of experienced bioinformaticians and biomedical scientists who are using a wide range of next-generation sequencing technologies (e.g., genome, transcriptome, epigenome and single-cell sequencing) to support world-class biomedical research and clinical collaborations in precision medicine.

    RESPONSIBILITIES

    Your Tasks:
    • Data processing. Manage a constant flow of sequencing data (terabytes per week) being transformed into valuable information
    • Data analysis. Work with customers and collaborators on the analysis, interpretation, and visualization of the generated data
    • Data management. Develop workflows, databases, and web infrastructure to keep track of data, analyses, and projects
    • Software development. Implement cutting-edge software and analysis pipelines for genome data analysis
    • Technology development. Contribute bioinformatically to the development of new next-generation sequencing assays
    • Training and outreach. Provide customer support, teach collaborating scientists how to analyze their data, help organize workshops
    • Optional: Contribution to the Austrian SARS-CoV-2 genome sequencing initiative at CeMM (www.sarscov2-austria.org)
    • Optional: Getting more deeply involved in individual research projects, lead bioinformatic analyses, contribute to paper writing
    • The Biomedical Sequencing Facility (www.biomedical-sequencing.org)

    REQUIREMENTS

    Your Profile:
    • Training in bioinformatics, computer science, genome biology, physics, or another quantitative field (Master and/or PhD)
    • Strong programming skills (any language) and experience working with large volumes of data
    • Prior experience with next-generation sequencing data and high-throughput bioinformatics is a plus
    • High accuracy and reliability in the processing of large-scale data, solid understanding of quantitative methods
    • Friendly, collaborative mindset, and motivation to work in an international, interdisciplinary environment
    • Team player with strong communication skills and a proactive "getting things done" mentality
    • Written and oral communication skills in English (German language skills are not required)

    TERMS & COMPENSATION

    We Offer:
    • Work within an experienced, interdisciplinary, and international team at one of Austria's leading research institutes
    • Ample opportunities to contribute and gain experience in a key area of biomedical research and precision medicine
    • An inspiring workplace with an international setting, strong team spirit, and an excellent work climate
    • A wide range of social, cultural, and sports activities organized by the institute
    • Excellent employee benefits including full insurance coverage (health, accident, retirement), health care services, subsidized cafeteria
    • Starting annual gross salary of at least EUR 55,000 (the salary will reflect the successful candidate's qualifications and can be higher)
    • Flexible start date. Open-ended full-time contact available after an initial trial period. Support for relocating to Vienna is provided.

    HOW TO APPLY

    Please apply online (cemm.jobbase.io/job/frqtjjc2) with cover letter, CV, academic transcripts, and contact details of 3 referees. Applications will be reviewed on a rolling basis. Any application received by 31 December 2021 will be considered.

    ABOUT US

    The successful candidate will be part of the Biomedical Sequencing Facility (BSF) based at CeMM. The BSF is Austria's first and leading center of expertise for next-generation sequencing in biomedicine. Led by Christoph Bock (bocklab.org) and with a dedicated team of staff scientists, the BSF contributes to biomedical research and whole genome medicine in Vienna, Austria, and internationally. The BSF is equipped with the latest technology for high-throughput genomics (Illumina NovaSeq, Oxford Nanopore, 10X Genomics, etc.) and powerful scientific computing infrastructure. The BSF's mandate includes a strong focus on technology development, contribution to study design and bioinformatic data analysis, as well as training and teaching best practices in sequencing technology and genomic medicine. Furthermore, it supports biomedical scientists and clinicians in the development of custom NGS protocols and in the bioinformatic analysis of the resulting datasets.

    The Institute (www.cemm.at):
    CeMM is one of Europe's leading biomedical research institutes. CeMM researchers routinely publish important discoveries in top journals. Over the last seven years, this included >10 papers in Nature/Cell/Science/NEJM and >30 papers in Nature/Cell sister journals – with a team of 120-150 scientists. Research at CeMM is exceptionally collaborative and has strong focus on medical impact, based on a profound molecular understanding of diseases such as cancer and immune disorders. CeMM is part of the Austrian Academy of Sciences and a founding member of EU-LIFE. It is located at the center of one of the largest medical campuses in Europe, within walking distance of Vienna's historical city center. A study by "The Scientist" put CeMM among the top-5 best places to work in academia worldwide (www.the-scientist.com/feat[...]40676). Vienna is frequently ranked the world's best city to live. It is a United Nations city with a large English-speaking community. The official language at CeMM is English, and >49 different nationalities are represented at the institute. CeMM promotes equal opportunity and harbors a mix of different talents, backgrounds, competences, and interests.

    BACKGROUND

    NuProbe USA is hiring two NGS Bioinformatics Scientists for its Houston (TX) location.

    NuProbe is the US-based R&D subsidiary of NuProbe Global, a company devoted to the development of novel non-invasive DNA and RNA diagnostic assays.

    Currently, NuProbe has several products based on NGS, qPCR, and sanger technologies. The Innovation team is developing new technologies based on NGS and qPCR for next stage products and services. The successful candidate will have the opportunity to join NuProbe, working under the guidance of Innovation team lead to contribute to the new technology development.

    RESPONSIBILITIES

    • (30% - 50%) Bioinformatics, NGS Data Analysis (Python, MATLAB)
    • (50% - 70%) Leading projects and performing wet lab experiments including, but not limited to NGS library preparation, sequencing, PCR, qPCR, and nucleic acid extraction

    REQUIREMENTS

    • PhD or postdoc in Biology, Biochemistry, or related field
    • Relevant bioinformatics experience in NGS and genomics data analysis, as well as using bioinformatics databases
    • Familiar with Python or MATLAB
    • Familiar with NGS library preparation, PCR, qPCR relative wetlab skills
    • 1 – 3 years of relevant wet-lab and dry-lab experience
    • Leadership or potential leadership, teamwork
    • We are looking for a highly motivated person, with the enthusiasm necessary to learn and grow with us

    TERMS

    Full-time on-site Mon-Fri

    LOCALE

    Houston 77054

    COMPENSATION

    $70,000 – $100,000

    HOW TO APPLY

    Please send resume to elise.deleon[at]nuprobe.com.

    DEADLINE

    ASAP – We need to hire immediately.

    RESPONSIBILITIES

    U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab) has an opening for a Bioinformatics Computing Consultant to join the team. In this exciting role, you will work as part of the Data Science and Informatics Department's Advanced Analysis Group.

    The successful candidate will be responsible for enhancing the scientific productivity of users through problem management; code and workflow optimization, debugging and scaling; strategic project support; documentation; training; third-party applications and library support; resource and workload analysis; user communication and requirements gathering. You will also play a key role in establishing JGI's computing strategy through evaluating and recommending high-end computing technology and software.

    You will work with other groups, scientists, and vendors to develop innovative solutions that resolve user requirements. Using a unique set of knowledge, skills, and experience, you will help research, evaluate, and develop new software infrastructure and analysis tools to support JGI's mission of accelerating scientific discovery through the production of high-quality data, as well as platforms to enable data analysis at scale.

    What You Will Do:
    • ​Provide technical guidance and courteous consulting services to the users and staff at the DOE JGI.
    • ​Develop solutions for complex user problems and provide one-on-one code debugging, optimization, and porting help. Resolve and manage consulting questions in a timely manner and follow up on longer-term problems working with vendors, partners, and other JGI staff to implement solutions. Convey user feedback and concerns to other JGI staff.
    • ​Educate and train users by creating content for the JGI docs website with online tutorials and documentation, giving presentations, and attending conferences. Communicate with users about new opportunities and capabilities in software and systems and advise them in effectively transitioning to new technologies.
    • ​Keep abreast of developments and research in the bioinformatics and high-performance scientific computing field, writing technical papers as appropriate.
    • ​Work independently and as part of the Data Science and Informatics Department to diagnose problems with scientific workflows, collect information on system performance, and educate users on best practices.
    • ​Engage in User-centered design practices to ensure software infrastructure meets the needs of the scientific community.
    • ​Be part of a team that provides high-quality support to the scientific community.

    REQUIREMENTS

    What is Required:
    • ​Bachelor of Science degree in Bioinformatics, Computer Science, Computational Science, Applied Sciences, or equivalent experience with a minimum of 8 years of related experience.
    • ​Experience with shell/PERL/Python application programming.
    • ​Experience with workflow management systems and data-intensive computing.
    • ​Strong technical and collaboration skills to create and deploy innovative ways of allowing our diverse user base to effectively utilize the unique data resources that JGI provides.
    • ​Demonstrated ability to work independently as well as collaboratively in large projects and contribute to an active intellectual environment.
    • ​Excellent oral and written communication skills.
    • ​Understand user needs and show initiative, tact, and good judgment in developing solutions to problems.

    TERMS & COMPENSATION

    • ​This is a full time 2 year term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
    • ​This position will be hired at a level commensurate with the business needs; and skills, knowledge, and abilities of the successful candidate.
    • ​This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
    • ​We offer a flexible schedule and hybrid work.

    LOCATION

    The primary location for this role is Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at lbl.taleo.net/care[...]94306 and follow the on-line instructions to complete the application process.

    POLICY

    Based on University of California Policy – SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit covid.lbl.gov for more information.

    Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, diversity.lbl.gov/ideaberkeleylab/) and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

    Equal Opportunity and IDEA Information Links:
    Know your rights, click here (www.dol.gov/ofcc[...]t.htm) for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision (www.dol.gov/ofcc[...].html) under 41 CFR 60-1.4.

    BACKGROUND

    Extended microbiome characterization by the exploitation of the microbial intra-community synergies – towards better understanding of the Exposome

    In recent years the more focus has been placed on human exposome and how it affects human health and well-being. Exposome understood as the set of human environmental exposures (complementing the genome) from conception onwards includes: a general external environment, a specific external environment, and internal environment factors. In all three categories, an alive part of the exposome are different microbiomes, e.g. urban microbiome, skin microbiome, gut microbiome.

    There are many efforts around the world to pursue the knowledge behind many different types of microbiomes and to extract the information directly from metagenomes. Projects such as MetaHIT, Human Microbiome Project or American Gut Project/Microsetta Initiative had led to the growth of information about plenty of gut connected diseases such as obesity, inflammatory bowel syndrome or ulcerative colitis. Similar insight has been gained by projects focused on skin microbiota (The Human Skin Microbiome Project), environmental microbiome (Earth Microbiome Project), urban and subway microbiomes (MetaSUB International Consortium metasub.org), and many more. However, only a few of them had also considered establishing interactions between microorganisms among themselves, with the environment, and with human beings as one of the main goals.

    Microbiomes are diverse, dynamic, and complex parts of exposomes that are crucial for determining health. The composition of these biomes by nature is strongly related to the ecological niche they occupy and thus synergies and anergies are here dominant factors. Thus, the goal of the project is to extend our knowledge about interactions within and between features that arise in three complementary views on the microbiome: view through the lenses of compositional/taxonomical profile (i.e., abundance of microbial species), view through the lenses of functionalities related to the phenomena under scrutiny and view using variables derived directly from the samples (i.e., sequences obtained from a sample). Where in the last view no prior knowledge of microbial genomes and sequences of functional proteins are used.

    In particular, we want to explore synergistic interactions between features and by this go beyond currently available approaches that are ill-fitted to analyse metagenomic data as they are not exploiting the existence of these relations.

    Specifically, we will investigate synergies in three exposome related use-cases:
    • Anomaly detection in microbiomes – identification of resistomes for AMR studies
    • Patient stratification – usage of microbiota profiles for establishing health status of the patient
    • Calculation of distances between microbiomes – prediction of the geographical origin of the sample
    The proposed type of analysis in the context of selected use-cases can lead to the discovery of new functionalities or new species that are relevant for the interesting phenomena.

    RESPONSIBILITIES

    Your work will be focused on bioinformatic analysis of available and newly acquired metagenomic microbiome data in defined use cases in order to exploit microbial intra-community synergies. You will be closely collaborating with our partners from University of Białystok responsible for development of MultiDimensional Feature Selection (MDFS) solution capable to identify microbial synergies. You will be also responsible for follow up machine learning based analysis and support in results contextualization. You are going to work closely with a PhD students and other Group members involved in this project.

    As the data are coming from various collaborations/consortia/projects you will be also involved in active collaboration with those, especially with MetaSUB International Consortium (metasub.org).

    The position will be funded by National Science Centre SONATA BIS 10 programme.

    REQUIREMENTS

    The successful candidate will:
    • Have PhD degree in computer science, biology, bioinformatics, automatic control, physics, mathematics or related disciplines
    • Have excellent written and oral communication skills in English
    • Have an expertise in at least one programming language (esp. Python)
    • Have an expertise in metagenomic data analysis, big data exploration, or in machine learning
    • Have an ability to collaborate
    • Enjoy interdisciplinary work
    • Understand the importance of communication and interactions with other members of the Group, collaborators and other members of the Centre

    COMPENSATION

    We offer:
    • Competitive salary commensurate with experience (according to National Science Centre regulations)
    • Opportunity to collaborate with world-class researchers from MCB and institutions such as Weill Cornell Medicine, ETH Zurich, University of Białystok, Acibadem University, East China Normal University
    • Scientific and professional mentorship
    • Position 100% focused on research and development (no compulsory teaching)
    • Opportunity to work on an ambitious and important scientific problem with interdisciplinary applications
    • Opportunity and support to participate scientific meetings across the globe
    • Flexible working time
    • Opportunity to work (partly) remotely

    HOW TO APPLY

    Please send an email to mcb[at]labaj.org (in email title please include "SONATA BIS Research Associate" and your first and last names) with documents as specified here: mcb.uj.edu.pl/docu[...]357a8

    DEADLINE

    17th December 2022

    ABOUT US

    The Group:
    We are a young bioinformatics group which research interests cover the methodological advances in data science and their application to topical biomedical challenges, with the focus on advancing transcriptomics and metagenomics on the road to precision medicine.

    In this manner we have played a lead role in the SEQC consortium co-ordinated by the U.S. Food and Drug Administration (FDA) for the benchmarking of largescale gene expression profiling technologies, including RNA-Seq. Currently, in the second phase of SEQC we are investigating the complementarity of targeted RNASeq and genome sequencing for refined cancer diagnosis. We are also active in the MetaSUB International Consortium where we do focus on establishing environmental metagenomics assays in healthcare as well as on enabling the use of environmental microbiome analysis for forensic purposes. We also extensively collaborate with local and international research groups and companies to grow and deliver cutting-edge, open and reproducible research which would serve the community.

    bioinf.mcb.uj.edu.pl/groups/pawelab
    scholar.google.com/cita[...]AAAAJ
    orcid.org/0000-0002-4994-0234

    Institution:
    Małopolska Centre for Biotechnology (MCB) is a flagship biotechnology institute of Southern Poland and one of the most promising biomedical institutes in Central/Eastern Europe. It is part of the Jagiellonian University, and its excellence is based on three main areas: computational biology, structural biology and plant biology. The first area, computational biology, has recently been undergoing rapid growth, with a recent start of several groups, including Microbial Genomics (Dr. Rafał Mostowy), Structural and Functional Genomics (Dr. Tomasz Kościółek), and Transcriptomics/Metagenomics (myself). The institute will also profit from the interactions with the nearby industry (Ardigen). Microbiome is a nascent field in Central/Eastern Europe and at the moment Kraków, especially MCB with 3 groups oriented around different facets of microbiome research, are rising as the leaders in this field.

    MCB offers an international and collaborative environment with access to state-ofthe-art infrastructure in both experimental and computational biology. MCB hosts many world-class research groups, including the Max Planck Research Group in Structural Biology (Glatt Lab), the Bionanoscience and Biochemistry Group (Heddle Lab), the Plant Molecular Biology Group (Yamada Lab) or the Virogenetics and Virology Group (Pyrć Lab).

    BACKGROUND

    Do you want to play a key role in redefining the future of cancer care? Join MSK's Center for Molecular Oncology's (CMO) Informatics/Software Engineering team as we meet the challenge of fighting cancer in the modern era. We will define a new model of care using software. You will support the multiple CMO engineering teams in delivering continuous value, growing efficiency and productivity so that stronger data can be provided to researchers in a timelier manner.

    You will help developers set up their CI/CD pipeline, automate their builds, and test and deploy code to production. You are a highly-skilled DevOps Engineer who's constantly seeking to automate everything. You will also help establish DevSecOps practices by integrating security testing into the deployment pipeline.

    RESPONSIBILITIES

    What you'll do!
    • Work with engineers/bioinformaticians/researchers to containerize existing applications and help build ETLs.
    • Build and maintain CI/CD pipelines as a service for various different applications.
    • Deploy and configure containers; automate releases.
    • Build and manage Infrastructure as Code and use configuration management tools in a cloud environment such as AWS.
    • Be involved in implementing new system-level tools as identified by research needs.
    • Collaborate with the High Performance Computing (HPC) team to isolate issues related to the cluster and resolve requirements for the purpose of implementing development- and operation-critical tools.

    REQUIREMENTS

    Who you are!
    • Deeply technical. You understand application architecture and can design, implement, and support highly available systems.
    • Someone with curiosity about cancer research.
    • Can debug, fix, and run Linux-based systems.
    • Have solid communication skills to collaborate with and serve the various teams in the CMO, consisting of researchers, engineers, doctors, analysts, and scientists.
    • Have a strong willingness to keep up on the latest and greatest technologies that emerge.
    You have:
    • Bachelor's degree in Computer Science, Engineering, related field or professional work experience.
    • Solid understanding of Linux-based systems.
    • Knowledge of Docker and/or Singularity, as well as Kubernetes, OpenShift or similar container orchestration.
    • Experience and familiarity with Cloud Architecture (AWS or Azure) preferred.
    • Experience with high-performance compute clusters (such as LSF or SGE) preferred.
    • Proficiency in various programming languages such as Python and Java.

    COMPENSATION

    Benefits:
    Generous Vacation, Sick time + 12 holidays to recharge & refuel | Internal Career Mobility & Performance Consulting | Medical, Dental, Vision, FSA & Dependent Care | 403b retirement savings plan match | Tuition Reimbursement | 12 Weeks Parental Leave & Adoption Assistance | Fitness Discounts & Wellness Program | Resource Networks | Life Insurance & Disability | Hybrid Remote Work force

    HOW TO APPLY

    For more details and to apply, please click this link: careers.mskcc.org/jobs[...]neer/

    DESCRIPTION

    We are looking for a highly motivated and talented postdoctoral researcher, specialized in comparative genomics and sequence analysis. In your role, you will work on exciting research projects – you will be directly collaborating with our team of wet-lab scientists who are generating novel data (whole-genome sequences, RNAseq transcriptome data, Illumina, 454, PacBio,...). These collaborations also allow your computational results to be experimentally validated.

    About the lab:
    The lab for Systems Biology of Kevin Verstrepen is a research team at VIB & University of Leuven. Our team focuses on genomics, genetics, epigenetics, transcriptomic, and evolution, using yeast as a model. We combine wet-lab and computational research to investigate how biological systems work and evolve.

    Example publications include:
    J. Helsen, K. Voordeckers, L. Vanderwaeren, T. Santermans, M. Tsontaki, K.J. Verstrepen* and R. Jelier*. Gene loss predictably drives evolutionary adaptation. MBE 2020. DOI: doi.org/10.1[...]aa172 (IF 14.8)

    A. Jariani, L. Vermeersch, B. Cerulus, G. Perez-Samper, K. Voordeckers, T. Van Brussel, B. Thienpont, D. Lambrechts and K.J. Verstrepen (2020). A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. eLife 2020;9:e55320 DOI: doi.org/10.7554/eLife.55320 (IF 7.5).

    B. Gallone, J. Steensels, S. Mertens, M.C. Dzialo, J.L. Gordon, R. Wauters, F.A. Theßeling, F. Bellinazzo, V. Saels, B. Herrera-Malaver, T. Prahl, C. White, M. Hutzler, F. Meußdoerffer, P. Malcorps, B. Souffriau, L. Daenen, G. Baele, S. Maere and K.J. Verstrepen (2019). Interspecific hybridisation facilitates niche adaptation in beer yeast. Nature Ecology and Evolution. DOI: doi.org/10.1[...]997-9 (IF 11).

    Gallone B, Steensels J, Prahl T, Soriaga L, Saels V, Herrera-Malaver B, Merlevede A, Roncoroni M, Voordeckers K, Miraglia L, Teiling C, Steffy B, Taylor M, Schwartz A, Richardson T, White C, Baele G, Maere S, Verstrepen KJ. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.Cell (2016).

    Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, Van Pee M, van der Zande E, Meert W, Yang Y, Zhu B, Marchal K, DeLuna A, Van Noort V, Jelier R, Verstrepen KJ. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PLoS Genetics (2015)

    The lab is located at Leuven University, one of the oldest and most prominent universities in Europe consistently ranked within the top 50 worldwide universities. Leuven is located 10 miles from Brussels, with frequent direct train connections to Brussels airport.

    REQUIREMENTS

    Essential:
    • You have a Ph.D. degree in Bioinformatics, Computational Biology, or related.
    • You have hands-on experience with or a strong interest in bioinformatics programming, including Linux, scripting) and R.
    • You have experience with the analysis of next-generation sequence data such as whole-genome sequencing, CNV, Structural variation, and RNA-Seq.
    • You are fluent in English, for both written and oral communication.
    Key personal characteristics:
    • As a postdoc, you have a strong research output (peer-reviewed publications in high-quality journals (e.g. Genome Research, Cell, Science, Nature journals, ...)
    • You are enthused about scientific research and have a strong interest in studying biology using genomics and systems biology approaches.
    • You must have good, open communication skills and be willing to collaborate with multiple other researchers from our team.

    TERMS & COMPENSATION

    • The ability to work on scientifically exceptional and high-impact research topics
    • Full-time appointment as a postdoctoral fellow at VIB / KU Leuven, a highly-ranked research institute with a competitive pay scale and benefits (health insurance, sports facilities, ...)
    • A stimulating and supportive international research environment (with English as the main language)
    • Various training opportunities within VIB and KU Leuven to broaden your expertise and skills
    • State-of-the-art infrastructure
    • Job is available immediately, starting date is negotiable.

    HOW TO APPLY

    Motivated candidates are asked to apply online (jobso.id/eb69).

    Additional requirements:
    Please upload your full CV including a list of your scientific publications and motivation letter. Please add the contact details of at least two references.

    More information: www.kuleuven.be/verstrepen

    POLICY

    Our institute greatly values diverse standpoints and promotes an inclusive environment in which everyone is respected.

    Submitter

    BACKGROUND

    The post holder provides high calibre bioinformatics research support to external researchers and industrial partners by enabling analysis, facilitating access to datasets and ensuring optimal use of the internal data within the organisation. The post holder will act as a second line of support for users of the Research Environment. They will be intimately familiar with the data and applications.

    They will be joining a team that are also responsible for the stewardship of genomic data and its effective flow through products into the various research products. The role includes elements of a bioinformatician and data analyst, ensuring that our users have an excellent customer experience.

    RESPONSIBILITIES

    Key Accountabilities Include:
    • Understanding the datasets and the research environment, and being both a superuser and advocate internally and externally.
    • Understanding the needs of customers (academic, NHS and industry); working with customers to ensure that their scientific projects are successful.
    • Carrying out custom analyses on demand.
    • Managing data; supporting data generation, intake, and extraction through airlocks.
    • Supporting users with how to use our software and data.
    • Keeping track of customer relationships and being the internal authority on specific customer issues, needs, and future plans.
    • Providing high calibre troubleshooting of problems for customers, appraise customers and internal options and execute solutions, co-ordinating with internal teams when necessary.
    • Contributing to the development of the Research Environment through identifying unmet customer needs, suggesting solutions, and improving supporting material.
    • Collaborating internally as part of squads or teams as part of the Research and Ecosystems tribe
    • Know and understand the meaning behind our virtues of Empathy, Integrity, Focus, Connection, Speed, Curiosity, Impact and embody them in all aspects of your role

    REQUIREMENTS

    Essential Skills Required Include:
    • Passionate disposition to service
    • Extensive experience in analysis of large-scale genomic data using bioinformatics tools and pipelines.
    • Demonstrable experience in using next generation sequencing data.
    • Competence in R, Python or similar language appropriate for large-scale genomics analysis.
    • Strong communication skills, both written and verbal and excellent facilitation, influencing and presentation skills.
    • Good customer-service orientation, disposition to help, and experience in working with customers, preferably in the scientific/pharma industry.
    • Excellent team working skills and comfortable working as part of matrix teams and as part of external teams to ensure delivery.
    • Experience with high-performance computing or cloud-scale data processing.
    • Adaptable to an ever-evolving working environment
    • Excellent attention to detail

    COMPENSATION

    There are some great benefits on offer with this role including the opportunity to work with one of the most ground-breaking genomics organisations in the country. There is a substantial pension scheme, competitive salary and generous holiday allowance.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Bioinformatics, Research, Support, Pipelines, Cancer, Analysis, Customers, NGS, Data, Troubleshooting, Python, AWS, Cloud, Nextflow, Genomics, Software, Pharma, NHS, London

    BACKGROUND

    Contribute to engineering the next generation thermophilic bacterial cell factories

    Do you have a biology related PhD, and do you want to make an impact clearly beyond the average, for yourself and the world? While joining DTU Biosustain you will help finding sustainable solutions to some of the biggest challenges in the history of mankind, and you will do it surrounded by state-of-the-art equipment and world-class scientists from all over the world.

    You will be part of a unique EU funded project with a 40 mill. Euro budget. During the next five years we will among others build a nearly full-scale fermentation plant with collaboration partners in Trondheim, Norway. The plant will be designed to fixate 10.000 tons of CO2 per year during production while enabling best-in-class experiment and testing opportunities. As such, you will get the best of two worlds – basic research and a direct link to the industry and the making of real-life products.

    Analyze and improve performance of enzymes of engineered metabolic pathways:
    You will be part of a science team headed by prof. Alex Toftgaard Nielsen aiming to create the foundation for production of valuable chemicals from renewable resources. We will be 5-8 in Denmark and approx. the same at our sister team in Norway. Besides internal collaboration, you will work in close collaboration with industrial partners, since the final goal of the project is technology application in large-scale fermentation facilities.

    RESPONSIBILITIES

    More specifically, you will contribute to engineering the next generation thermophilic bacterial cell factories. You and your team colleagues will combine methods from diverse fields such as systems and synthetic biology, computational modelling, strain engineering, biochemistry and fermentation technology to construct robust and highly efficient production strains and processes. Your research will pave the way for e.g. development of sustainable solvents used in the global plastic industry.

    Your overall focus will be on working with the enzymes of the engineered metabolic pathways to analyze and improve their performance. Your tasks will include:
    • Develop assays for characterizing kinetic parameters of pathway enzymes
    • Analyze and compare protein structures in silico
    • Enzyme engineering based on structural information and enzymatic properties of protein libraries
    • Presenting results on a regular basis
    • Potentially travelling to Trondheim several times a year to meet with Norwegian science peers and Engineers working to build the new plant

    REQUIREMENTS

    PhD with experience within methods for determining enzyme kinetics:
    We are looking for an ambitious Scientist that likes to create results via knowledge sharing and teamwork with due respect to professional and cultural differences. At the same time, you must be able to define the road map and be the primary driver of turning ideas into action. Additionally, you must be good at designing and setting up experiments and bring a strong motivation for working with high throughput data. Additionally, your CV comprises:
    • PhD in Computational Biology, Bioinformatics, Biochemistry, Molecular Biology, or equivalent
    • Demonstrated experience within methods for determining enzyme kinetics
    • Experience with computational protein analysis and modeling
    • Motivation for building skills within genome scale modelling of metabolism
    • High level English skills, written and spoken

    TERMS & COMPENSATION

    DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

    The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

    The period of employment is 2 years preferably starting at the beginning of 2022.

    You can read more about career paths at DTU here: www.dtu.dk/engl[...]paths

    HOW TO APPLY

    Your complete online application must be submitted no later than 1 December 2021 (Danish time).

    Please apply at www.career.dtu.dk

    Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:
    • Application (cover letter)
    • CV
    • Academic Diplomas (MSc/PhD)
    • List of publications
    Applications received after the deadline will not be considered.

    Further information:
    If you would like additional information about the position, please contact Prof. Alex Toftgaard Nielsen at atn[at]biosustain.dtu.dk. Then we can set up an additional phone call to ensure your understanding of the job and your many opportunities.

    If you are applying from abroad, you may find useful information on working in Denmark and at DTU at "DTU – Moving to Denmark" (www.dtu.dk/engl[...]nmark).

    ABOUT US

    The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain):
    Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at biosustain.dtu.dk.

    Technology for people:
    DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN's 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

    POLICY

    All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

    BACKGROUND

    Do you want to break new ground at the absolute forefront of science?

    Have you completed a PhD in Microbiology, Fermentation Technology, Molecular Biology or equivalent and are you looking for the best place to set your scientist career on tracks? If so, you have found it.

    You will be working alongside a unique EU funded project with a 40 mill. Euro budget. The goal is to engineer the next generation thermophilic bacterial cell factories and by that enable production of valuable chemicals from renewable resources. We are confident that we e.g. will be able to develop sustainable solvents used in the global plastic industry and by that replace the use of enormous amounts of fossil-based components.

    Focus on anaerobic and aerobic bacteria in artificially designed communities
    You will be part of a science team headed by prof. Alex Toftgaard Nielsen at DTU Biosustain where you will be surrounded by state-of-the-art equipment and world-class scientists from all over the world. We will be 5-8 in Denmark and approx. the same at our sister team in Norway.

    RESPONSIBILITIES

    More specifically, you will contribute to engineering the next generation thermophilic bacterial cell factories. You and your team colleagues will combine methods from diverse fields such as systems and synthetic biology, computational modelling, strain engineering, biochemistry and fermentation technology to construct robust and highly efficient production strains and processes.

    You will especially be working with anaerobic and aerobic bacteria in artificially designed communities that will efficiently convert selected substrates into valuable chemicals. In particular, your tasks will include:
    • Designing functional bacterial communities based on metabolic interactions
    • Cultivation of various strains and optimization of growth conditions and media
    • Fermentation of selected strains and co-cultures in bioreactors at different scales
    • Presenting results on a regular basis

    REQUIREMENTS

    PhD with experience from working with anaerobic organisms and fermentation:
    We are looking for a colleague that likes to create results via good and positive team work. As part of this you must thrive in a multi-disciplinary, multi-cultural and highly interactive environment where knowledge sharing and collaboration are key to succeed. As you will be trusted to drive own tasks forward (micro management is not the way we work), you must be very good at planning not only your own tasks but also when involving multiple stakeholders. Additionally, your CV comprises:
    • PhD in Microbiology, Fermentation Technology, Molecular Biology or equivalent
    • Demonstrated working experience with anaerobic organisms
    • Motivation for building skills within fermentation technology in bioreactors and investigating microbial consortia using various techniques
    • Motivation for designing and studying next generation of consortia-based production systems
    • Motivation for building skills within Gram positive and/or thermophilic bacteria
    • High level English skills, written and spoken

    TERMS & COMPENSATION

    DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

    The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

    The period of employment is 2 years preferably starting at the beginning of 2022.

    You can read more about career paths at DTU here: www.dtu.dk/engl[...]paths

    HOW TO APPLY

    Your complete online application must be submitted no later than 1 December 2021 (Danish time). Please apply at www.career.dtu.dk

    Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:
    • Application (cover letter)
    • CV
    • Academic Diplomas (MSc/PhD)
    • List of publications
    Applications received after the deadline will not be considered.

    Further information:
    If you would like additional information about the position, please contact Prof. Alex Toftgaard Nielsen at atn[at]biosustain.dtu.dk. Then we can set up an additional phone call to ensure your understanding of the job and your many opportunities.

    If you are applying from abroad, you may find useful information on working in Denmark and at DTU at "DTU – Moving to Denmark" (www.dtu.dk/engl[...]nmark).

    ABOUT US

    The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain):
    Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at biosustain.dtu.dk.

    Technology for people:
    DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN's 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

    POLICY

    All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

    BACKGROUND

    Make the world a better place via as part of unique EU funded 40 million Euro project

    If you have a PhD in Computational Biology, Bioinformatics, Microbiology, Molecular Biology, or equivalent and you are considering the best way forward for your future career, you do not need to think any longer. Embarking on this project will provide you with the best of two worlds – basic research and a direct link to the industry and the making of real-life products.

    During the next five years we will among others build a nearly full-scale fermentation plant in Trondheim, Norway. The plant will be designed to fixate 10.000 tons of CO2 per year during production while enabling best-in-class experiment and testing opportunities. As such, the plant is as a match of the world-class facilities at DTU Biosustain, your new workplace. Here you can look forward to unfolding your skills surrounded by state-of-the-art equipment and world-class scientists from all over the world.

    Generate omics data and integrate them to understand the cell on a systems level:
    As part of DTU Biosustain your overall objective is to find sustainable solutions some of the biggest challenges in the history of mankind – create the foundation for production of valuable chemicals from renewable resources. You will do so as part of a new science team headed by prof. Alex Toftgaard Nielsen. We will be 5-8 in Denmark and approx. the same at our sister team in Norway.

    RESPONSIBILITIES

    More specifically, you will contribute to engineering the next generation thermophilic bacterial cell factories. You and your team colleagues will combine methods from diverse fields such as systems and synthetic biology, computational modelling, strain engineering, biochemistry and fermentation technology to construct robust and highly efficient production strains and processes. Your research will pave the way for e.g. development of sustainable solvents used in the global plastic industry.

    You will play your important role by generating omics data and integrating them to gain an understanding of the cell on a systems level for further engineering and optimization of strain performance. Your tasks will include:
    • Generation and computational analysis of the omics datasets (transcriptomics, proteomics, metabolomics, etc.)
    • Analyzing data using genome scale computational models
    • Processing and visualizing large data sets
    • Identifying targets for genome engineering to boost strain performance
    • Potentially be involved in engineering of the production organisms
    • Present results on a regular basis
    • Travelling to Trondheim several times a year to meet with Norwegian science peers and Engineers working to build the new plant
    When joining us, you can look forward to being part of a Center with multiple world-class Scientists with a shared passion for breaking new ground. Our environment is first and foremost characterized by cross-organizational collaboration and knowledge sharing. Besides internal collaboration, you will work in close collaboration with industrial partners, since the final goal of the project is technology application in large-scale fermentation facilities.

    REQUIREMENTS

    PhD in the area of biology and bioinformatics:
    To succeed at DTU Biosustain, you must simply love to share ideas and collaborate – and be able to do with respect for and understanding of professional and cultural differences. This also calls for your good communication skills. Additionally, you must be good at designing and setting up experiments and bring a strong motivation for working with high throughput data. Additionally, your CV comprises:
    • PhD in Computational Biology, Bioinformatics, Microbiology, Molecular Biology, or equivalent
    • Computational background (for example Python, R)
    • Demonstrated experience with working on omics datasets
    • Experience with statistical data analysis
    • Motivation for building skills within genome scale modelling of metabolism and metabolic engineering
    • High level English skills, written and spoken

    TERMS & COMPENSATION

    DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

    The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

    The period of employment is 2 years preferably starting at the beginning of 2022.

    HOW TO APPLY

    Your complete online application must be submitted no later than 1 December 2021 (Danish time).

    Please apply at www.career.dtu.dk

    Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:
    • Application (cover letter)
    • CV
    • Academic Diplomas (MSc/PhD)
    • List of publications
    Applications received after the deadline will not be considered.

    You can read more about career paths at DTU here: www.dtu.dk/engl[...]paths

    Further information:
    If you would like additional information about the position, please contact Prof. Alex Toftgaard Nielsen at atn[at]biosustain.dtu.dk. Then we can set up an additional phone call to ensure your understanding of the job and your many opportunities.

    If you are applying from abroad, you may find useful information on working in Denmark and at DTU at "DTU – Moving to Denmark" (www.dtu.dk/engl[...]nmark).

    ABOUT US

    The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain):
    Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at biosustain.dtu.dk.

    Technology for people:
    DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN's 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

    POLICY

    All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

    BACKGROUND

    Lawrence Berkeley National Lab's (LBNL) Environmental Genomics & Systems Biology Division has an opening for a Computational Biology Postdoctoral Fellow to join the Department of Energy (DOE) Systems Biology Knowledgebase (KBase) team. The successful candidate will be supervised by Principal Investigator, Adam Arkin and Scientist, Paramvir Dehal.

    In this exciting role, you will work with the KBase and Research team leads in collaboration with targeted users to develop advanced functionality and analysis in KBase. In this role, you will develop and execute novel machine learning methods for predictive biology for microbes, plants, and their communities. You will collaborate with computational scientists and biologists to develop new GPU-enabled infrastructure on the National Energy Research Scientific Computing Center (NERSC)'s new Cray supercomputer, "Perlmutter", and you have the opportunity to pursue and lead towards publication of novel genomics-based research that leverages the KBase Knowledge Engine and Relation Engine.

    The Department of Energy Systems Biology Knowledgebase (KBase) is a computational platform designed to meet the key challenges of systems biology: predicting and designing biological function. KBase integrates numerous biological datasets and analysis tools in a unified, extensible system that allows researchers to collaboratively generate and test hypotheses about biological functions and interactions. The project's long-term goal is to help researchers understand how plants and microbes interact with and affect each other and environmental processes and how these interactions could be harnessed for sustainable bioenergy and environmental solutions. KBase is a multi-institutional collaboration involving about 30 researchers at four national laboratories (LBNL, Argonne, Brookhaven, and Oak Ridge) and several universities.

    Work will be performed at Lawrence Berkeley National Laboratory, a national lab that offers a research environment similar to academic institutions with a reasonable work/life balance. You will work with a diverse and talented team of biologists, computer scientists, and developers, and will have many opportunities to broaden their knowledge and meaningfully expand their collaborative network. Travel to other KBase sites for two-day planning meetings will occur several times a year.

    RESPONSIBILITIES

    What You Will Do:
    • With KBase leadership, collaborate with targeted KBase users and other stakeholders to identify high value science that can be performed with suitable extensions to the KBase platform and data sets.
    • Develop, package, and apply new and community computational methods in the KBase platform, which will be shared and disseminated across the microbiome community.
    • Work with the KBase team to develop the integrated data science platform to support inference across system reference source and shared user data.
    • Work with targeted users to perform sophisticated analyses of heterogeneous biological data of plants, microbes and their communities to discover and predict biological function and behavior and compare against experimental observations.
    • Publish scientific papers in peer-reviewed journals and present findings at seminars and conferences.
    • Collaborate with other members of the project research team, both internal and external to Berkeley Lab and develop new collaborations as appropriate to further the scientific goals of the program.

    REQUIREMENTS

    What is Required:
    • Ph.D. within the last three years in computer science, data science, machine learning, chemical engineering, bioengineering, chemistry, biochemistry, chemical biology, plant biology, microbiology, bioinformatics, computational biology, or related field.
    • Strong background in programming, data science and/or computational biology.
    • Proven ability to perform independent research and organize data for publication and presentations.
    • Demonstrated ability to interact effectively with technical and scientific staff.
    • Ability to work independently and in a team environment.
    • Demonstrated ingenuity in dealing with complex problems.
    • Demonstrated strength and efficiency in technical writing.
    Desired Qualifications:
    • Strong track record in developing software tools.
    • Strong experience with software engineering best practices.
    • Experience/familiarity with AGILE project management.

    TERMS & COMPENSATION

    • This is a full-time 2 year postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 3 years of paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.
    • This position is represented by a union for collective bargaining purposes.
    • Salary will be predetermined based on postdoctoral step rates.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
    • Flexible work options are available.

    LOCATION

    Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]12849 and follow the on-line instructions to complete the application process.

    POLICY

    Based on University of California Policy – SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit covid.lbl.gov for more information.

    Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, diversity.lbl.gov/ideaberkeleylab/) and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

    Equal Opportunity and IDEA Information Links:
    Know your rights, click here (www.dol.gov/ofcc[...]t.htm) for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision (www.dol.gov/ofcc[...].html) under 41 CFR 60-1.4.
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