Bioinformatics specialist job description

The Bioinformatics Specialist I helps to advance computational component of biomedical research at the department and throughout the hospital. Works closely with other investigators to answer key biological questions by performing genome scale computational analyses. The background must demonstrate a proven ability to work collaboratively and perform high quality analyses of large-scale experimental data in a timely manner. Contributes code to shared computational infrastructure and is expected to meet high software development standards. Evaluates existing computational methods and serve as a knowledge resource to collaborators seeking advice about the best tool for a particular problem.

In addition, under the supervision of the Director and with the help of senior members, manages research collaborations, designs Bioinformatics workflows, selects tools and statistical approaches, and executes projects. Demonstrates good understanding of biological problems and in-depth knowledge of computational methods for next-generation sequencing analysis. Demonstrates mature interpersonal skills in communicating with collaborators and driving collaborative research.
KEY RESPONSIBILITIES:

* Provides collaborative advanced Bioinformatics analysis in support for the research projects at the Department of Molecular Biology and Partners in general
* Drives the Bioinformatics component of the collaborative projects using computation (Linux/Unix environment, Perl, Python, R, or other scripting languages), statistics, good understanding of biological problems, and in-depth knowledge of methods for the analysis of high-throughput biomedical data, with the primary emphasis on next-generation sequencing methods

* Interprets and translates computational results into biologically relevant conclusions and hypotheses. Discusses biological questions, problems, and outcomes with wet-lab collaborators
* Addresses scientific ideas and questions of wet-lab collaborators and implements of them in Bioinformatics workflows in real time under the guidance of the Director
* Clearly and succinctly communicates basic ideas and design of performed computational analyses to biologists and clinicians
* Works on his/her own Bioinformatics research projects in connection with the Director and senior members

SKILLS NECESSARY:

* Expertise in genomic data analysis - particularly ChIP-seq, RNA-seq, polymorphism discovery, and other NGS methods.
* Demonstrated understanding of statistics.
* Expertise working in Unix/Linux environments.
* Experience with Perl, Python, or other scripting languages.
* Excellent skills in oral presentation and good writing skills; ability to clearly and succinctly communicate basic ideas of computational analyses to biologists and clinicians.
* Strong ability and experience in interpreting computational results and translating these results into biologically relevant conclusions and hypotheses.

COMPENTENCIES/LICENSES/DEGREE/EXPERIENCE REQUIREMENTS:

* BS in computational biology, bioinformatics, cell biology, or a related field required, MS or PHD strongly preferred.

* Minimum 2 years of directly related experience expected.

Exciting opportunity to study the impact of metagenomics in understanding the human microbiome in health and disease. Labcorp is pursuing new avenues in this science to create clinical tests with utility for general well-being as well as disease conditions ranging from gut disorders to autoimmune diseases to cancer. We are expanding our microbial test offerings to include metagenomics- and metatranscriptomics-based tests. This position will focus on the research, development and implementation of our metagenomics pipeline on a cloud-based environment that allows for rapid development, deployment, scaling and accessibility. Areas of focus will include microbiome from various human sources such as the gut, nose, skin etc. as well as general wellbeing and various disease conditions. The successful candidate for this role will lead the development of our metagenomics and metatranscriptomics analysis capabilities.
Essential Duties and Responsibilities:


Develop and implement a metagenomics analysis pipeline using open source as well custom developed in-house tools that incorporates the latest algorithms and validated tools for microbiome analysis Research and development of a Labcorp database of annotated reference sequences for microbiome analysis based on expert knowledge combined with natural language processing strategies Source publications and open source datasets to develop disease-specific microbiome abundance databases Continuously aggregate and build Labcorp's own database of microbiome data using the metadata as well as the results of microbiome tests performed by Labcorp Research, develop and implement novel applications of our microbiome tests in combination with the vast amount of other test data and results that Labcorp already has Work with other groups, such as our AI team, to adopt and implement the latest Machine learning and AI tools to microbiome analysis


Minimum Education & Previous Experience Required:


Master's degree required, PhD preferred in Computational Biology/Bioinformatics, Computer Science, Molecular Biology, Physics, Engineering or related field Must be able to provide evidence of relevant research expertise in the form of presentations, software, technical publications, and/or knowledge of applications. PhD with 0-2 years' experience or Master with at least 2 years' experience in a biotechnology setting.


Knowledge, Skills & Abilities:


Proven track record of proficiency in data analysis and statistical learning Proficient in biological sequence analysis and analysis of next-generation sequencing data Proficiency with Python, R, Linux environment highly desirable Experience with Laboratory Developed Tests (LDT) highly desirable Programming experience in Java, Python or Perl and experience with rational and non-structure databases is highly desirable Familiarity with one or more machine learning libraries or frameworks such as: PyTorch, Tensorflow. Experience using cloud technologies such as AWS with tools such as S3, EC2, Lambda, Athena, etc. Experience with NGS data analysis with a focus on metagenomics, such as genome assembly, taxonomy assignment, abundance calculation, etc. Demonstrated success in technical proficiency, scientific creativity, collaboration with others and independent thought Knowledge of using professional concepts to contribute to development of company's concepts and principles and to achieve objectives in creative and effective ways; works on extremely complex problems in which analysis of situations or data requires an evaluation of intangible variables; exercises independent judgment in developing methods, techniques and evaluation criteria for obtaining results; acts independently to determine methods and procedures on new assignments and may oversee and manage the activities of lower level personnel


Physical Demands and Environmental Conditions:


Regularly works with a computer for approximately 6-8 hours a day Must be able to read and understand scientific and complex directions


Labcorp is proud to be an Equal Opportunity Employer:


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We are currently seeking a highly skilled Bioinformatics Specialist I to work full-time in the lab of Dr. Evan Eichler at University of Washington School of Medicine. The Eichler lab is interested in the disease and evolutionary impact of gene duplication and other complex forms of human genetic variation. Specifically, they apply advanced genome sequencing methods to understand how segmental duplications give rise to new genes and recurrent rearrangements associated with the neurodevelopmental delay, including autism. More information can be found on the lab website.

The Bioinformatics Specialist I will collaborate with the Investigator, postdoctoral fellows, and students to develop, implement, and execute computational methods and tools to assess the organization of recent segmental duplications and structural variation using next-generation Illumina and long-read technologies.

This role will focus on the discovery of genetic variation relevant to neurocognitive disease, including autism, and will work as part of sequencing consortia to develop methods to sequence and assemble genomes at higher quality. The successful candidate will independently perform scientific investigative procedures applying professional judgment, interpreting experimental results, guiding lab members through bioinformatics methods and analyses, and preparing research reports for presentation or publication.

For consideration for this position, please apply directly through the application website and do not contact the lab directly. Please be sure to include a cover letter with your application.

Responsibilities
Develop and maintain algorithms and computational tools to detect duplications, copy number variants, and single-nucleotide polymorphisms using data generated from genome sequencing projects. (40%) Create tools to create, manage, and analyze next-generation sequencing datasets using massively parallel computing infrastructure (2500+ CPUs). (20%) Develop programs and/or scripts, including graphical visualization software, to facilitate large-scale data mining of the genome, genetic, and expression databases. (15%) Collaborate with postdoctoral and doctoral researchers and work independently on research projects as assigned by the Investigator. The latter will include the preparation of summaries and reports to be included in publications. (15%) Integrate analysis data into existing genome browser. (10%)

Lead Responsibilities (if applicable)
Supervise and manage massively parallel computing infrastructure including 2,500+ CPUs, 3+ PB of shared storage, and standalone web and database servers in collaboration with departmental IT staff.Deploy and manage shared software and reference resources.Guide the work of junior-level programmer analysts as well as computational students as needed.

Qualifications
Education
Bachelor's degree in bioinformatics, computer science, or similar discipline is required. Master's degree is preferred.
Experience
At least 2-3 years of relevant research experience in bioinformatics and/or computational biology is required.Experience in genomics research is required including at least 3 years of experience developing computational methods and tools used in bioinformatics research.In-depth understanding of data structures, algorithm design, and software implementation Experience with PacBio, Oxford Nanopore, 10X, or Strand-seq technologies desired but not required Extensive experience in two or more programming languages (Python, R, Java, C/C++, Perl, etc.); experience with Python and its scientific libraries (NumPy, SciPy, Pandas, Snakemake).An understanding of common bioinformatics file formats (FASTQ, SAM/BAM, VCF, BED).

Knowledge, Skills, and Abilities
Proficient skill with integrating data and systems.Proficient skill with existing bioinformatics software tools (e.g., BWA, GATK, BLAST, CLUSTALW, MEGA), particularly data mining of whole-genome shotgun sequence data analysis.Skilled with Linux/Unix and comfortable working in a command line environment.Ability to perform independent analyses and report findings to both national and international collaborative groups.Technical proficiency and collaborative ability as well as independent thought.Ability to develop innovative processes to achieve goals. Reviews work activities to determine where new information could improve processes or move projects forward.Ability to work independently and as part of a multidisciplinary team.Strong organizational skills with exceptional attention to detail.Strong multitasking and project management skills.Ability to be flexible and effectively adapt to changing priorities.
Physical Requirements:Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.Please Note:This job description sets forth the job's principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

Compensation and Benefits
Our employees are compensated from a total rewards perspective in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our Benefits at HHMI site to learn more.

HHMI is an Equal Opportunity Employer