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    Submitter

    BACKGROUND

    Paramount are currently supporting a global pharmaceutical organisation with the exciting developments within their data science and translational medicine group in the UK. This company are at the forefront of drug discovery, supporting both early and late development projects in therapeutic areas such as the central nervous system (CNS). The data science team themselves are highly skilled in the analysis and interpretation of omics and screening data, advanced data analytics and quantitative methods.

    RESPONSIBILITIES

    The Post Doc Bioinformatician will apply advanced analytical capabilities to biological domain understanding to reveal mechanistic insight into disease and drug action. You will establish genomic data processing pipelines and analytical plans to inform target identification, validation and biomarker discovery.

    Additional responsibilities:
    • Affect new target identification, target validation, biomarker discovery and patient stratification using omics data.
    • Process, analyse and interpret data from omics studies across the portfolio.
    • Develop approaches to utilize state of the art tools and technologies, or develop new methods where appropriate, to enable the above.

    REQUIREMENTS

    You will be part of a highly motivated, multi-disciplinary team all driven by a passion to improve decision making in Drug Discovery by leveraging advanced data science methods. The position has a high potential of extension, as others have been in the past, the company are keen to help the successful candidate grow and develop as an early career bioinformatics scientist. This is an excellent opportunity for a PhD graduate or someone with 1-3 years experience in academia who would like to gain experience in a pharmaceutical company.

    What we are looking for:
    • A thorough understanding of bioinformatics, statistics, data mining, and visualization of biological data types and the standard tools used in these domains. Expertise in pre-processing, integration and analysis of different omic data types (e.g. proteomics, gene expression, SNP, metabolomic, epigenetic data, etc.)
    • Expertise in methods pertinent for functional interpretation of omics data e.g. pathway enrichment, functional module detection, causal reasoning
    • Familiarity with specific strategies e.g. (eQTL analysis) for analysis of multiple omic data types as well as advanced statistical and machine learning methods
    • Proficiency in a range of programming languages such as Python or R
    • Ability to interpret and communicate efficiently the outcomes of analytical work to a non-expert audience in order to trigger efficient decision-making

    TERMS

    12-month contract (Potential to Extend)

    HOW TO APPLY

    Please contact Harvey on +44 121 616 3407 or email huppal[at]pararecruit.com for more information or to discuss applying for this role.

    Keywords: Bioinformatics, Computational Biology, Screening, Informatics, Statistics, Analysis, Biological Data, Data Analytics, Molecular, Omics, Berkshire, UK, Genomics, Human Genetics, Pharmaceutical

    BACKGROUND

    To perform data management, quality control, data processing, data analysis and other bioinformatics-related tasks on high-dimensional data in coordination with study investigators and other computing and bioinformatics staff in the assigned department. To determine applicable commonly-available, widely-accepted and well-understood bioinformatics tools and technologies. To stay abreast of recent literature and other new developments, incorporating into existing data analysis protocols and pipelines in support of high quality, reproducible research in any science discipline or disease.

    RESPONSIBILITIES

    • Performs data and analysis-related tasks, including but not limited to (a) processing next-generation sequence data (NGS) applications including RNA-seq, single-cell RNA-seq (e.g. 10x) and B cell receptor repertoire sequencing, (b) processing flow cytometry data, (c) performing quality control and troubleshooting, (d) performing downstream analyses, and (e) recommending, creating and maintaining local bioinformatics databases, as well as making use of public databases
    • Develops and implements software workflows, pipelines and tools, and analytical procedures supporting bioinformatics analysis
    • Participates in informatics projects providing evaluation, design and building of databases, web applications and other services to support the needs of the investigators
    • Identifies and resolves technical issues and proposes upgrades to current software
    • Evaluates and identifies new technologies for implementation
    • Interfaces with high-performance computing staff as needed
    • As part of the research team in particular, (a) assists with the development of grant applications, presentation of results and scientific papers for publication, (b) participates in formal and informal training activities, and (c) maintains knowledge of current changes and developments in the bioinformatics fields through publications, communicating with subject matter experts, and attending related workshops and conferences
    • Provides consultation and training on bioinformatics-related concepts, applications and tools
    • Performs other duties as assigned

    REQUIREMENTS

    Bachelor's degree in Bioinformatics, Biological Sciences, Computer Science or a related field required. Work experience may NOT substitute for education requirement.

    PREFERENCES

    The preferred candidate will possess the following:
    • Ability to work as part of a team
    • Knowledge of theoretical and applied statistics, and molecular biology
    • Knowledge of bioinformatics
    • Analytical skills, problem-solving and troubleshooting skills
    • Critical attention to detail
    • Exceptional organizational skills
    • Excellent verbal and written communication skills
    • Demonstrated experience in a biological/biomedical field if a Computer Science graduate
    • Demonstrated computer/software-development skills if a Biology graduate
    • Experience with at least one data-rich biological platform, e.g.: RNA-seq, scRNA-seq, ATAC-seq, CHiP-seq, Rep-seq, Microbiome, Metabolomics, Multiparameter Flow Cytometry
    • Demonstrated experience in:
      • A technical computing platform (e.g. Matlab, R)
      • A programming language (e.g. Perl, Python, Java)
      • Databases (e.g. relational, like MySQL or associative, like Neo4j)
      • High-performance computing

    TERMS

    Full-time

    LOCALE

    Birmingham, AL

    COMPENSATION

    Salary range: $47,486.40 - $74,484.80

    HOW TO APPLY

    Applications can be submitted here: uab.taleo.net/care[...]ng=en

    BACKGROUND

    A position for a doctoral candidate is available in Leila Taher's new lab at the Institute for Biomedical Informatics at Graz University of Technology (Austria, www.bioinfo.tugraz.at). We develop and apply regulatory genomics and systems biology approaches to analyze large biological datasets. Our long-term goal is to gain novel insights into the mechanisms and evolution of differential gene expression, in particular in the context of disease.

    RESPONSIBILITIES

    Misregulation of gene expression can cause a broad range of diseases, including cancer. In keeping with the key role that enhancers play in gene regulation, many groups have shown that enhancers are enriched for disease-associated common genetic variants. Thus, genes with redundant enhancers can be expected to be buffered against the effects of disruptive regulatory mutations. The successful candidate will study the evolution of redundant enhancers in human regulatory networks and develop machine learning approaches to model the effects of mutations within redundant enhancers. The data involved in these analyses will be obtained from public data repositories (e.g., ENCODE) or generated by some of our experimental collaborators.

    The position is intended to give promising candidates the opportunity to pursue advanced research in Functional Genomics leading to a doctoral degree in Natural (Dr. rer. nat.) or Technical (Dr. Techn.) Sciences. Doctoral candidates are expected to explore and address open research questions in the field of Bioinformatics, contribute to existing projects in the Institute for Biomedical Informatics, present their work at conferences, write scientific articles describing their findings, support teaching, undertake duties in academic self-administration, and actively participate in the activities of the group.

    REQUIREMENTS

    Master's level degree in Bioinformatics, Informatics in the Natural Sciences, Applied Computer Sciences, Molecular Biology, Bioengineering or equivalent.

    In addition, the ideal candidate should have
    • Good programming skills (e.g., Perl, Python, R; see "Beginning Perl for Bioinformatics" by James D. Tisdall and "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck)
    • A proven knowledge of Molecular Biology at the level of Benjamin Lewin's "Genes XII"
    • A solid understanding of statistics
    • Familiarity with UNIX/Linux, including shell scripting
    • Experience
      • With the analysis of NGS data, building NGS pipelines (e.g., Snakemake) and using bioinformatics tools; and/or
      • In the field of (human) genomics
    • A high level of organization and attention to detail
    • The willingness and ability to work individually and as part of a team
    And be
    • Proficient in both written and oral English
    • Creative
    • Self-motivated, with strong work ethics
    • Open-minded
    Command of the German language is not a requirement but would be an advantage. Practical experience with sequencing technologies (in particular, Oxford Nanopore Technologies) and/or Machine Learning would be valuable assets.

    TERMS & COMPENSATION

    The position is for a fixed term of 4 years and will be paid according to category B1 of the collective agreement for employees of Austrian universities. This currently results in a monthly gross salary in the amount of € 2.864,50 (14 x per year), which may increase on the basis of previous experience.

    HOW TO APPLY

    Please, send an e-mail to applications.csbme[at]tugraz.at indicating the position identifier "7200/20/003" in the subject. An application package must contain the following documents (in English, all in one PDF file):
    1. A cover letter with a short explanation for how this position fits into your interests and career aspirations
    2. Your CV
    3. Copies of your transcripts and certificates
    4. Contact information for two references

    Only complete applications will be considered.

    DEADLINE

    February 11, 2020

    BACKGROUND

    A postdoctoral fellow position is available immediately in the Department of Pathology at Harvard Medical School/Beth Israel Deaconess Medical Center to study resilience in Alzheimer's disease. The position is funded by an NIH R01 research grant entitled "The Alzheimer's Disease Resiliome: Pathway Analysis and Drug Discovery under the direction of Dr. Winston Hide (Systems RNA medicine), Noncoding RNA Laboratory, Beth Israel Hospital, together with collaborators Dr. Doo Yeon Kim and Dr. Rudolph Tanzi (Massachusetts General Hospital). We seek to understand the manner in which some individuals appear to be resilient to the pathologies associated with the onset of Alzheimer's disease and to use that information to promote healthy aging and decrease the severity of neurodegenerative diseases. The laboratory primarily uses computational modeling of neurodegenerative diseases prior to validating results with collaborators in vitro, and in mouse models.

    RESPONSIBILITIES

    The postdoctoral trainee will apprehend and curate Alzheimer's disease datasets from collaborators and the public domain to evaluate and synthesize molecular signatures and so integrate models that pertain to concepts of disease and resilience. Datatypes will include but are not restricted to, mRNAs, miRNAs, ncRNAs, single-cell and tissue-level transcriptomes, methylation, acetylation and genome variant data. Integrated molecular signatures from human subject data, and from model organoid data, will be assessed and incorporated into pathway-disease-drug network models. The project is expected to expose several layers of pathological pathway cascades, and these will need to be evaluated and modeled. A major role will be to predict, test, and provide prioritized intervention strategies, such as drugs, miRNAs and potential diagnostics.

    REQUIREMENTS

    • PhD in a quantitative field related to bioinformatics (e.g. with a specialization in bioinformatics related to genetics, neurosciences, disease modeling, pathway modeling)
    • Extensive experience working with multi-omic datasets
    • Ability to generate computational disease models and hypotheses
    • Superb communication skills
    • Ability to work independently and as part of a team
    • Ability to drive a research project from design stages to data analysis, figure preparation and manuscript writing
    • A passion for scientific research
    • Strong organization and time-management skills
    • Meticulous attention to detail
    • Excellent working knowledge of R and other scripting languages
    This position is a fundamentally important one and we are seeking a highly motivated individual who relishes a challenge and is not shy about diving into complex datasets.

    Additional expertise:
    • Sound knowledge of statistics
    • Experience with manipulating and curating Alzheimer's transcriptome datasets
    • Experience using large-scale datasets to rank gene and pathway candidates, and to define key network events that may be driving a disease process
    • Extremely comfortable with network-orientated bioinformatics
    • Knowledge of the aging and neurodegeneration research field
    • A strong understanding of genetics
    • Experience with human-derived model systems

    TERMS

    The position is available immediately and can be renewed annually.

    HOW TO APPLY

    Email applications including curriculum vitae, a summary statement of personal objectives and research interests, PDFs of your best two papers, and the names and email addresses of three references directly to: whide [at] bidmc [dot] harvard [dot] edu

    Submitter

    BACKGROUND

    This is a great opportunity working with a well-funded early stage biotech company who have identified novel tumour-specific antigens derived from reactivated endogenous retroviral sequences. They are using this discovery to enable the development of a range of pharmaceutical products including vaccines, biologics and cell therapies. Importantly, these pharmaceuticals are non-personalised and thus able to broadly impact the needs of oncology patients.

    This is an exciting opportunity to join an organisation that aims to support efforts to acquire and interrogate immunopeptidomic data from primary human tissue in order to discover, validate and quantify novel cancer-specific (neo) antigens. The ideal candidate will oversee the processing and analysis the genomic pipeline used to identify cancer-specific transcripts. They will be responsible for the analysis of genomics and transcriptomic data using existing software packages and through the development of novel algorithms. They will also be responsible for integrating data output for further analysis.

    A successful candidate will have a PhD in Bioinformatics or a related subject and have an interest in the developing field of immuno-oncology. You will also have a working knowledge of genomics methods and the ability to work with NGS data in a HTC environment.

    REQUIREMENTS

    • Experience of software development in a life sciences commercial/academic environment
    • Knowledge of R and/or Python scripting languages
    • Knowledge of genomic data analysis, specifically RNA Seq
    In addition to the above, the following skills/experiences are desirable:
    • Experience with version control systems e.g. Bitbucket
    • Practical knowledge of workflow management e.g. Snakemake, Nextflow
    • Experience of the Amazon Web Services (AWS) environment
    • Knowledge of Database Development/Management
    Additional criteria include:
    • The ability to communicate results clearly and effectively and to discuss scientific ideas within the work environment
    • An active interest in supporting scientific research
    • The ability to work on several projects in parallel
    • Excellent record keeping and precision driven work approach
    • The ability to work in a team

    COMPENSATION

    There are great benefits on offer with this role including a competitive salary, pension, holidays and more.

    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, Bioinformatician, Genomics, Pipelines, RNA, Python, Version Control, Bitbucket, Snakemake, AWS, Database, Development, London, Immunology, Oncology, NGS

    DESCRIPTION

    Human cells perform highly complex tasks but the map of cellular regulation that controls these processes is surprisingly poorly known. In diseases, these processes are disturbed and targeted interference is required to rebalance disease. Such interference can only result in effective disease eradication with minimal side effects when the map of cellular regulation is known in sufficient detail. We will employ Phenosaurus, a large collection of ~130 genome-wide haploid screens and advanced computational inference to reconstruct this map. Phenosaurus is a genotype to phenotype map that contains the strength of association between every gene and 130 quantitative protein readouts in haploid human cells. We envisage charting the regulatory map using two approaches. First, we will identify functional units. We will determine gene-gene similarity based on Phenosaurus phenotypic profiles and fuse these similarities with independent co-data sources such as protein-protein interaction maps, co-expression maps and gene ontologies to identify high confidence functional units (complexes and pathways). Second, we will identify regulatory interactions between functional units and genes. As many associations in Phenosaurus are indirect i.e. mediated by e.g. 'master regulators', we will employ network inference approaches, such as the PC algorithm, guided by co-data sources to identify (master) regulators and their associated interactions. High confidence predictions emerging from these analyses, such as protein complex or pathway membership (first approach) and new putative regulatory interactions with master regulators (second approach) will be validated experimentally. Importantly, this project provides the opportunity to develop novel computational approaches associated with data fusion, network inference and effective application of co-data.

    RESPONSIBILITIES

    You will research and benchmark the latest algorithms, develop new algorithms and help design validation and follow-up experiments. You will be working closely with fellow computational scientists of the Wessels group (ccb.nki.nl) experimentalists in the Brummelkamp group and scientists of Scenic Biotech BV (scenicbiotech.com) a biotech startup.

    LOCALE

    You will be part of the Netherlands Cancer Institute (NKI), a world-class cancer research institute residing under the same roof as the Antoni van Leeuwenhoek cancer hospital in the vibrant city of Amsterdam. The NKI provides an open, lively and stimulating environment with access to top-notch facilities, including high-performance computing and with many opportunities to interact with colleagues at social events, attend high-quality seminars and perform translational research.

    REQUIREMENTS

    • A degree or advanced skills in bioinformatics, or a related discipline
    • A degree or a high level of proficiency in (molecular) biology
    • Proficiency in R, Python and data base management
    • Experience in interacting with molecular biologists
    • Highly motivated

    HOW TO APPLY

    Please send applications by email to Lodewyk Wessels (l.wessels[at]nki.nl) and use "#application #postdoc" in the subject line. Include a CV, motivation letter and the names and contact information of at least two references in your application.

    DEADLINE

    1 March 2020

    Submitter

    BACKGROUND

    This is a great opportunity for a collaborative and self-motivated bioinformatician to spearhead cancer evolutionary genomics analysis and the design and operation of the bioinformatics NGS pipeline for the TRACERx Renal cancer and associated programmes within this organisation. The role is ideally suited for a creative individual with a strong interest in cancer genomics, cancer evolution, software development and testing, database analysis, and automation within a high throughput academic setting. A successful candidate will have strong software engineering and programming skills and be keen to apply these skills to the field of cancer genomics and cancer evolutionary biology.

    RESPONSIBILITIES

    Key responsibilities include:
    • Lead on the running and development of the NGS analysis pipelines.
    • Evaluate and provide software, databases, protocols and methods to aid in the analysis of genomic and genetics experiments from academic and commercial sources.
    • Develop methodologies and techniques to address analysis issues and implement software and data resources in relation to these technologies.
    • Lead the bioinformatics analysis of projects with a view to high impact publications investigating cancer evolution and the interface with the immune microenvironment and novel profiling methods.
    • Provide consultation and communication in data analysis, statistics, genomics and other areas of bioinformatics, to other members of the team.
    • Produce thorough but concise written documentation of algorithms, validations, SOPs, and other processes and procedures as required.
    • To liaise and coordinate between various working groups involved in the sequencing of clinical samples to ensure the delivery of high-quality sequence data in a time efficient manner.
    • To record all experiments in an accurate, timely and clearly presented manner, and use this to prepare data summaries and reports as and when required.
    • To attend, and report research results at regular group and (inter)national meetings.

    REQUIREMENTS

    Qualifications, experience and competencies:
    • Higher degree in a relevant subject with an extensive analytical component e.g. bioinformatics, statistics, molecular biology
    • Fluent in at least one of the following programming languages: Python or R
    • Familiarity with the application of statistical techniques to biological data
    • Considerable experience of using bioinformatics in a biological field, ideally translational research projects
    • Demonstrable experience of NGS analysis methodologies and protocols
    • Experience of interaction with investigators on scientific projects and working in a collaborative environment
    • Experience of managing a large analysis project over a number of years is desirable.
    • Works with minimal supervision, organising and prioritising own workload
    • Excellent communication skills within a research environment, building highly effective working relationships with team and customers.
    • Excellent scientific analysis skills
    • Evidence of independent and original contribution to research
    • Ability to manage projects to timelines, analyse, present and write up data in a timely manner
    • Good presentation skills
    • Excellent inter-personal skills and commitment to team-work
    • Experience in the field of evolutionary biology/cancer evolution is desired
    • Experience with machine learning is desirable

    PREFERENCES

    Qualifications, experience and competencies:
    • An understanding of programming, particularly with regard to big data, data visualisation and data-mining techniques within a genomic or genetical environment
    • Knowledge of genetics, model organisms, cancer biology
    • A broad comprehension of high throughput genomic technologies
    • Experience of having managed a large bioinformatics project
    • Experience of supervising or mentoring other members of the team
    • Experience of monitoring and allocating resources within a project

    COMPENSATION

    There are great benefits on offer with this role including a competitive salary, pension, holidays and more.

    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: Principal, Bioinformatician, Genomics, Cancer, Analysis, NGS, Human, Software, Testing, Pipeline, Biology, Analysis, Python, Statistics, Algorithms, Validation, SOP, WGS, WES, London

    DESCRIPTION

    The Laboratory of Genetics and Genomics at the National Institute on Aging (NIA) at NIH is recruiting for a postdoctoral position in the lab of Dr. Maragkakis. The lab is interested to understand the high-dimensional regulation in cells as a key component of discovering the mechanistic basis of the physiology and diseases of aging. The lab employs experimental and computational approaches to discover fundamental biological mechanisms that control RNA stability and dynamics (relevant publication www.nature.com/arti[...]042-8). Of particular interest to the lab is the interaction between regulatory processes such as miRNAs, RNA binding processes and mRNA decay. Projects are data-driven and highly integrative. Your role will be to lead, develop and apply advanced computational methods for genomics research, large-scale data integration and analysis of sequencing data from novel technologies such as nanopore sequencing (dRNA-Seq), CLIP-Seq, CAGE, etc. The appointed postdoctoral fellow will have the option to work side-by-side with experimentalists and will have opportunities to train on wet biology. More information can be found in the lab webpage www.nia.nih.gov/rese[...]-unit.

    REQUIREMENTS

    • PhD in bioinformatics, biostatistics, computer science, mathematics or related discipline
    • Strong background in computer science and machine learning
    • Excellent programming skills (e.g. Python, R, Go)
    • Research background evidenced by at least one first-author publication
    • Outstanding interpersonal and communication skills

    LOCALE

    Baltimore, Maryland, United States

    HOW TO APPLY

    Interested candidates should submit their curriculum vitae (CV) by email to Dr. Maragkakis at emmanouil.maragkakis[at]nih.gov. Reference "EMRecruit" in the email subject line.

    DEADLINE

    Application are evaluated on rolling basis. Position will remain open until filled.

    POLICY

    DHHS and NIH are Equal Opportunity Employers. The NIH is dedicated to building a diverse community in its training and employment programs.

    BACKGROUND

    Bioinformatics Developer, Plant and Fungal Trees of Life Project (PAFTOL)

    Kew is the world's leading botanic gardens, at the forefront of plant and fungal science, a UNESCO World Heritage Site and a major visitor attraction. We want a world where plants and fungi are understood, valued and conserved – because our lives depend on them. We use the power of our science and the rich diversity of our gardens and collections to provide knowledge, inspiration and understanding of why plants and fungi matter to everyone.

    RESPONSIBILITIES

    The successful candidate will be an active member of PAFTOL's multi-disciplinary team. The post holder, together with PAFTOL's other bioinformatics staff, will be responsible for completion of the design and build of software systems and data analysis necessary to ensure the long-term operation of the PAFTOL project.

    REQUIREMENTS

    You will be an excellent bioinformatician or software engineer with appropriate professional experience and a proven background in genomic data manipulation, ideally in a research environment. You will have a track record of helping to design and build robust bioinformatics pipelines, with good knowledge of distributed compute environments and workflow management systems. Experience of phylogenomics is desirable but not essential. You will be a proven team player, with the ability and appetite to help deliver project outputs, outreach, and to train and support researchers and students as required.

    TERMS

    Fixed term, 18 month contract
    Hours of work: Full time

    LOCALE

    Royal Botanic Gardens Kew, London, United Kingdom.

    COMPENSATION

    £34,933 - £37,865 per annum depending on skills and experience.

    We offer a fantastic range of benefits including a broad range of Learning and Development opportunities, with access to the Civil Service training curriculum, generous annual leave entitlement for new starters, family friendly policies, a choice of competitive pensions and flexible benefits scheme as well as free entry into a wide range of national museums and galleries.

    HOW TO APPLY

    Please visit careers.kew.org/vaca[...].html

    DEADLINE

    Monday 3rd February 2020

    POLICY

    We are committed to equality of opportunity and welcome applications from all sections of the community. We guarantee to interview all disabled applicants who meet the essential criteria for the post.

    BACKGROUND

    A postdoctoral researcher position (up to 3 years) in evolutionary bioinformatics is available at the Technische Universität Braunschweig, Germany (research group of M. Vences: www.tu-braunschweig.de/en/z[...]ology) with collaborations at the Ludwig-Maximilians-Universität in Munich, Germany.

    The aim of the postdoctoral project is the development of concepts and bioinformatic tools for taxonomic data, in the framework of the DFG-funded "Taxon-Omics" priority program (SPP 1991; www.taxon-omics.com).

    This encompasses
    (1) developing and implementing tools for user-friendly archiving and retrieving of specimen-based information from data repositories, for taxonomic use and re-use;
    and
    (2) developing a software pipeline that formalizes an integrative taxonomy workflow: using diverse kinds of data and combining various species delimitation approaches.

    The research will be embedded in the DFG-funded Taxon-Omics priority program (SPP 1991), in which some 27 research projects are producing an array of data, from high-throughput imaging and chemotaxonomy to genomics, from protists, plants, fungi, and animals. The cutting-edge approaches to taxonomy in this program and the diversity of taxa and data, provide an ideal environment for collaborative research, and a unique opportunity to produce high-visibility methods. The research environment in this priority program is international and operates in English; international applicants are encouraged to apply.

    RESPONSIBILITIES

    (1) Development of software pipelines and tools (90%)
    • Conceptual development
    • Implementation in a programming language, e.g. in R, C++, Python
    • Simulation studies
    • Collaboration with research groups in the Priority Program
    • Proof-of-principle studies with empirical data sets
    • Writing scientific publications
    (2) Organizational tasks in the priority program (10%)

    REQUIREMENTS

    • A doctoral degree in a relevant discipline, e.g. biology, mathematics, physics, or informatics

    PREFERENCES

    Ideally, the researcher should combine as many as possible of the following skills:
    • Expertise or interest in biological systematics, taxonomy, or another field of evolutionary biology
    • Familiarity with relevant programming languages
    • Experience with research data management and data repositories
    • Experience with machine learning approaches
    • Experience with analysis of genomic data
    • Excellent oral and written communication skills in English
    • Original research publications in peer-reviewed international journals

    LOCALE

    The postdoctoral researcher will be based at TU Braunschweig, but will spend extended periods at the Ludwig-Maximilians University in Munich, working with biodiversity-informatics experts there. A close collaboration with the team of GFBio (www.gfbio.org) is envisaged.

    COMPENSATION

    Salary will be paid according to Remuneration level 13 of the Wage Agreement for Public Service in the Federal States (TV-L).

    HOW TO APPLY

    Applications should be sent until 31st January 2020 to Miguel Vences (by email: m.vences[at]tu-braunschweig.de) and include (1) a cover letter explaining your background and motivation, (2) a CV, and (3) email addresses of two references.

    DEADLINE

    31st January 2020

    BACKGROUND

    The Stanford Research Computing Center (SRCC) is seeking outstanding applicants for the position of HPC System Engineer/Administrator. Based in Polya Hall on the Stanford campus, you will join a dynamic and growing team of technology specialists supporting the computational and data needs of Stanford's research community. This role will focus primarily on the management and support of an HPC cluster and multi-petabyte storage platform that provides essential infrastructure for Stanford's bioinformatics and genomics communities.

    The successful candidate will be someone who:
    • Has built, managed, secured and supported scalable HPC clusters before and is comfortable with handling all aspects of that, from racking servers, to configuring networking, to installing software for end-users to providing one-on-one instruction and support
    • Has managed large-scale research storage platforms
    • Thrives when working in an academic environment
    • Is passionate about technology and is driven by challenge and intellectual curiosity
    • Is self-motivated to learn, sometimes on your own time
    • Has user support experience and actually likes working with end-users on a daily basis
    • Is thorough, detail-oriented, documents well, and understands the importance of documentation
    • Isn't afraid of hardware
    • Loves problem-solving
    • Understands the need to ensure the usability of systems from the end-users' perspectives
    • Works independently but also collaborates within and across teams
    • Has a sense of humor
    The SRCC is jointly sponsored by University IT (UIT) and the Office of the Dean of Research. The SRCC team of 18 cyber infrastructure professionals offers research computing platforms, hosting, consultation, tool and software development, system engineering, and system administration in support of computational and data-intensive research across the Stanford campus.

    RESPONSIBILITIES

    Job Purpose:
    This position will provide system administration, engineering and specialized technical consultation for existing and future systems and services for research computing workloads. The position will also specifically have responsibilities for department or faculty- owned research computing HPC cluster and server environments, including filesystems and storage platforms, Linux server environments, job schedulers, scientific tools, and application software.

    Core Duties:
    • Support and administration of research computing clusters, servers and storage systems, including installation, network and security configuration, monitoring, maintenance, application software build/configuration, upgrading, patching, and complex user problem solving. Those systems may be in Stanford data centers or in Stanford research labs and units.
    • Provision computing platforms and associated storage and networking for research environments, incorporating novel technical solutions as needed to meet research requirements. Install, test and configure software tools, libraries and compilers to meet researchers' needs.
    • Customize environments as requested by research teams, with specific focus on the optimization of end-users' experiences
    • Provide advanced cyberinfrastructure training and consultation for faculty, postdocs and graduate students across a wide-array of university research units and departments.
    • Ensure systems are configured and managed in accordance with Stanford policies and any regulatory requirements specific to data sources and classifications.
    • Conceive, design, develop, optimize, integrate, and maintain information technology at a complex level.
    • Troubleshoot highly complex problems for which the analysis and resolution require extensive knowledge of many diverse system components
    • Develop long range technology plans.
    • Provide leadership and IT solutions for complex problems
    • Other duties may be assigned.
    The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

    REQUIREMENTS

    Bachelor's degree and eight years of related increasingly technical work experience or a combination of education and relevant experience. Strong, demonstrated knowledge of Linux and demonstrated experience managing complex multiuser HPC clusters and large-scale research storage environments are required as well.

    Knowledge, Skills and Abilities:
    Advanced knowledge of Linux is required; experience managing, using, supporting and consulting on research computing cyber-infrastructure in an academic or research environment is strongly preferred. Proven ability to deliver outstanding system and service administration and end-user support in a thorough and timely manner is needed. This position requires that you be able to juggle multiple competing priorities, work quickly and accurately, and demonstrate initiative in conceptualizing and moving technical projects successfully to completion. The position must be able to do independent analysis, troubleshooting and problem resolution, but also must work collaboratively with other team members and across organizational group boundaries.

    This position requires hands-on experience building and supporting multi-tenant Linux servers/clusters and their associated networks, file systems and storage devices in production research environments. Specifically, this technical knowledge needed to be successful in this position includes:
    • Expert demonstrated knowledge of clustered Linux systems, including securing systems, and day-to-day troubleshooting, monitoring, support, software packaging, and working within industry-wide best practices
    • Experience administering, configuring, and supporting HPC clusters, including systems with accelerators, and high performance file systems and storage. This includes hardware installation, configuration, upgrades and repairs
    • Knowledge of and experience utilizing data and system security techniques, practices and standards as they relate to HPC systems, storage and networks
    • Experience installing and supporting parallel computing environments (e.g. OpenMPI, MVAPICH, etc.)
    • Hands-on experience installing, configuring and supporting job schedulers and resource managers (e.g., SLURM, OGE, LSF, Torque, Maui, etc.)
    • Familiarity with deploying virtualization technologies and basic knowledge of container technologies
    • Exceptional written and verbal communication skills
    • Experience using shell scripts, programming languages (Python), and programming automated system management tools, both at a general level (e.g. Puppet) and at a cluster-level (e.g. Rocks)
    • Experience installing, configuring, managing and supporting GPFS parallel file systems is desired but not required
    • Familiarity with TCP/IP, Internet Routing Protocols, private and public networks, VLANs, Firewalls, Load Balancers, addressing schemes, subnet creation and subnet masking. Proven ability to troubleshoot basic network issues and communicate and work with a team of network engineers to solve possible network design issues in HPC
    • Familiarity with the intersection of storage and networking disciplines: i.e. transport media, speeds of media, storage networks, IP based storage delivery, other storage delivery technologies
    • Experience with some the following applications: Git, Apache, Kerberos, LDAP
    • Software installation and maintenance experience supporting research codes and clients
    • Exceptional client service and communication, focusing on proactive system administrator actions and interactions to reduce or remove barriers to clients' efficient use of resources to advance research

    ABOUT US

    Why Stanford is for You:
    Imagine a world without search engines or social platforms. Consider lives saved through first-ever organ transplants and research to cure illnesses. Stanford University has revolutionized the way we live and enrich the world. Supporting this mission is our diverse and dedicated 17,000 staff. We seek talent driven to impact the future of our legacy. Our culture and unique perks empower you with:
    • Freedom to grow. We offer career development programs, tuition reimbursement, or audit a course. Join a TedTalk, film screening, or listen to a renowned author or global leader speak.
    • A caring culture. We provide superb retirement plans, generous time-off, and family care resources.
    • A healthier you. Climb our rock wall or choose from hundreds of health or fitness classes at our world-class exercise facilities. We also provide excellent health care benefits.
    • Discovery and fun. Stroll through historic sculptures, trails, and museums.
    • Enviable resources. Enjoy free commuter programs, ride-sharing incentives, discounts and more!

    TERMS

    Schedule: Full-time
    Employee Status: Regular
    Grade: M

    LOCALE

    Business Affairs: University IT (UIT), Stanford, California, United States

    COMPENSATION

    The hiring range for this position is $135,000 - $150,000.

    HOW TO APPLY

    We invite you to apply for this position by visiting apptrkr.com/1765095. To be considered, please submit your resume and a cover letter along with your online application.

    Job Code: 4770
    Requisition ID: 85728

    To be considered for this position please visit our web site and apply on line at the following link: apptrkr.com/1765095

    POLICY

    Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.

    Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

    www.jobelephant.com
    jeid-597fa09cf4a1a148bd82defd7ac8bffc

    BACKGROUND

    A position for a doctoral candidate is available in Leila Taher's new lab at the Institute for Biomedical Informatics at Graz University of Technology (Austria, www.bioinfo.tugraz.at). We develop and apply regulatory genomics and systems biology approaches to analyze large genomic datasets. Our long-term goal is to gain novel insights into the mechanisms and evolution of differential gene expression.

    RESPONSIBILITIES

    Tasks:
    Gene expression is primarily controlled at the level of transcription, which is mediated by transcription factor activity and changes in the chromatin structure. Chromatin structure is largely determined by histone modifications and DNA methylation, collectively known as epigenetic marks. Large international efforts such as the ENCODE (www.encodeproject.org) and FANTOM (fantom.gsc.riken.jp) projects are now generating a wealth of transcriptomic and epigenomic data that should enable us to elucidate the mechanisms underlying health and disease. However, the analysis of these data is not trivial. In particular, repetitive regions in the genome pose an enormous challenge to current bioinformatics tools. It has been estimated that approximately two-thirds of the human genome consists of repeats or repeat-derived sequences, and a predominant part of these sequences are transposons. The successful candidate will develop computational tools to aid the genome-wide characterization of sequences of transposon origin.

    The position is intended to give promising candidates the opportunity to pursue advanced research in Functional Genomics leading to a doctoral degree in Natural (Dr. rer. nat.) or Technical (Dr. Techn.) Sciences. Doctoral candidates are expected to explore and address open research questions in the field of Bioinformatics, contribute to existing projects in the Institute for Biomedical Informatics, present their work at conferences, write scientific articles describing their findings, undertake duties in academic self-administration, and actively participate in the activities of the group.

    REQUIREMENTS

    Master's level degree in Bioinformatics, Informatics in the Natural Sciences, Applied Computer Sciences, Molecular Biology, Bioengineering or equivalent.

    In addition, the ideal candidate should have:
    • Good programming skills (e.g., Perl, Python, R; see "Beginning Perl for Bioinformatics" by James D. Tisdall and "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck)
    • A proven knowledge of Molecular Biology at the level of Benjamin Lewin's "Genes XII"
    • A solid understanding of statistics
    • Familiarity with UNIX/Linux, including shell scripting
    • Experience with the analysis of Illumina NGS data, building NGS pipelines (e.g., Snakemake) and using of bioinformatics tools
    • A high level of organization and attention to detail
    • The willingness and ability to work individually and as part of a team
    And be:
    • Proficient in both written and oral English
    • Creative
    • Self-motivated, with strong work ethics
    • Open-minded
    Command of the German language is not a requirement.

    TERMS & COMPENSATION

    The position is for a fixed term of three years and will be paid according to the standards of the Austrian Science Fund (FWF, www.fwf.ac.at/de/f[...]etze/).

    HOW TO APPLY

    Please, send an e-mail to funcgenfau[at]gmail.com addressed to Leila Taher and with the subject "PhD BIOINFO NANTES". An application package must contain the following documents (in English, all in one PDF file):
    1. A cover letter with a short explanation for how this position fits into your interests and career aspirations
    2. Your CV
    3. Copies of your transcripts and certificates
    4. Contact information for two references

    Only complete applications will be considered.

    Contact: Leila Taher (funcgenfau[at]gmail.com)

    DEADLINE

    Applications are due immediately. Position will remain open until filled.

    BACKGROUND

    MeInBio is a PhD research training group at the University of Freiburg and the Max Planck Institute of Immunobiology and Epigenetics Freiburg. It aims at a dual education in bioinformatics and wet laboratory methods to explore the spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods. For the start of the second generation of PhD students in September, 2020, MeInBio is now accepting applications to 13 PhD positions (funded for three years).

    We offer:
    • Exciting modern research projects in well equipped laboratories using state-of-the-art technologies (stem, cancer and prokaryotic cells, single cell and high-throughput sequencing, high-resolution imaging, bioinformatics)
    • Tandems between wet laboratory and bioinformatics groups with an extensive stay in the lab of the respective other field
    • Different model organisms for conceptual learning and scientific exchange
    • Professional and efficient supervision secured by a thesis advisory committee
    • Regular courses in bioinformatics and wet laboratory techniques
    • Additional "soft skills" courses and gatherings of all research training group members for scientific exchange

    REQUIREMENTS

    We are looking for junior researchers with expertise either in life sciences (molecular biology, cell biology, molecular medicine, biochemistry), or in bioinformatics/ informatics/ statistics. Our dual education profile requires a strong interest for training in the respective other field.

    Candidates should:
    • Have an excellent recent university degree in one of the fields mentioned above
    • Be passionate about science and highly motivated
    • Have a strong affection to acquire both, biological and informatics knowledge
    • Be fluent in written and spoken English

    HOW TO APPLY

    For further details concerning the positions, information on the individual research groups, as well as the application procedure please refer to www.meinbio.uni-freiburg.de.

    Only online applications through the MeInBio web site will be considered.

    For more information please contact christine.hacker[at]anat.uni-freiburg.de.

    DEADLINE

    Feb, 15, 2020

    BACKGROUND

    We invite applications for one Edson Foundation Postdoctoral Research Scholar in the ASU-Banner Neurodegenerative Disease Research Center (NDRC) at Arizona State University. The goal of the Edson foundation is to fund research that will find new discoveries and solutions to better the quality of life for people affected by neurodegenerative diseases.

    As a prestigious Edson Postdoctoral Research Scholar, you will have a primary mentor in the NDRC, but will have the opportunity to collaborate with other investigators. The NDRC prides itself on producing high impactful research through collaborations. The selected candidate will work on projects utilizing highly dimensional genomic data, especially next-generation sequencing data for multilevel "omics" data analyses, with a focus on the identification of genes/drug targets implicated in neurodegenerative diseases, especially Alzheimer's disease.

    We will begin reviewing applications January 27, 2020 and will continue to review incoming applications on a biweekly basis until the position is filled.

    RESPONSIBILITIES

    • Write and optimize computational pipelines (scripts) for whole genome/exome sequencing, RNA-seq, and/or microarray.
    • Organize, prepare and analyze data; develop hypotheses to be tested and ways of testing it.
    • Prepare and present the results of research, in scientific conferences and journals.
    • Assist with grant preparation and reporting.

    REQUIREMENTS

    Applicants must have a PhD by May 31st, 2020 in bioinformatics, genomics, computational biology, biostatistics, epidemiology or related field to be considered.

    PREFERENCES

    • Experience with Linux/Unix based systems, developing shell scripts/command-line interface, demonstrable experience in large-scale data analysis and utilization of high-performance computing systems
    • Formal training/experience in analyzing next generation sequencing (NGS) or microarray data for gene expression, genotyping or epigenetics
    • Experience with scientific computing and data visualization tools and scripting languages such as Python/Perl/R/Matlab, and understanding of intermediate level of statistics
    • Excellent communication skills
    • Experience in genomic data analysis of neurodegenerative diseases is desired but not required.

    ABOUT US

    For the fifth year in a row, ASU has been named the most innovative school in the nation, recognizing the university's culture of groundbreaking research and partnerships, as well as its commitment to helping students thrive in college and beyond. U.S. News and World Report has named ASU as the most innovative university all five years the category has existed.

    ASU Knowledge Enterprise advances research, innovation, strategic partnerships, entrepreneurship, and international development. Our success arises from solutions-focused, interdisciplinary research; an entrepreneurial approach that is embedded in every school and department; and a commitment to transform society in a positive way. research.asu.edu

    The Biodesign institute is home to the ASU-Banner Neurodegenerative Disease Research Center (NDRC). This is a collaboration between ASU and Banner Health that was officially entered into in July 2015. The goal of NDRC is to develop a world-class research center that houses basic and translational researchers to address challenges in the etiology, prevention, diagnosis and treatment of neurodegenerative diseases. We share a strong desire to collaborate in an effort to advance the scientific and clinical fight against Alzheimer's disease and other neurodegenerative diseases and to make meaningful contributions to the understanding and promotion of healthy aging, as well as establish an organization that unites clinical and basic research in an effort to bridge the gap between discovery and delivery of health care of affected populations. ASU serves as the basic research arm and Banner Health serves as the clinical research arm of the partnership.

    HOW TO APPLY

    Applicants are responsible for including a cover letter, CV, and the names of three professional references in the application through the Interfolio website (apply.interfolio.com/72796). Emailed applications will not be accepted.

    DEADLINE

    Application deadline is January 27, 2020. Applications will continue to be accepted on a rolling basis for a reserve pool. Applications in the reserve pool may then be reviewed in the order in which they were received until the position is filled.

    POLICY

    A background check is required for employment. Arizona State University is a VEVRAA Federal Contractor and an Equal Opportunity/Affirmative Action Employer. All qualified applicants will be considered without regard to race, color, sex, religion, national origin, disability, protected veteran status, or any other basis protected by law.

    (See www.asu.edu/aad/[...].html and www.asu.edu/titleIX/.)

    In compliance with federal law, ASU prepares an annual report on campus security and fire safety programs and resources. ASU's Annual Security and Fire Safety Report is available online at www.asu.edu/poli[...]t.pdf You may request a hard copy of the report by contacting the ASU Police Department at 480-965-3456.

    Equal Employment Opportunity Statement:
    A background check is required for employment. Arizona State University is a VEVRAA Federal Contractor and an Equal Opportunity/Affirmative Action Employer. All qualified applicants will be considered without regard to race, color, sex, religion, national origin, disability, protected veteran status, or any other basis protected by law.

    BACKGROUND

    About the Job:
    The Institute for Health Informatics at the University of Minnesota invites applications for multiple Postdoctoral Associate positions from candidates with a Ph.D or equivalent degree in bioinformatics or related disciplines. The translational genomics and bioinformatics group directed by Dr. Steven S. Shen, M.D., Ph.D., is seeking outstanding scientists who are interested in working in a research program studying the genome wide mapping of epigenetic elements and the mechanism of gene expression regulation in mammals.

    The ideal candidate should have experience in bioinformatics and computer programming, especially NGS data analysis. Familiarity with public DNA/RNA sequencing data repository will be needed to study the distribution of genome-wide epigenetic elements and the correlation with gene expression control. The candidate must have the ability to define research questions and develop experiment designs to address those questions. The candidate should have experience presenting research results through publications and presentations.

    About the Department:
    The Institute for Health Informatics at the University of Minnesota is a well-balanced program with significant achievements in teaching, clinical programs and research. The University of Minnesota is one of the highest ranked public universities in research. The successful applicant will receive training in, and be expected to participate in the design, implementation and evaluation of experiments related to on-going NIH funded research. The University of Minnesota shall provide equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression.

    RESPONSIBILITIES

    • Develop research questions based on genome-wide distribution of epigenetic elements and the control mechanism of gene expression (20%)
    • Collect data (20%)
    • Analyze data (30%)
    • Write manuscripts for publications (15%)
    • Collaborative research projects (15%)

    REQUIREMENTS

    Minimum qualifications:
    • PhD in bioinformatics, computer science, mathematics, or related science field
    • Expertise in DNA/protein sequencing data, NGS data, genomics and epigenetic data analysis,
    • Excellent interpersonal skills and ability to work collaboratively with others.
    • Excellent oral and written communication skills
    Preferred qualifications:
    • Experience working gene expression profiling, DNA and histone methylation
    • Experience in genome wide DNA and histone marker discovery
    • Experience in machine learning technology
    • Experience statistical analysis of experimental data
    • Record of presenting research results through publications and conference abstracts

    HOW TO APPLY

    Applications must be submitted online (hr.myu.umn.edu/jobs/ext/326907), or search for Job ID # 326907 (hr.myu.umn.edu/psc/[...]eId=1). To be considered for this position, please click the Apply button and follow the instructions. You will be given the opportunity to complete an online application for the position and attach a cover letter and resume.

    Additional documents may be attached after application by accessing your "My Activities" page and uploading documents there.

    To request an accommodation during the application process, please e-mail madso009 at umn (dot) edu or employ at umn (dot) edu or call (612) 624-UOHR (8647).

    COMPENSATION

    $50K – 65K (commensurate with experience)

    POLICY

    Diversity:
    The University recognizes and values the importance of diversity and inclusion in enriching the employment experience of its employees and in supporting the academic mission. The University is committed to attracting and retaining employees with varying identities and backgrounds.

    The University of Minnesota provides equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression. To learn more about diversity at the U: diversity.umn.edu.

    Background Check Information:
    Any offer of employment is contingent upon the successful completion of a background check. Our presumption is that prospective employees are eligible to work here. Criminal convictions do not automatically disqualify finalists from employment.
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