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  • Career Center - Summary

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    BACKGROUND

    About us: OSTHUS is a leader in Scientific Informatics. Our customers are the top companies in the pharmaceutical, bioinformatics and life science industries. With sites in Europe, the US and Asia, we offer a modern, exciting and attractive working environment. Using state-of-the-art methods and technologies, we work on future-oriented projects in the areas of Big Data, Machine Learning and AI. Personal development, innovation and diversity are of great importance to us as well as to our customers and employees.

    RESPONSIBILITIES

    • Data architecture consulting at the interface between science and information technology
    • Working in demanding project environments at leading national and international companies in the life science sector
    • Leading role in the development and definition of digital data and information architectures.
    • Development, advice, and implementation of data integration solutions according to customer requirements
    • Providing leadership in the implementation of data-centric solutions taking into account modern cloud, semantic and database technologies
    • Expansion and strengthening of our partner and academic network
    • Support in establishing and intensifying our customer relationships

    REQUIREMENTS

    • Completed studies in computer science, chemical, medicinal or bioinformatics (PhD is an advantage)
    • At least 6 years of professional experience in the field of data or information architecture consulting or knowledge management
    • Experience in the pharmaceutical or chemical industry
    • Sound knowledge and experience with common SQL and NoSQL database technologies
    • Experience with one or more of the following topics: data modeling, metadata management, or semantic data management (RDF, triple stores, graphs)
    • Knowledge of ontologies and terminologies commonly used in the chemical industry and the life science sector
    • High customer orientation, strong communication skills and a confident manner
    • Very good spoken and written German and English skills
    • Limited willingness to travel

    COMPENSATION

    Your benefits:
    • Diverse portfolio of tailored training and professional and personal development measures offered by our in-house Academy
    • The possibility to acquire a job bike
    • Joint breakfast on Friday
    • Attractive salary extra: ticket plus card
    • Positive working culture including regular social activities
    • ...and much more!

    HOW TO APPLY

    E-Mail your résumé, your salary expectations and your desired starting date to career[at]osthus.com. Refer to "Senior Consultant Information Architecture (m/f/d)" in the subject line.

    Your personal contact: Ivonne Braun

    OSTHUS GmbH
    Eisenbahnweg 9-11
    52068 Aachen

    BACKGROUND

    About us: OSTHUS is a leader in Scientific Informatics. Our customers are the top companies in the pharmaceutical, bioinformatics and life science industries. With sites in Europe, the US and Asia, we offer a modern, exciting and attractive working environment. Using state-of-the-art methods and technologies, we work on future-oriented projects in the areas of Big Data, Machine Learning and AI. Personal development, innovation and diversity are of great importance to us as well as to our customers and employees.

    RESPONSIBILITIES

    • Management and implementation of complex cloud transformation programs in the environment of leading pharmaceutical and chemical companies
    • Impact analysis of the effects of cloud technologies on business organizations
    • Development of cloud architecture and technology strategies in intensive exchange with customers
    • Technology-agnostic consulting with a focus on the development of value-adding solutions
    • Digital architecture management for digital transformation and new business or process models
    • Support in establishing and intensifying customer relationships

    REQUIREMENTS

    • Completed studies in computer science, informatics or natural sciences with computer science as a minor
    • At least 6 years of professional experience in consulting
    • Good knowledge in cloud transformation, cloud-based architecture and enterprise architecture
    • Relevant certifications like TOGAF, IAS or similar is an advantage
    • Sound knowledge of common cloud technologies such as MS Azure, AWS or Oracle Cloud
    • Knowledge or experience with marketable, cloud-based solutions in the laboratory and life science informatics environment
    • High customer orientation, strong communication skills and a confident manner
    • Very good spoken and written German and English skills
    • Limited willingness to travel

    COMPENSATION

    Your benefits:
    • Diverse portfolio of tailored training and professional and personal development measures offered by our in-house Academy
    • The possibility to acquire a job bike
    • Joint breakfast on Friday
    • Attractive salary extra: ticket plus card
    • Positive working culture including regular social activities
    • ...and much more!

    HOW TO APPLY

    E-Mail your résumé, your salary expectations and your desired starting date to career[at]osthus.com. Refer to "Senior Cloud Consultant (m/f/d)" in the subject line.

    Your personal contact: Ivonne Braun

    OSTHUS GmbH
    Eisenbahnweg 9-11
    52068 Aachen

    DESCRIPTION

    The Molecular Characterization Laboratory (MoCha) is part of Leidos Biomedical Research's Clinical Research Directorate (CRD) at the Frederick National Laboratory for Cancer Research. The MoCha Laboratory is responsible for providing high-level research in support of the NCI-Cancer Diagnostics Program (CDP) within the Division of Cancer Treatment and Diagnosis (DCTD). MoCha's major activities include development and application of genomic assay platforms for use in DCTD-sponsored national clinical trials and preclinical studies.

    This position is essential to the success of MoCha and on-site presence in Frederick, MD and occasionally in Shady Grove (Rockville, MD) is required.

    RESPONSIBILITIES

    The Bioinformatics Analyst IV serves as the technical authority on computational issues related to the assigned projects/programs.

    Duties include:
    • Validate and maintain genomic analysis pipelines for exome, whole genome and RNA-seq data generated from the mocha lab and/or collaborator(s) and help provide biological interpretation of the genomic analysis to advance the understanding of cancer
    • Responsible for the organization and management of large genomic datasets, and the integration of data from multiple sources
    • Supervise and collaborate with other bioinformatics team members to ensure the quality of work and the prioritization of projects to meet deadlines
    • Interacts with management to define strategies for genomic data analysis including hypothesis generation and testing of predictive biomarkers of drug response
    • Interacts extensively with intramural laboratories at the NIH and extramural scientists
    • Responsible for generating scientific opinions, identifying potential resources or constraints, and proposing strategies for exploiting available databases and program data generated at the molecular and cellular levels

    REQUIREMENTS

    • Possession of a Bachelor's degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in a related field (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency.
    • In addition to the education requirements, a minimum of eight (8) years of related computational experience in a biological/medical research laboratory environment with a strong background in bioinformatics application development is required
    • Must possess experience in analysis of next generation sequencing (NGS) data (including quality metrics, mapping, variant calling, quantitation of gene expression and biological interpretation)
    • Experience in analysis of large genomic data sets including integration with data available from public or private sources
    • Hands-on experience in data processing and analyzing sequencing and expression and other array data including quality and biological assessment are also essential
    • Experience in a computer cluster environment is required
    • Proficiency in bash shell scripting and in one or more of the programming languages such as R, C/C++, PYTHON, PERL, JAVA, SQL and bioinformatics tools and database management is essential
    • Must be proficient in several genomic data analysis tools such as GATK, Samtools etc., as well as biological pathway/functional analysis
    • Expertise in statistical analysis of complex biological data is critical to success
    • Experience and demonstrated success in a team-oriented environment and excellent communication skills (written and oral) are also required
    • Ability to identify and solve complex problems. Proven knowledge of cancer biology demonstrated through peer reviewed publications is required
    • Must be able to obtain and maintain a security clearance

    PREFERENCES

    • Experience in algorithm development for NGS data analysis. In-depth understanding of molecular biology techniques, oncology and clinical research
    • Experience in data integration, database construction, application development and visualization
    • Experience in porting applications to a web environment and working with workflow tools and applications are also desired

    HOW TO APPLY

    Please apply at the following link: leidosbiomed.csod.com/ats/[...]d=914.

    POLICY

    Equal Opportunity Employer (EOE) | Minority/Female/Disabled/Veteran (M/F/D/V) | Drug Free Workplace (DFW)

    DESCRIPTION

    Within Leidos Biomedical Research Inc., the Clinical Monitoring Research Program Directorate (CMRPD) provides high-quality comprehensive and strategic operational support to the high-profile domestic and international clinical research initiatives of the National Cancer Institute (NCI), National Institute of Allergy and Infectious Diseases (NIAID), Clinical Center (CC), National Heart, Lung and Blood Institute (NHLBI), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Center for Advancing Translational Sciences (NCATS), National Institute of Neurological Disorders and Stroke (NINDS), and the National Institute of Mental Health (NIMH). Since its inception in 2001, CMRPD's ability to provide rapid responses, high-quality solutions, and to recruit and retain experts with a variety of backgrounds to meet the growing research portfolios of NCI, NIAID, CC, NHLBI, NIAMS, NCATS, NINDS, and NIMH has led to the considerable expansion of the program and its repertoire of support services. CMRPD's support services are strategically aligned with the program's mission to provide comprehensive, dedicated support to assist National Institutes of Health (NIH) researchers in providing the highest quality of clinical research in compliance with applicable regulations and guidelines, maintaining data integrity, and protecting human subjects. For the scientific advancement of clinical research, CMRPD services include comprehensive clinical trials monitoring, regulatory, pharmacovigilance, protocol navigation and development, and programmatic and project management support for facilitating the conduct of 400+ Phase I, II, and III domestic and international trials on a yearly basis. These trials investigate the prevention, diagnosis, treatment of, and therapies for cancer, influenza, HIV, and other infectious diseases and viruses such as hepatitis C, tuberculosis, malaria, and Ebola virus; heart, lung, and blood diseases and conditions; parasitic infections; rheumatic and inflammatory diseases; and rare and neglected diseases. CMRPD's collaborative approach to clinical research and the expertise and dedication of staff to the continuation and success of the program's mission has contributed to improving the overall standards of public health on a global scale.

    The Clinical Monitoring Research Program Directorate (CMRPD) provides bioinformatic support to the National Cancer Institute's (NCI's), Center for Cancer Research (CCR), Surgery Branch (SB).

    RESPONSIBILITIES

    • Works closely with the staff to develop and support the application of software tools needed for the analysis of complex datasets derived from high-throughput whole genome, whole exome, and RNA-seq analysis of tumor and T cell populations
    • Provides detailed analysis of complex datasets and provide summaries to SB Senior Investigators, post-doctoral fellows, and clinical fellows as needed
    • Works with the Principal Investigators to set goals, devise specific plans, and periodically review progress in projects to assist in the research and development of novel targeted immunotherapies
    • Focuses on generating and optimizing software tools used for the analysis of complex datasets derived from analysis of patient tumor and peripheral blood samples
    • Develops and optimizes a sequencing pipeline used to identify mutated T cell epitopes along with a variety of other software tools for analyzing high throughput sequencing data
    • Maintains expert knowledge of scientific principals and concepts, new and emerging computational methods and technologies and medical imaging principals
    • Initiates and prepares new research plans, proposals or methodologies
    • Develops new methods and validates the reliability of the methodology
    • Develops data triage and quality control evaluations for complex level assignments
    • Responsible for development and implementation of Standard Operating Procedures
    • Develops formal reporting of data utilized in presentations and/or publications
    • Conduct presentations of data at seminars and meetings
    • May supervisor lower level technical staff
    • This position is located in Bethesda, Maryland

    REQUIREMENTS

    • Possession of a Bachelor's degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in biomedical science/bioinformatics/math/computer related field (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency.
    • In addition to the education requirements, a minimum of eight (8) years of progressively responsible relevant experience
    • Strong background in Bioinformatics
    • Demonstrates proficiency coding in either R or Python
    • Experience with relevant scientific software applications such as Varscan and Annovar that are used for the analysis of high throughput sequencing results in order to optimize a pipeline used to identify somatic mutations that encode epitopes recognized by tumor-reactive T cells.
    • Proficiency with software packages such as Partek, which contains a variety of statistical tools for analyzing complex cell populations, including hierarchical clustering tools that will facilitate the classification of cells based upon gene expression patterns, gene ontology enrichment tools to group genes on the basis of their molecular function, and a chromosomal viewer that facilitates the visualization of chromosomal mapping data and copy number variation
    • Experience with working in a cGMP-like environment, which is needed to carry out studies that are relevant to patient treatments
    • Must be able to obtain and maintain a security clearance

    PREFERENCES

    • Master's degree preferred
    • Basic knowledge and a degree in Computer Science
    • Experience with molecular biology techniques, clinical research and project management
    • Experience with next-generation sequence analysis
    • Proficiency in a variety of bioinformatics analysis tools
    • Excellent presentation skills that include written, oral communication
    • Experience with a variety of analysis tools that include Tophat, Samtools, Varscan and Annovar
    • Experience performing expression analysis
    • Experience working with single cell data
    • Familiarity with methods for T cell receptor sequence analysis

    HOW TO APPLY

    Please apply to the following link: leidosbiomed.csod.com/ats/[...]d=944.

    POLICY

    Equal Opportunity Employer (EOE) | Minority/Female/Disabled/Veteran (M/F/D/V) | Drug Free Workplace (DFW)

    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.

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