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    Latest announcements

    At the Medical University of Vienna in IT-Systems & Communications with the code: 10510/20 we are looking to fill a position of a full-time Scientific Computing System Administrator (f / m / d) (according to the collective agreement – employment group IVa), with an expected starting date on January 4th 2021 limited to a period of 3 months with the option of permanent employment.

    RESPONSIBILITIES

    Maintenance and operational maintenance of the central scientific computing cluster (Linux, CPU and GPU systems); Support (second and third level support) of the employees of the department and the scientific working groups of the MedUni who work at the cluster in the field of high performance computing (HPC), artificial intelligence (AI), machine learning (ML) and imaging; Proactive identification of needs, planning, development and implementation of solutions; Script creation to increase operational efficiency; further implementation and operation of the cloud computing environment with a focus on scheduling and resource accounting, and GPU computing with special consideration of the scientific computing needs of the key users (HPC, AI, ML, imaging).

    REQUIREMENTS

    Training or professional experience with a focus on IT, ideally a degree in computer science or a comparable discipline or HTL Matura, at least 1 year of relevant or 3 years of related professional experience, sound knowledge of (HPC) computing and server support (Linux derivatives), knowledge: Linux, Network, scripting, virtualization, optional knowledge of SAN and file server technologies.

    Desired qualifications: Willingness to learn, the joy of building new systems (CEPH, Cluster, SLURM, GPU Computing, ...), team spirit, solution orientation, flexibility, customer orientation, willingness to communicate, a high degree of initiative.

    With the same qualifications, the recruitment of applicants with reduced earning capacity is supported.

    LOCALE

    The Medical University of Vienna campus is within walking distance of Vienna's historical city center. Vienna is frequently ranked the world's best city to live. It is a United Nations city with a large English-speaking community.

    COMPENSATION

    The monthly minimum remuneration for this is currently 2,673 euros gross (14x per year) and may increase on the basis of the collective agreement provisions through the crediting of job-specific previous experience and other remuneration components associated with the specifics of the job.

    HOW TO APPLY

    The official job posting is on the homepage of Medical University of Vienna (german): www.meduniwien.ac.at/web/[...]0/20/

    The information according to the General Data Protection Regulation can be found at www.meduniwien.ac.at/date[...]ungen.

    Information regarding the General Data Protection Regulation is available at www.meduniwien.ac.at/date[...]en_en.

    Code: 10510/20

    Please send your detailed application with the code: 10510/20 by December 9, 2020 to:
    bewerbungen[at]meduniwien.ac.at
    or by post to:
    Medical University Vienna
    Personnel and Personnel Development Department
    1090 Vienna, Spitalgasse 23
    www.meduniwien.ac.at/web/[...]ngen/

    ABOUT US

    The Medical University of Vienna is a leading international research institution in the field of biomedical research. As part of an interdisciplinary research focus in the field of medical imaging, machine learning and precision medicine, a cluster system for scientific / high performance computing is used and in the process of being expanded.

    DESCRIPTION

    The University of Vermont, founded in 1791, is a premier research university internationally acclaimed for excellence in medicine, biology, and health science. It is one of original "Public Ivies", and the fifth oldest university established in New England (after Harvard, Yale, Dartmouth and Brown). The University of Vermont College of Medicine is the 7th oldest medical school in the nation.

    The University of Vermont College of Medicine Department of Microbiology and Molecular Genetics is looking for multiple research positions, including postdoctoral fellows, graduate students, and research assistants, with experience or interests in multi-omics and bioinformatics research of human disease to join our newly-funded projects including disease risk discovery, bioinformatics development, and translational medicine. The applicants will join a highly collaborative team to analyze newly generated multi-omics data (genome, transcriptome, epigenome, phenome, etc.) from patient blood, postmortem brains, neurons, and mice. We are fully committed to supporting applicants' research and career development. Various research training opportunities, including grant and manuscript writing, will be provided. We also have various internal trainee fellowships available that the applicants can apply immediately. The applicants are expected to present in national and international conferences and prepare manuscripts to publish. Applicants with quantitative biology background (genomics, bioinformatics, data science, etc.) are especially encouraged to apply.

    Applicants with the following bioinformatics experience are particularly invited to apply:
    • Use high-throughput sequencing (HTS) data analysis pipelines
    • Process FASTQ/BAM files in Linux servers
    • Perform advanced statistical correlation tests and pathway analyses using various packages
    • Prepare figures using R packages
    • Understand importance to verify all analyses/results (rigor of research) and complete within deadlines
    Applicants with the following expertise or interests are highly encouraged to apply:
    • Use existing pipelines to process whole-genome sequencing and RNA-Seq FASTQ/BAM files to genotype and to quantify expression of transposable elements (TEs)
    • Quickly learn how to use new TE- or endogenous retrovirus (ERV)-related pipelines
    • Develop new pipeline to improve HTS-based TE or ERV analyses
    • Use or develop single-cell/-nucleus or long read sequencing data analysis pipelines
    • Use standard pipelines to process DNA methylation .idat files
    • Know standard molecular verification of HTS findings (e.g., qPCR/ddPCR)

    LOCALE

    The University of Vermont is located by the beautiful Lake Champlain. Burlington is one of the best cities to live in the U.S. Competitive salary or stipend will be provided.

    HOW TO APPLY

    To apply, please send CV to: dawei.li[at]uvm.edu (please highlight related research experience or interest in your email). The positions are available till filled. The job updates can be seen online (www.uvm.edu/geno[...]s.pdf).

    BACKGROUND

    The Division of Genetic Medicine at the University of Washington in Seattle is currently recruiting for a Research Scientist/Engineer 3 (RSE3) in the Chong Lab. The RSE3 position will be in the field of human genetics. The RSE3 will research and develop machine learning methods that integrate genetic and phenotypic data to assist in diagnosis of and research into the causes of rare genetic conditions (also called Mendelian conditions, or rare diseases). The RSE3 will collaborate with clinical experts and researchers in human genetics and machine learning/data science. This position is for a Research Scientist, but a postdoc position is a possibility, depending on further discussion and the right fit.

    RESPONSIBILITIES

    Job duties include but are not limited to:
    • Testing standard machine learning models (e.g., NMF, LDA, random forest, decision trees)
    • Feature engineering (different vectorization methods to accommodate domain-specific data)
    • Research, design, and create custom models to handle data with dependent relationships (e.g. ontologies)
    • Adapting or developing and validating simulated and real datasets for use in model evaluation
    • Enhancing data collection and extraction procedures for relevant data
    • Assessing models for bias due to correlated noise
    • Performing statistical analyses with traditional and machine learning methods
    • Contribute to preparation of research manuscripts, reports, presentations, reviews, and summaries
    • Actively participate and present summaries of work progress at group meetings
    • Other duties as assigned

    REQUIREMENTS

    • Master's Degree in Computer Science, Data Science, Biostatistics, Computational Biology, Genetics or related field or three or more years of relevant work experience
    • Basic understanding of genetics (e.g. rare/Mendelian vs complex traits, modes of inheritance)
    • Ability to communicate clearly in written and oral communications is essential
    • Must be comfortable working independently, taking the initiative to explore possible solutions, and doing both as part of a team
    • Expertise in common data science toolkits (e.g. Python, scikit-learn)
    • Excellence with machine learning techniques, particularly NMF, LDA, and decision trees
    • Flexibility to take on additional tasks as necessary to accomplish team goals
    Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.

    PREFERENCES

    • Familiarity with genetic mutation nomenclature/concepts and clinical finding terminology
    • Experience developing custom probabilistic models and/or experience applying deep learning methods to build context-aware recommender systems

    TERMS

    Full Time

    LOCALE

    Seattle, WA but relocation to Seattle is flexible during the COVID-19 pandemic.

    HOW TO APPLY

    Application through UW Hires: bitly.com/ML4rare

    DEADLINE

    Applications are open until position is filled.

    POLICY

    We especially encourage applications from groups traditionally underrepresented in STEM.

    As a UW employee, you have a unique opportunity to change lives on our campuses, in our state and around the world. UW employees offer their boundless energy, creative problem solving skills and dedication to build stronger minds and a healthier world.

    UW faculty and staff also enjoy outstanding benefits, professional growth opportunities and unique resources in an environment noted for diversity, intellectual excitement, artistic pursuits and natural beauty. All of which has allowed the UW to be nationally recognized as a "Great College to Work For" for six consecutive years.

    The UW Department of Pediatrics is dedicated to improving the health of all children by educating physicians of the future, advancing research, advocating for children, and providing the nation's best pediatric clinical care. We are committed to building a diverse and inclusive faculty and staff.

    BACKGROUND

    The Novo Nordisk Foundation for Biosustainability (DTU Biosustain) at the Technical University of Denmark is seeking highly motivated PhD candidates with an interest in computational approaches to microbial systems biology for the purposes of strain design.

    We are looking to fill four positions in the newly established "Microbial Reconstruction Unit", headed by DTU Biosustain CEO Prof. Bernhard Palsson and CSO Prof. Lars Keld Nielsen. Reconstructions are collections of organism-specific knowledge, such as the set of all metabolic reactions that take place within an organism or the set of all experimentally-determined protein structures. These reconstructions are invaluable resources for rational design of microbial strains for a host of applications, but their availability outside model organisms is limited.

    In the Microbial Reconstruction Unit, we are developing new organism-specific reconstructions, computational tools, and databases to empower the development of microbial strains in non-model organisms for several applications, including small molecule production, bioactive compound production, and microbial foods. The team is working on a range of organisms including fermentation organisms such as Lactobacillus and Streptomyces, and C1 organisms such as acetogens, methanotrophs, and cyanobacteria.

    RESPONSIBILITIES

    Developing genome scale models:
    You will work as part of an interdisciplinary team focusing on a group of organisms, e.g., acetogens, to develop a highly curated set of reconstructions of the individual organisms. This involves working with a number of big data sources (e.g., genomes, transcriptomes, Phenotype MicroArrays), existing databases and a range of existing annotation pipelines. The end product is a high quality reconstruction that captures all codifiable information about the organism and makes it available for computational modelling. You will use these models to explore the inherent potential of the organisms as well as the potential for rational design.

    Your role will primarily be to perform computational modelling, write scientific publications, as well as take 30 ECTS points of relevant PhD courses as required in Danish PhD programs.

    REQUIREMENTS

    Two-year master's degree (120 ECTS points) or equivalent in bioengineering, computational biology or bioinformatics:
    We are looking for candidates with a two-year master's degree (120 ECTS points) or equivalent in a relevant discipline. You will have experience in computational modelling for metabolic systems with substantial knowledge of metabolic biochemistry. You will also have intermediate skills in Python programming ideally with some experience interfacing databases and R scripting.

    Collaboration is an integral part of this project and we expect that you can demonstrate a track-record for successfully collaborating with your peers. At the same time, reconstruction demands periods of exacting individual detail work and it is important that you draw satisfaction from this mode of work as well.

    TERMS & COMPENSATION

    Salary and terms of employment:
    The period of employment is three years. 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.

    HOW TO APPLY

    Please submit your online application no later than 9 December 2020 (Danish time).

    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:
    • A letter motivating the application (cover letter)
    • Curriculum vitae
    • Grade transcripts and BSc/MSc diploma
    • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)
    Candidates may apply prior to obtaining their master's degree but cannot begin before having received it.

    Applications and enclosures received after the deadline will not be considered.

    Approval and Enrolment:
    The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide (www.dtu.dk/engl[...]guide).

    Further information:
    If you would like additional information about the position, please contact Professor Bernhard Palsson at palsson[at]eng.ucsd.edu or Professor Lars Keld Nielsen at lars.nielsen[at]uq.edu.au. You can read more about DTU Biosustain at www.biosustain.dtu.dk.

    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 12,000 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.

    POLICY

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

    BACKGROUND

    Do you want to help drive the next generation of genome scale reconstruction?

    The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) is seeking highly motivated researchers with an interest in computational approaches to microbial systems biology for the purposes of strain design.

    We are looking to fill four positions in the newly established "Microbial Reconstruction Unit", headed by DTU Biosustain CEO Prof. Bernhard Palsson and CSO Prof. Lars Keld Nielsen. Reconstructions are collections of organism-specific knowledge, such as the set of all metabolic reactions that take place within an organism or the set of all experimentally-determined protein structures. These reconstructions are invaluable resources for rational design of microbial strains for a host of applications, but their availability outside model organisms is limited.

    RESPONSIBILITIES

    You will join a dynamic team developing new organism-specific reconstructions, computational tools, and databases to empower the development of microbial strains in non-model organisms for several applications, including small molecule production, bioactive compound production, and microbial foods. Half the team will work on key fermentation organisms such as Lactobacillus and Streptomyces, while the other half will work on C1 metabolism in organisms such as acetogens, methanotrophs, and cyanobacteria. Everybody will be involved in advancing reconstruction software as well as reconstructions of the model organism E. coli.

    Develop genome scale models for non-model organisms:
    As a member of the Microbial Reconstruction Unit, you will be building organism-specific computational resources to empower microbial strain design workflows. You will work closely with the Principle Investigators (PIs) and teams to coordinate efforts within strain design projects.

    Specific tasks include:
    • Reconstructing metabolic networks of target organisms from genome annotations and experimental literature to enable metabolic modeling applications.
    • Annotating protein structure and genome sequence information for the analysis of sequence variation.
    • Construction of organism-specific databases from internal and public -omics datasets (e.g. genomics, transcriptomics, proteomics, metabolomics, and sequencing) to empower strain design projects.
    • Transcription regulatory analysis of organism gene and protein expression data
    • Contribution to development and implementation of computational methods and tools described above.
    • Participation in a team environment as part of a large academic organization developing computational tools and workflows for strain design.
    • Organization of (bi-)weekly project updates to lab management.

    REQUIREMENTS

    PhD degree in engineering, bioinformatics, or similar field:
    We are looking for a colleague with previous experience working with metabolic network reconstructions, with substantial knowledge of metabolic biochemistry. This includes familiarity with methods for computational modelling of metabolism, including constraint-based and kinetic modelling, and an understanding of the relevant methods such as linear programming and matrix decomposition.

    Most of our programming is in Python/Pandas and intermediate level programming skills are essential. Experience interfacing databases and R scripting will be an advantage but not required.

    Additionally, your CV will demonstrate ability to:
    • Communicate technical information to internal/external audiences at various levels (undergraduates to senior scientists) and from various backgrounds (technical and non-technical personnel).
    • Work independently and as part of a team.
    • Successfully work on multiple concurrent projects and meet deadlines.

    TERMS & COMPENSATION

    Salary and terms of employment:
    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 three years.

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

    HOW TO APPLY

    Please submit your online application no later than 9 December 2020 (Danish time).

    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 CV, cover letter, diploma and if relevant list of publications.

    Further information:
    If you would like additional information about the position, please contact Professor Bernhard Palsson at palsson[at]eng.ucsd.edu or Professor Lars Keld Nielsen at lars.nielsen[at]uq.edu.au.

    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 12,000 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.

    POLICY

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

     

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