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    BACKGROUND

    The laboratory of Dr. Shaun Mahony in the Biochemistry and Molecular Biology Department at Penn State is seeking a Computational Scientist to develop machine learning applications in the area of regulatory genomics. The primary focus of the Computational Scientist position is to contribute to the ongoing development of a scalable genome segmentation method that can characterize regulatory states using large collections of regulatory genomic datasets generated across many cell types. Developing and applying the computational analysis platform will be carried out in close collaboration with the laboratories of Dr. Ross Hardison and Dr. Frank Pugh. Prior experience developing machine learning applications and/or regulatory genomics analysis methods is preferred, but not required. Strong programming experience in a common language (such as Java, Python, C/C++, Perl, or R) is required, as is prior software development experience. Experience with Linux and git is strongly preferred. This is a fixed-term appointment funded for one year from date of hire with possibility of reappointment across multiple years

    RESPONSIBILITIES

    The successful candidate will be responsible for designing, developing, and testing software that performs integrative analyses across large collections of regulatory genomics datasets (i.e. ChIP-seq, ATAC-seq, etc). Specifcally, the project aims to scale up a machine learning platform that consistently characterizes regulatory states across different cell types in order to enable efficient application to large numbers of cell types. This project will be executed in collaboration with other Mahony lab members, and will also involve maintaining active collaborations with wet-lab biologists. The Computational Scientist will also have the opportunity to co-author research reports for presentation or publication, and to participate in other professional development opportunities.

    REQUIREMENTS

    Strong programming experience in a common language (such as Java, Python, C/C++, Perl, or R) is required. Prior software development experience is also required. Experience with Linux and git is strongly preferred. Prior experience developing machine learning applications and/or regulatory genomics analysis methods is preferred, but not required.

    LOCALE

    University Park, Pennsylvania, USA

    TERMS

    This position will be filled as a level 2 or 3, depending upon the successful candidate's competencies, education, and experience. A level 2 appointment typically requires a Bachelor's degree or higher in a field of study with focus on computational research methods plus two or more years of related experience, or an equivalent combination of education and experience. A level 3 appointment typically requires a Master's degree or higher in a field of study with focus on computational research methods plus four or more years of related experience, or an equivalent combination of education and experience.

    HOW TO APPLY

    Interested individuals should upload their curriculum vitae and a personal statement of background and interests to one of the following job postings:
    psu.jobs/job/82740 (level 2)
    psu.jobs/job/82742 (level 3)

    DEADLINE

    Review of applications will begin immediately and continue until the position is filled.

    POLICY

    Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status.

    OVERVIEW

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Knowledge Systems Group (KSG) at Dana-Farber Cancer Institute seeks a Bioinformatics Engineer to help build a new open-source software to enable precision cancer medicine. The Bioinformatics Engineer is an exceptional candidate who has both bioinformatics experience and extensive software engineering experience. We operate at the crossroads of cancer genomics and software, and are looking for that rare individual who has experience and passion for both. Our platforms are focused on mining of cancer genomic data sets, matching patients to clinical trials, and building cloud-based infrastructure for sharing of immunologic data.

    RESPONSIBILITIES

    • Design and develop software, databases and interfaces for analyzing and manipulating genomic and immunologic data, and matching patients to clinical trials.
    • Design and develop Application Programming Interfaces (APIs), microservices, and asynchronous queuing systems.
    • Orchestrate cloud-based services via modern devops frameworks.
    • Develop new Python software modules, developed via best practices, including unit testing, automated build processes and code reviews.
    • Design and develop cloud-based bioinformatic workflows, e.g. for whole exome sequencing and RNASeq data.
    • Implement bioinformatic workflows using workflow specification languages, e.g. WDL / CWL / Snakemake.
    • Work independently, and with external experts, to understand novel biological data types and help the software team with the implementation of them in our projects.

    REQUIREMENTS

    • Bachelor's or Master's Degree in Computer Science, Bioinformatics, Computational Biology or a related field
    • 2+ years of software engineering experience in the bioinformatics or cancer genomics space
    • Expert knowledge of Python
    • Expert knowledge of relational and non-relational databases, especially MongoDB
    • Strong interest in contributing to biological research with clinical applications
    • Experience in modern software development technologies, including distributed versioning systems, continuous integration, and Agile programming practices
    The candidate must demonstrate excellent communication skills, outstanding personal initiative and the ability to work effectively as part of a team. Ability to meet deadlines and efficiently multitask is a must.

    PREFERENCES

    Any of the following would be significant plusses: Experienced knowledge of Javascript and any modern Javascript library, especially React. Cloud computing experience, e.g. Amazon, Google Compute, or Digital Ocean. Any cloud devop framework experience, such as Kubernetes. User interaction design and data visualization. Experience with bioinformatics workflow software such as WDL / CWL and Snakemake.

    ABOUT US

    Check out our web site at: bcb.dfci.harvard.edu/knowledge-systems/

    HOW TO APPLY

    Apply here: www.Click2apply.net/9mj88ct53mdfq5g5

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI106933074

    OVERVIEW

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Department of Data Sciences within the Dana-Farber Cancer Institute is seeking a Team Lead, Bioinformatics Engineering.

    The Team Lead is an exceptional candidate who has deep software engineering experience and bioinformatics expertise, combined with proven team leadership experience. Candidate must have prior experience building scalable, cloud-based platforms for running and managing Next Generation Sequencing (NGS) pipelines, and must have prior experience managing a small team of bioinformatics engineers. This is an exciting opportunity that will impact thousands of patients across Dana-Farber and we need a creative leader, who can take our tumor profiling and precision oncology efforts to the next level.

    The team lead will be responsible for recruiting and managing a small team of bioinformatics engineers, to build new computational solutions for cancer genomics at DFCI. This includes a new cloud-based genomics platform for running and managing NGS pipelines. The lead will be responsible for selection of appropriate technological approaches, but we expect the successful candidate to drive the use of cloud-native solutions, with an emphasis on containerized workflows and a service-oriented architecture.

    RESPONSIBILITIES

    • Design and develop a new hybrid on-premise and cloud-based genomics platform for executing and managing NGS pipelines.
    • Design and develop Application Programming Interfaces (APIs), microservices, and asynchronous queuing systems.
    • Orchestrate cloud-based services via modern devops frameworks.
    • Develop new Python software modules, developed via best practices, including unit testing, automated build processes and code reviews.
    • Implement bioinformatic workflows using workflow specification languages, e.g. WDL / CWL / Snakemake.
    • Recruit and manage a small team of bioinformatics engineers.

    REQUIREMENTS

    • Bachelor's or Master's Degree in Computer Science, Bioinformatics, Computational Biology or a related field
    • Prior experience building scalable, cloud-based platforms for running and managing Next Generation Sequencing (NGS) pipelines
    • 5+ years of bioinformatics engineering experience in an academic or industry setting
    • 2-3 years experience managing a small team of bioinformatics engineers
    • Demonstrated ability to work in an agile, research environment while building production-grade software
    • Expert knowledge of Python
    • Prior experience building bioinformatic workflows using workflow specification languages, e.g. WDL / CWL / Snakemake
    • Experience in modern software development technologies, including distributed versioning systems, continuous integration, and Agile programming practices
    • Expert knowledge of relational and non-relational databases
    • Demonstrated ability to communicate and present technical ideas and plans to non-technical stakeholders

    HOW TO APPLY

    Apply Here: www.Click2apply.net/3hvq8wmfy3f9fwr2

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI106932834

    OVERVIEW

    A two-year Postdoc position is available in the Gorodkin lab (ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (rth.dk) at Department of Veterinary and Animal Sciences (ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. The Postdoc position concerns bioinformatics analyses of transcriptomic data from neurodegenerative diseases. The position is available from 1 March 2019 or as soon as possible thereafter.

    You will be a team player working with great excitement, and a key person in the project essential for obtaining successful results. The Postdoc position is part of the Indo-Danish NeuroStem project, which aims to discover RNA mediated regulation in neurodegeneration through stem cell models. The Postdoc will be interacting closely with the Group for Stem Cells and Embryology (ivh.ku.dk/engl[...]ells/). See neurostem.dk for details. The Neurostem project is supported by Innovation Fund Denmark. The project holds strong synergy to the BrainStem center: brainstem.dk.

    Background:
    The NeuroStem project aims at identifying the underlying neuronal pathology of causative genes and regulatory elements to obtain novel functional insight in Alzheimer's and Parkinson's diseases that can enable improved treatment. Transcripts will be extracted from neurons derived from iPSC, previously generated from patient skin fibroblasts. In cases where the patients carry specific disease-causing mutations, the iPSCs are gene corrected using CRISPR/Cas9 (isogenic control) allowing for strict comparisons of diseased and isogenic neuronal cells. In addition neurons from engineered healthy control iPSC, into which the genetic mutation is introduced, will be part of the analyses to circumvent the low numbers of samples due to rare mutations. Finally neurons from sporadic iPSC will be investigated to identify novel disease causative genes and pathways as well as validation of common pathways affected in both sporadic and familial forms of Alzheimer's disease.

    Job description:
    The project takes outset in differential expression analysis of transcripts between disease and gene edited and healthy control neurons. This involves detection and analysis of coding and noncoding transcripts as well as structured RNA and other regulatory elements. From the differential expression analysis, relevant pathways will further be included to obtain candidates for downstream functional analysis in terms of knock-out and knock-in experiments. In addition to transcriptome analysis and gene network methods in silico methods concerning structured RNA and RNA-RNA interactions will be can be incorporated in the integrated pipelines and relevant method development be included in the project.

    REQUIREMENTS

    The applicant should hold the professional as well as personal skills and qualifications as stated below:
    • A completed PhD degree in bioinformatics, computer science or in a similar area
    • General background knowledge of biological areas of genome structure and transcriptomes
    • Strong experience with script languages such as Perl or Python (or similar)
    • Strong experience with the Linux/Unix environment, command lines and shell scripting
    • Solid experience with transcriptome analysis
    • Good interpersonal skills
    • Excellent in English both in writing and speech

    PREFERENCES

    Candidates fulfilling one or more of the following qualifications will be prioritised:
    • Strong experiences with transcriptome data analysis
    • Algorithmic insight broad and for RNA (2D) structure
    • Experience with transcriptomic data from neurodegenerative diseases
    • Experience in at least one of the following programming languages: C, C++ or Java
    It is recommended that the applicant address the qualification requirements one by one in the cover letter.

    TERMS & COMPENSATION

    Salary and other terms and conditions of appointment are set in accordance with the Agreement between the Ministry of Finance and AC (Danish Confederation of Professional Associations) or other relevant professional organisations. The position is covered by the "Memorandum on Job Structure for Academic Staff at the Universities" of June 28, 2013.

    The gross basic salary range for Postdoctoral Fellows is DKK 33,766 to DKK 35,552 per month (level 6 to 8). To the basic salary a supplement could be negotiated, dependent on the candidate's experience and qualifications. An additional 17.1 % monthly contribution to pension will be paid by the employer. Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark for the last 10 years.

    The position is limited to a two-year period.

    LOCALE

    RTH is located on Frederiksberg Campus; however, as part of the NeuroStem project research visits to project partners will be a part of the Postdoc employment. Our research environment is highly international and stimulating. We frequently organise seminars, workshops, PhD summer schools with international speakers and have retreats with our international collaborators.

    ABOUT US

    Part of the International Alliance of Research Universities (IARU), and among Europe's top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

    HOW TO APPLY

    Apply by clicking "Apply online" below. Please note that only online applications will be accepted.

    Applications – in English – must include:
    • Cover letter detailing your motivation and background for applying for the specific Postdoc project
    • CV
    • Diploma and detailed transcripts of records
    • Other information for consideration, e.g. list of publications, peer reviewed and other
    • Personal Recommendations (if any)
    • A maximum of 3 relevant scientific works which the applicant wishes to be included in the assessment
    The deadline for applications is 10 February 2019. Any applications received after this time or incomplete will not be considered.

    Receipts of the applications will be acknowledged, and the applicant will be kept continuously informed of the progress of the application.

    The further process:

    Shortlist: After the expiry of the deadline for applications, the authorised recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at employment.ku.dk

    Assessment: The selected applications will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities and the University of Copenhagen's guidelines 2013. The Assessment Committee makes a non-prioritised assessment of the academic qualifications and experience with respect to the mentioned area of research, techniques, skills and other requirements listed in the advertisement.

    Please note that the applicant will be contacted if the assessment committee requires further documentation.

    Apply online: candidate.hr-manager.net/Appl[...]=true

    Questions: For further information about the scientific content of the position please contact Professor Jan Gorodkin, email gorodkin[at]sund.ku.dk, phone +45 23375667.

    POLICY

    The University of Copenhagen wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of personal background.

    DESCRIPTION

    Our lab is interested in transcriptome and epigenetic changes that occur in a time-dependent manner during pregnancy and how those can influence autoimmune disease. We are seeking a highly motivated and creative postdoctoral fellow to examine changes in coding and non-coding RNA patterns over time (based on RNA-seq data) in the context of human pregnancy and autoimmune disease. The successful applicant will perform original research in computational biology, assessing computational methods and developing/implementing analytical pipelines to infer underlying molecular mechanisms. He/She will take a lead in the project management, data analysis and interpretation of results within the context of the biological problem being investigated, and will collaborate with other team members. The ideal candidate is expected to report the scientific results by writing scientific papers and effectively communicate with peers. For more info, see www.chori.org/Prin[...].html.

    REQUIREMENTS

    Applicants must have a Ph.D. in bioinformatics, computational biology, statistics, human genetics or related field, and a sound understanding of biology, data science and statistical modeling. Must be proficient in statistical and programming languages such as R and Python, and familiar with Linux and high performance computing. Preference will be given to candidates with prior experience in analyses of RNA-seq data, other omics data, co-expression analyses, and with a thorough understanding of biological systems. Strong problem solving abilities and excellent verbal and written communication skills are required.

    HOW TO APPLY

    Please email cover letter, curriculum vitae, and the names and contact info of three references to: Damini Jawaheer, Ph.D. (djawaheer[at]chori.org).

    BACKGROUND

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Knowledge Systems Group (KSG) at Dana-Farber Cancer Institute seeks a Senior Software Engineer to help build open-source software to enable precision cancer medicine.

    The Senior Software Engineer is an exceptional candidate who, in addition to software experience has an interest in applying their skills to tackling problems in human health. We operate at the crossroads of cancer genomics, software, and medicine. Our platforms are focused on mining of cancer genomic data sets, matching patients to clinical trials, and building cloud-based infrastructure for sharing of immunologic data.

    RESPONSIBILITIES

    • Design and develop software, databases and interfaces for analyzing and manipulating genomic and immunologic data, and matching patients to clinical trials.
    • Work towards the paradigm of a microservices architecture where services communicate via APIs.
    • Orchestrate cloud-based services via modern devops frameworks.
    • Develop in Python while adhering to the best practices of automated testing at all steps and code reviews.
    • Build and maintain cloud based data processing workflows, incorporating open source tools for scheduling, monitoring and resource management.

    REQUIREMENTS

    • Bachelor's or Master's Degree in Computer Science or a related field
    • 4+ years of software engineering experience
    • 4+ years of Python coding experience
    • Working knowledge of relational and non-relational databases, especially MongoDB
    • Strong interest in contributing to biological research with clinical applications
    • Experience with containerization of software (Docker, Kubernetes, etc.)
    • Experience in modern software development technologies, including distributed versioning systems, continuous integration, and Agile programming practices
    • The candidate must demonstrate excellent communication skills, outstanding personal initiative and the ability to work effectively as part of a team. Ability to meet deadlines and efficiently multitask is a must.

    PREFERENCES

    Any of the following would be significant plusses: Experienced knowledge of Javascript and any modern Javascript library, especially React. Cloud computing experience, e.g. Amazon, Google Compute, or Digital Ocean. Any cloud devop framework experience, such as Kubernetes. User interaction design and data visualization.

    Apply Here: www.Click2apply.net/czqbgw8phnhvrnrf

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI106798437

    OVERVIEW

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Department of Data Sciences within the Dana-Farber Cancer Institute seeks a Director, NGS Bioinformatics to lead the development of Next Generation Sequencing (NGS) efforts for Profile, our institutional cancer sequencing platform. We are seeking an exceptional candidate who has deep experience in developing NGS methods, pipelines and experience leading a team of computational biologists. This is an exciting opportunity that impacts thousands of patients across Dana-Farber and we need a creative leader, who can take our tumor profiling and precision oncology efforts to the next level.

    RESPONSIBILITIES

    • Oversee the continued development of all institutional NGS cancer sequencing efforts, including targeted capture assays, RNA-seq, whole exome, whole genome and cfDNA.
    • Oversee the necessary validation, and QC associated with each of our NGS assays.
    • Oversee new bioinformatics analyses, including tumor mutational load analysis, viral signature detection, and improved methods for detecting structural rearrangements.
    • Recruit and manage a team of computational biologists, focused on NGS bioinformatics.
    • Interface with the Bioinformatics Platform Group, which will be developing a new scalable, cloud-based platform for running all NGS sequencing pipelines.
    • Interface with Clinical Genomics and Data Sharing Teams at DFCI, to ensure that results of NGS sequencing have maximal clinical and research impact.
    • Interface with faculty within the Department of Data Sciences to ensure the rapid adoption and integration of new NGS analysis algorithms.

    REQUIREMENTS

    • PhD (or equivalent) in computational biology, bioinformatics, or related fields
    • 10+ years of NGS bioinformatics experience in an academic or industry setting
    • Proven experience in building NGS methods and pipelines at an academic sequencing center or industry
    • Publication record in NGS and cancer genomics
    • Proven experience in leveraging best practices from the genomics community, e.g. GATK, Mutect, etc.
    • Proven experience in managing a team of computational biologists
    • Excellent interpersonal communication and writing skills
    • Excellent organization skills, including the ability to organize teams
    • Exceptional attention to detail
    • Strong leadership skills
    The candidate must also demonstrate outstanding personal initiative, work effectively as part of a team, meet deadlines, and efficiently multitask.

    HOW TO APPLY

    For consideration, please submit a cover letter and resume.

    Apply Here: www.Click2apply.net/rt2ck933z3wfhbtf

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI106797186

    Submitter

    BACKGROUND

    Bioinformatics, Permanent, Central London!

    Paramount are working in partnership with Genomics England to help expand their team – after successfully completing the 100,000 Genomes Project recently they are working together with the NHS to launch the World's First Genomic Medicine Service. This will transform the way patients are cared for in the future.

    A fantastic position has become available in their Production team for a Bioinformatics Operations Manager to ensure smooth operation of the bioinformatics pipeline in accordance with ISO 15189 standards, supporting formulation, implementation and delivery of the bioinformatics operating strategy.

    This role would be ideal for a candidate with extensive bioinformatics experience who has some team leadership skills as well.

    RESPONSIBILITIES

    You will be accountable for the optimal day-to-day running of the results pipeline, updating senior and external stakeholders on pipeline status, reporting to the quality team and being accountable for facilitating problem resolution and continuous improvements.

    Your main responsibilities will involve:
    • Leading a team specialised in operating the bioinformatics pipelines and clinical interpretation to ensure smooth processing and return of results to the NHS
    • Monitoring delivery and conducting operational trouble shooting using bioinformatics tools and implementing varied and sustainable continuous improvements that drive successful KPI delivery
    • Constantly reviewing and seeking to improve operational performance and efficiency, meeting both current and future bioinformatics business requirements
    • Interfacing with operations teams within other functions across Genomics England
    • Ensuring the reporting of the pipeline status is up-to-date
    • Working to continuously improve operational processes and promoting a quality
    • Deputising for the Head of Production as required

    REQUIREMENTS

    The ideal Bioinformatics Operations Manager should fulfil the following criteria:
    • Knowledge of working within an ISO accredited lab (essential)
    • Experience running operations in a large company or laboratory, preferably within IT (essential)
    • Solid skills set in Bioinformatics (essential)
    • Strong record of leadership of multiple stakeholder groups while under tight timelines
    • Solid expertise of using continuous improvement methods in an operational setting to achieve operational objectives
    • Data management, operational and scientific problem-solving skills
    • Must have demonstrated excellent ability to interface with customers and internal teams
    • Knowledge of JIRA and Confluence desirable, as well as exposure to Lean processing
    In return you will receive a competitive salary and work in a fantastic location, with the opportunity to contribute the creation of a new Genomic Medicine Service now that the 100,000 Genomes Project has been completed. This would be a perfect opportunity for someone who is looking for a new challenge, and has several years' experience in Bioinformatics (with managerial and operations experience).

    HOW TO APPLY

    Only candidates who are eligible to work in UK (UK/EU passport and/or indefinite leave to remain) will be considered.

    If you're interested in the role and think you could be a good fit, please apply and send your up-to-date CV to Anna (alauterjung[at]pararecruit.com; +44 121 616 3469).

    Keywords: Bioinformatics, Operations, Manager, ISO, laboratory, pipeline, stakeholder, operating strategy, quality, clinical interpretation, troubleshooting, SOP, Standard Operating Procedure, Genomics, production, ISO 15189, London, 100,000 Genomes Project, UK

    BACKGROUND

    We seek a highly motivated individual with a track-record of statistical models and/or computational tools development dedicated to the analysis of high throughput sequencing data, comparative genomics, functional genomics, or a related field. We are looking for applicants excited about combining life sciences and computation to analyze gene expression regulation. The successful candidate will be collaborative, independent, with strong enthusiasm for research, and should have experience in programming (mainly Python, R, and bash) dedicated to the analysis of large-scale genomics data with a strong publication record. Being familiar with gene expression regulation in general, DNA methylation, and TF binding is an advantage.

    The appointment is a full-time position and is made for a period of up to three years

    The main purpose of the fellowship is to qualify researchers for work in higher academic positions within their disciplines.

    RESPONSIBILITIES

    The candidate will be expected to establish her/his independent research topic within the scope of the group's research interests.

    REQUIREMENTS

    • Applicants must hold a degree equivalent to a Norwegian doctoral degree in computational biology, bioinformatics, biostatistics, computer science, or a related field. Doctoral dissertation must be submitted for evaluation by the closing date. Appointment is dependent on the public defence of the doctoral thesis being approved.
    • Strong publication records (including 1st authorship) with evidence for writing scientific manuscripts independently
    • Proficiency in programming (Python, R, bash)
    • Ability to collaborate with researchers from different fields and at different career stages
    • Willingness to be part of a team to share knowledge and skills
    • Documented ability to communicate science
    • Knowledge of eukaryotic gene expression regulation
    • Knowledge of molecular biology
    • Experience with analysis of genomics data sets
    • High drive for science and desire to become an independent researcher
    • Fluent oral and written communication skills in English

    HOW TO APPLY

    The application must include:
    • A cover letter (outlining motivation, career goals, past achievements, summarizing scientific work and research interest)
    • A short research project proposal if available (max. 2 pages)
    • A CV (summarizing education, positions, and other qualifying activity)
    • Copies of educational certificates (academic transcripts only) a complete list of publications
    • List of reference persons: 2-3 references (name, relation to candidate, e-mail and phone number)
    The application with attachments must be delivered in our electronic recruiting system at www.jobbnorge.no/en/a[...]ation.

    Foreign applicants are advised to attach an explanation of their University's grading system. Please note that all documents should be in English.

    In assessing the applications, special emphasis will be placed on the documented, academic qualifications, the project proposal, and the quality of the project as well as the candidates motivation and personal suitability. Interviews with the best qualified candidates will be arranged.

    It is expected that the successful candidate will be able to complete the project in the course of the period of employment.

    Submitter

    BACKGROUND

    A world renowned institute in Boston are looking for a new Bioinformatics Engineer to join an applied genomics software and data sciences group, focused on enabling cancer genomics research and precision cancer medicine. This role will help to build a new open-source software to enable precision cancer medicine.

    The long-term goal is to work with multiple cancer centers to build one of the most comprehensive knowledgebases of genomic data integrated with detailed clinical data. This company hire talented clinicians and researchers in the mission of conquering cancer, HIV/AIDS and related diseases. Working with amazing partners and the best technologies, this is a fantastic group to be a part of.

    To take on this Bioinformatics Engineer position you should have both bioinformatics experience and extensive software engineering experience.

    RESPONSIBILITIES

    You will be working with platforms that are focused on mining of cancer genomic data sets. Additional responsibilities include:
    • Designing and developing software, databases and interfaces for analyzing and manipulating genomic data, and matching patients to clinical trials
    • Designing cloud-based bioinformatic workflows, e.g. for whole exome sequencing and RNASeq data
    • Design and develop Application Programming Interfaces (APIs), microservices, and asynchronous queuing systems
    • Arranging cloud-based services via modern dev-ops frameworks
    • Developing Python software modules, developed via best practices, including unit testing, automated build processes and code reviews

    REQUIREMENTS

    Experience required:
    • Bachelor's or Master's Degree in Computer Science, Bioinformatics, Computational Biology
    • 2+ years of software engineering experience in the bioinformatics or cancer genomics space
    • Expert knowledge of Python
    • Expert knowledge of relational and non-relational databases, such as MongoDB
    • Strong interest in contributing to biological research with clinical applications
    • Experience in modern software development technologies, including distributed versioning systems, continuous integration, and Agile programming practices
    • Excellent communication skills, and ability to work to deadlines

    HOW TO APPLY

    This position is available immediately and I would love to hear from you if you are interested. Please apply to this advert or sending through your resume to jpage[at]pararecruit.com

    Keywords: Bioinformatics Engineer, Precision Medicine, Cancer Genomics, Software Engineering, Bioinformatician, Python, Boston

    DESCRIPTION

    Computational and Systems biology group at the University of Nebraska (Lincoln, Nebraska, USA) is looking for a quantitatively trained and highly motivated post-doctoral researcher to expand and validate a virtual immune system: a mechanistic, multi-scale, and multi-cellular model of the immune system. In the model, immune cells are represented as discrete and autonomous entities in an agent-based framework in various compartments, while the extracellular environment is described as continuous concentrations by ordinary differential equations. Each cell is also modeled at additional molecular scales to capture the dynamics at the level of metabolism, gene regulation, and signal transduction, using various mathematical and computational approaches. In addition to life sciences research, we also develop technologies (such as Cell Collective) to make computational systems biology broadly accessible to users with varying computational background. More information about our group at helikarlab.org.

    The researcher will work in collaboration with other members of the group, and will have the opportunity to work on multiple projects in an international and a highly interdisciplinary setting with laboratory scientists, computer scientists, engineers, and mathematicians.

    REQUIREMENTS

    • PhD in a quantitative subject such as computational biology, bioinformatics, engineering, mathematics, physics, and computer science, or equivalent
    • Deep understanding of immunology
    • Mastery of modeling frameworks (at least one of differential equations, agent-based modeling, logical modeling, and constraint-based modeling) and their use in multi-scale modeling of complex biological systems
    • Strong expertise in parametric estimation
    • Computational and programming competence (e.g., C++, MATLAB, and LINUX)

    PREFERENCES

    • Strong biology background (e.g., metabolism, signal transduction, immunology, host-pathogen interactions)
    • Experience with extracting and manipulating large datasets from various databases, and integration of these data with predictive computational models
    • Experience with statistics and machine learning, especially in the context of multi-omics
    • Experience collaborating with wet-lab researchers

    TERMS

    The start date is immediate (but flexible depending on mutual agreement), and the position is open until filled. This position is for one year, with possibility to extend, pending performance review.

    LOCALE

    Lincoln, Nebraska, USA

    COMPENSATION

    Commensurate with experience.

    HOW TO APPLY

    If interested, please send a cover letter, CV, and contact information for three references to Dr. Tomas Helikar at thelikar2 at unl dot edu.

    DEADLINE

    February 15th. However, applications will be reviewed as they are received. So send yours in to ensure consideration for the position.

    POLICY

    The University of Nebraska has an active National Science Foundation ADVANCE gender equity program, and is committed to a pluralistic campus community through affirmative action, equal opportunity, work-life balance, and dual careers.

    DESCRIPTION

    The Wisconsin Institute for Discovery (WID) and the Department of Biostatistics and Medical Informatics (BMI) at the University of Wisconsin-Madison seek a tenure track assistant/associate/full professor whose research focuses on machine learning, or related areas of data science, to start in Fall 2019. We seek candidates with experience or a demonstrated interest in both machine learning algorithm development and collaborative applications of machine learning to biological problems, especially motivating methodological research through biological, clinical, and/or public health sciences applications.

    The Wisconsin Institute for Discovery provides a vibrant environment for interdisciplinary research. The Institute is dedicated to pushing the boundaries of fields to foster discovery and offers its researchers many opportunities and support for collaborative work with other Institute scientists and the rest of the UW-Madison campus.

    The University of Wisconsin-Madison is a world-class academic institution with an international reputation for basic, applied, and interdisciplinary research. UW- Madison regularly ranks in the top 10 or 12 among U.S. public universities, and regularly surpasses $1 billion in annual research expenditures. Madison provides a vibrant, culturally rich environment highly ranked in national surveys for quality of life. The BMI Department also provides an exceptional environment for academic activity and interdisciplinary collaboration. BMI faculty collaborate with scientists across UW and the State, including the Institute for Clinical and Translational Research, the UW Carbone Cancer Center, the Marshfield Clinic Research Foundation, the Wisconsin Institute for Discovery, and the Morgridge Institute for Research. BMI maintains strong ties to the world-class Departments of Computer Sciences and of Statistics, through which most of its PhD students have traditionally been trained. BMI is also home to a new PhD program in Biomedical Data Science.

    HOW TO APPLY

    Please see: go.wisc.edu/machine-learning for application procedures.

    DEADLINE

    To ensure full consideration, applications must be received by February 15, 2018.

    POLICY

    WID and BMI are committed to building diversity in our department and more broadly. We especially encourage female applicants and those from underrepresented minorities, and we are committed to the professional development and success of such individuals throughout their career.

    AA/EOE.

    Unless confidentiality is requested in writing, information regarding the applicants must be released upon request. Finalists cannot be guaranteed confidentiality.

    BACKGROUND

    EMBL is an international research organization covering many fields of modern biology. Five Computational Centres provide expertise, advice, and training for scientists across EMBL. We are looking for a statistician or data scientist to Head the EMBL Centre for Statistical Data Analysis.

    RESPONSIBILITIES

    • Statistical consulting for EMBL researchers
    • Teaching short courses on computational statistics / data science in biology
    • Collaboration on selected research projects with EMBL research groups
    As statistician/data scientist, you will be interested in statistical applications in modern biology, in computational method development for new technologies (single cell `omics, imaging, proteomics, microfluidics), in data visualization and data integration, and in method benchmarking and teaching. You will be co-affiliated with the research group of Wolfgang Huber (see www.huber.embl.de).

    The position also offers the opportunity to help shape future developments of `data science' in biology, such as publication and communication best practices.

    REQUIREMENTS

    A PhD or equivalent qualification in a quantitative science (statistics, mathematics, computer science, physics) with solid theoretical foundations in probability and applied statistics and some experience in data analysis of modern biological data. As our ideal candidate you should enjoy teamwork and be excited by providing consulting and teaching services at an advanced level in a world-class research environment. Excellent communication skills in written and spoken English are required.

    Candidates should have a solid understanding of programming concepts and multiple languages, including advanced R. Proficiency with scientific authoring frameworks such as LaTeX, Rmarkdown and HTML5 is a plus.

    TERMS

    3 years (renewable)

    LOCALE

    Heidelberg, Germany

    COMPENSATION

    Depending on experience and qualifications

    HOW TO APPLY

    Please visit www.embl.de/jobs[...]%5d=1

    DEADLINE

    10 March 2019

    RESPONSIBILITIES

    The candidate is expected to work on a variety of projects related to analysis of data from NGS, Mass Spectrometry, Flow Cytometry and other related modalities. The position expects hands-on work and a strong eye for detail. The candidate will be able to contribute to impactful work spanning patient care, clinical research, and new assay and method development.

    REQUIREMENTS

    A PhD in a quantitative field (statistics, math, bioinformatics, computer science, physics or similar) and work experience or post-doc experience handling high throughout genomics data.

    PREFERENCES

    Experience in working in inter-disciplinary groups and ability to author research publications are additional desired qualities.

    LOCALE

    The position is in Bangalore and reports to the Chief Scientific Officer.

    HOW TO APPLY

    Write to ramesh[at]strandls.com.

    Submitter

    BACKGROUND

    The CPRIT-funded UTHealth Cancer Genomics Core (CGC) at the University of Texas Health Science Center at Houston (UTHealth) has a non-tenure track Research Scientist position in the areas of human genetics.

    UTHealth is in the world-renowned Texas Medical Center (TMC) located in cosmopolitan Houston, Texas, the fourth largest city in the United States.The CGC core aims to provide next-generation sequencing (NGS) and advanced bioinformatics services to the cancer investigators in UTHealth, Texas Medical Center, and other Texas regions.

    RESPONSIBILITIES

    Design and conduct research in the area of complex disease genetics and next-generation sequencing based studies. The primary responsibilities include development of protocols for the library preparation and sequencing, instrument operation and maintenance, problem solving, training and supervising the laboratory technician, providing support and training of genome technologies and bioinformatics analysis to cancer and other investigators through UTHealth Cancer Genomics Core, assisting grant proposal development and manuscript writing

    REQUIREMENTS

    • Doctorate Degree. Two years of research experience in human genetics studies or related, and have verifiable publications within the field of the research project
    • Good knowledge in NGS platforms.Strong attention to detail, accuracy, scientific professionalism, and deadlines. Excellent communication skills both written and verbal
    • At least be familiar with one computer programming, excellent knowledge and skills in genomic technologies and genomic data analysis. Previous publication in genomics or bioinformatics

    LOCALE

    Houston, Texas

    COMPENSATION

    By experience

    HOW TO APPLY

    Apply at uth.taleo.net/care[...]ailto or at uth.referrals.selectminds.com/jobs/search/ and search keywords by 1800028Q for this position. Please feel free to send an email to zhongming.zhao[at]uth.tmc.edu to inquire any information.

    DEADLINE

    Open until the position is filled
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