Research Scientist Requirements:
- Ph. D in Bioinformatics, Biophysics, Biochemistry, CS, ECE or related field. Alternative degree fields will be considered if accompanied by equivalent experience as it relates to current NCSA projects.
- 1-3 years of experience in biological computing, such as genomics, transcriptomics, phylogeny, molecular modeling, computer simulation of biological processes, etc.
- Experience documenting projects, research effort and codes.
Senior Research Scientist Requirements:
- Ph. D. degree in Bioinformatics, Biophysics, Biochemistry, CS, ECE or related field. Alternative degree fields will be considered if accompanied by equivalent experience as it relates to current NCSA projects.
- 4-6 years of experience in biological computing, such as genomics, transcriptomics, phylogeny, molecular modeling, computer simulation of biological processes, etc.
- Experience with Bash, Linux command line, Python/Perl/R.
- Experience documenting projects, research effort and codes.
- Experience contributing to research articles and grant proposals.
- Ph.D. or BA/MS+3-5 years post graduate experience in Bioinformatics, Biochemistry, or related field; or in Computer Science with a focus on biological or pharmaceutical sciences.
- Background in molecular biology, biochemistry, or a related field ideally with an understanding of basic biotherapeutic discovery.
Applicants should hold a doctoral degree in Biomedical sciences, Pathology, Computer Sciences, Statistics, Engineering or related field. Preferred (but not required): working experience in AI, machine learning, predictive modeling, imaging analysis or digital pathology. Appointment rank will be commensurate with academic accomplishments and experience.
- MSc and PhD in bioinformatics, geobiology, molecular microbiology, geoecology or equivalent in all cases with a strong computational focus
- Specialized knowledge in next-generation sequencing data evaluation – ideally with a focus on eukaryotes
- Documented record in developing and applying bioinformatic algorithms and pipelines to complex environmental samples
- Capacity for interdisciplinary and international teamwork and excellent communication skills
- Documentable excellent publication and 3rd party funding records
- Polar fieldwork is a part of the project, so willingness / experience in outdoor activities is a bonus
- Proficiency in spoken and written English, German is an asset
- Ph.D. in Bioinformatics or Computational Biology. Postdoctoral experience in Bioinformatics, and or Computational Genomics. Experience teaching Introductory as well as advanced Bioinformatics Programming (Python and R) courses in the field, is preferred. Ph.D. in Bioinformatics, Computational Biology or related field(s).
- Strong research profile in Bioinformatics, with a focus on computational genomics and Next-Generation sequencing.
- Excellent Bioinformatics Programming skills in Python and R, as shown by quality publications and articles in the top journals.
- Excellent communication and interpersonal skills, and demonstrated ability to work in teams.
- Capable of establishing collaborative research programs involving undergraduate students. Evidence of experience spearheading or participating in experiential learning models a plus.
- Experience working with various stakeholders, such as students, faculty, staff, and administrators.
- Experience working with underrepresented minorities in STEM.
- 5-7 years of working experience.
- Demonstrated experience 3+ years in non-profit program management, preferably for a health or disease-focused organization, with experience planning and implementing targeted community engagement initiatives, supporting clinical trials recruitment, and/or other research/scientific projects management.
- At least 2 years, preferably 5, demonstrated supervisory experience, especially in supervising remote staff.
- Excellent interpersonal and communications (writing and speaking) skills. Comfortable working with a range of stakeholders; ability to build trust and relationships with partners. Ability to communicate complex ideas in a clear and straightforward manner, particularly for general audiences.
- Self-starter willing and able to take responsibility and ownership for producing timely and high-quality work with limited supervision. Ability to deconstruct complex problems and develop actionable plans.
- A team-oriented attitude, strong cross-functional collaboration skills and proven ability to work in a matrixed, global organization. Strong supervisory skills, especially in supervising remote staff.
- Strong organizational and project management skills; detail oriented. Proven ability to manage a large, complex workflow with multiple deadlines, data points, and priorities.
- High degree of professionalism, maturity, executive presence, business understanding, cultural awareness, and sensitivity to relationships, security, and confidentiality.
Education: Master’s Degree: Business Administration, Life Sciences, Data Science and/or Public Health
|DESCRIPTIONThe Department of Data Science within the Dana-Farber Cancer Institute is seeking a Team Lead, Bioinformatics Engineering for our Trial Matching Platform. The Team Lead is an exceptional candidate who has deep software engineering experience and cancer bioinformatics expertise, combined with proven team leadership experience. Candidates must have prior experience building data pipelines and software utilizing genomics data. Must have some exposure to management of engineers. This is an exciting opportunity that will impact thousands of patients across Dana-Farber and we need a creative leader who can help us drive precision oncology forward.|
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 cancer clinical trial matching system which recommends precision medicine clinical trials for patients. The lead will be responsible for learning existing technologies, improving the technologies when necessary and helping deliver new features and related products. The candidate will eventually lead the engineering efforts of multiple projects.RESPONSIBILITIESLearn, improve, and develop new features for precision medicine clinical trial matching software.Design, develop and maintain Application Programming Interfaces (APIs), microservices, and asynchronous queuing systems.Develop new and migrate legacy software to more modern devops frameworks.Develop new Python software modules, developed via best practices, including unit testing, automated build processes and code reviews.Recruit and manage a small team of bioinformatics engineers.REQUIREMENTSBachelor’s or master’s degree in Computer Science, Bioinformatics, Computational Biology or a related field.Prior experience building applications with genomics data.Experience with AI / ML is a bonus.3+ years of bioinformatics engineering experience in an academic or industry setting.1-3 years’ experience managing a small team of bioinformatics engineers.Expert knowledge of Python.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.
|BACKGROUNDAt the EMBL Hamburg Unit, we are seeking to recruit an experienced and highly motivated software engineer to develop, implement and provide new computational methods for structural modeling of large macromolecular complexes.|
The research at our Unit covers structural studies of large protein complexes using X-ray-based techniques, electron microscopy, and computational modeling. The recent AI-based modeling methods such as AlphaFold and RoseTTAfold have begun a new era in structural biology, in which accurate structural models can be built for many proteins. These new methods also create unprecedented opportunities for modeling large complexes based on experimental data. With this job opening, we aim to combine our expertise in integrative structural biology with these modeling methods to enable accurate modeling of large macromolecular complexes as a new EMBL platform.RESPONSIBILITIESYour role:To develop, implement and provide new methods for modeling the structure of large macromolecular complexes by leveraging tools like AlphaFold and RoseTTAfold and integrating experimental data such as electron microscopy, crosslinking, X-ray crystallography or small angle X-ray scattering.Incorporate the new methods in our modeling package AssemblineManage well-organized and tested software packagesTo test and apply these methods within ongoing research projects of internal and external collaborators.To support and train young researchers in using modeling methodsYou will be affiliated with the research group of Jan Kosinski, but your expertise will be accessible to all interested research groups and teams from the EMBL Hamburg Unit.REQUIREMENTSYou have:A PhD in an area related to structural biologyExcellent programming skills in Python, and track record in developing and applying computational tools in the structural biology fieldExperience in disseminating and managing software packagesStrong motivation to work in a highly collaborative and multidisciplinary environment of EMBLCompetence and commitment to contribute to teaching (workshops, tutorials, personal supervision) on the new modeling methods
- PhD in Bioinformatics or related quantitative science (Computer Science, Biology, Engineering, Math, Physics) and at least 3 years’ of work experience in Bioinformatics in industry or research
- Experience in teaching semester courses or workshops on a quantitative topic
- Expertise with Statistics and Machine Learning
- Experience with web server development and administration
- Experience with cloud computing and development (e.g. AWS, Google Cloud)
- Experience with NGS pipeline development
- BS/MS in computational discipline required
- Ability to independently plan and execute pipelines and workflows of high complexity required
- Knowledge of phenotype harmonization processes and associated resources such as ontologies required
- Knowledge of common NGS or other high-throughput data formats is required
- Strong UNIX/LINUX expertise required
- Expertise in applications written in common bioinformatics languages such as Python, R, Perl or similar required
- Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required
- Expertise with resources of genomic data sets and analysis tools, such as NCBI databases, UCSC Genome Browser, ENCODE, and others is required
- Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and deployment is required
- Knowledge with cloud computing concepts and applications is required
|BACKGROUNDMedical Science and Computing (MSC; a Guidehouse company) is currently searching for a Biomedical Informatics Data Specialist to provide support to the National Institutes of Health (NIH). This opportunity is a full-time position with MSC, and it is on-site in Rockville, MD.|
Key skills:3+ years of Python and Bash scriptingContribute code with team members using git and GitHubHigh Performance ComputingBuilding Bioinformatics pipelines with Snakemake (or similar tools)Handling and exploring large human VCF filesHuman Clinical GenomicsOMIM, Gnomad, ClinVar, HGMD, and other human databasesHigh level communication, documentation, organizational, and time-management skillsRESPONSIBILITIESWork closely with a small diverse team of scientists and engineers to deliver high-quality dataDocument and design data modelsExtract, integrate, and reconcile new data sources with existing knowledge basesPerform quality control on data to ensure that it meets requirementsWorking with the project team and an enterprise infrastructure team to test the impact of new functionality on dataExperiment with new data management technologies and systems and prototyping solutionWorking within the developer team to share knowledge, collaboratively developing best practicesWorking with Stakeholders, Users, and Project Managers to meet NIH Project Goals and MilestonesREQUIREMENTSBS. or higher degree in computational life sciences or related fieldDemonstrated expert fluency (3+ years working experience) in using Python for bioinformatics or biomedical informatics data management pipelinesExperience with Snakemake pipelinesProficiency in the use of UNIX/Linux and bash scriptingExperience with high performance computing and cloud environmentsExperience with common clinical genomic file formats (primarily VCF, but also BAM)Experience using Git and GitHub for tracking code changes and sharing contributions of multiple team membersDemonstrated experience extending the functionality of existing software; ability to learn an existing body of code and extend itExperience with annotating human genomes with annotations through scripting and the use of reference genome databasesKnowledge of public genomic databases such as OMIM, Gnomad, ClinVar, HGMD, othersExcellent communication skills and ability to work with users, including to develop and document requirementsExcellent organizational and time-management skillsExperience communicating with end users on software development projects
- Strong background and interest in cancer genomics.
- Strong background and interest in open access science.
- MS or PhD in bioinformatics or computational biology.
- Experience developing genomic and clinical data standards and ontologies.
- Experience managing genomic assay data, including single cell RNASeq and multiplex imaging.
- Experience managing complex bioinformatics projects, including stakeholder management, and ability to multitask multiple project deadlines.
- Working experience with data sharing platforms, including dbGAP or NCI Cloud Resources.
Only applicants who meet the following requirements will be considered for the positions.
1) A Ph.D. degree in a relevant scientific discipline or will defend Ph.D. in less than 6 months
2) U.S. citizenship or permanent resident or H-1 holder willing to convert to J-1 status or foreign applicant (through J-1 visa) or F-1 with OPT
3) Stayed in USA for 3 years in the last 5 years
4) Proficiency with at least one programming language (C, C++, Python, Perl, Java, etc.)
5) Experience with software packages of MatLab, SAS, R, or other statistical analysis programs
6) Excellent oral and written communication skills
7) Good judgment, clear sense of purpose, and accountability
- Advanced degree from accredited university or technical school or multiple years experience in molecular biology or related discipline
- Experience in standard genomics techniques (RNA-seq, ATAC-seq, DNA-seq) and library preparation
- Independent work ethic and desire to learn new methods and protocols
- Ability to manage your role in multiple collaborative projects
- Willingness to learn basic programming
- Ability to speak and write fluently in English, which is the working language at EMBL
- A PhD in an area related to structural biology
- Excellent programming skills in Python, and track record in developing and applying computational tools in the structural biology field
- Experience in disseminating and managing software packages
- Strong motivation to work in a highly collaborative and multidisciplinary environment of EMBL
- Competence and commitment to contribute to teaching (workshops, tutorials, personal supervision) on the new modeling methods
- Bachelor’s or master’s degree in Computer Science, Bioinformatics, Computational Biology or a related field.
- Prior experience building applications with genomics data.
- Experience with AI / ML is a bonus.
- 3+ years of bioinformatics engineering experience in an academic or industry setting.
- 1-3 years’ experience managing a small team of bioinformatics engineers.
- Expert knowledge of Python.
- 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.