RISE Bioinformatics Engineer

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JOB DESCRIPTION AND POSITION REQUIREMENTS:

The Institute for Computational and Data Sciences (ICDS) at Penn State is seeking a Bioinformatician or Computational Biologist for their  Research Innovations with Scientists and Engineers (RISE) Engagement team. You will be an integral contributor to a fast-paced and growing team of specialists supported by an exciting, ongoing $125 million Penn State investment in ICDS cyber-ecosystem, called “Roar”. With ICDS, our RISE team members have the unique opportunity to support and participate in groundbreaking academic research at Penn State.

This position will primarily focus on supporting a new interdisciplinary center, which sits at the intersection of Data Sciences and Molecular and Cellular Sciences. The center will serve as a leader in integrating various publicly accessible data sets, which diverse teams of scientists will synthesize to answer cutting-edge questions.

Work Arrangement: This position has the potential to be a hybrid of remote and on-site work, with a minimum of 3 days per week on-site.  This position may not be supportive of fully remote work.

This is a limited-term position funded for 3 years from the start date, with excellent chances of renewal.

As a RISE Bioinformatician or Computational Biologist, you would have the following responsibilities:

• Provide advanced engineering and support in the design and development of bioinformatics science gateways and pipelines, with a particular emphasis on analysis of mass spectrometry, genomics, transcriptomics, proteomics, and metabolomics datasets.

• Formulate and define the scope, objectives, and detailed specifications for bioinformatics projects. Collaborate with researchers to understand their data requirements and design custom solutions.

• Offer guidance and support on the selection and application of bioinformatics and computational biology tools and pipelines, especially those related to sequence alignment, gene expression analysis, and variant calling, following open and reproducible science best practices. Develop and maintain quality assurance protocols for workflows to guarantee the reliability and reproducibility of results.

• Stay up-to-date with the latest advancements in bioinformatics, computational biology, and available biological datasets.

• Work with the center project manager, scientific working groups, and graduate students to deliver work products on time and to predefined specifications.

• Provide technical expertise in the wrangling, harmonizing, and standardizing of existing biological datasets, including advanced experience with mass spectrometry data and/or next-generation sequencing data. Implement comprehensive quality control measures to ensure data accuracy and consistency.

• Project manage graduate students who will work with you to support data science efforts.

Education and Experience: This position will be filled at an Intermediate or Advanced Professional level, depending on the successful candidate’s experience and education or an equivalent combination.

• Minimum education and experience are a Bachelor’s degree in Computational Biology or Bioinformatics, and 1+ years of experience, or an equivalent combination of education and experience.

• Candidates with a PhD in Bioinformatics, Computational Biology, or a related discipline and 3+ years of experience, or an equivalent combination of education and experience are strongly preferred.

Skills and Abilities:

• Advanced expertise in Python and/or R for complex data analysis, scripting, and statistical modeling, with a particular focus on sequence alignment algorithms, structural prediction, gene expression analysis, and variant calling. Additional proficiency in languages like Perl or C++ is beneficial for systems-level bioinformatics applications.
• Mastery in using bioinformatics or computational biology software (like BLAST, GATK, Bioconductor)
• Experience in working with large-scale biological databases using SQL or NoSQL, with strong skills in big data analytics, ETL processes, and the ability to extract meaningful insights from complex datasets.
• Understanding of genetic principles, molecular biology techniques, and genomic databases.
• Familiarity with next-generation sequencing (NGS) data, its analysis, interpretation, and integration with mass spectrometry and other omics data.
• Practical experience with any of the following datasets: XL-MS (PRIDE), AlphaFold (EBI), M.S.A., DMS (MAVE), P.P.I. (STRINGS), Metabolic networks (KEGG), Expression (GEO, SRA), Seq-methods (e.g., Hi-C, CRISPRi, etc.)

In addition, our desired qualifications and skills include but are not limited to the following:

• Proven track record of publications in peer-reviewed journals and/or conference proceedings, demonstrating significant contributions to the field.
• Expertise in machine learning algorithms for pattern recognition and predictive modeling in biological data.
• Experience developing new bioinformatics tools as dictated by research needs.
• Experience with high-performance computing (HPC) environments, parallel computing, and cloud-based computational resources.
• Experience with software containerization, workflow management systems, and adherence to open and reproducible science practices.
• Proficiency in creating sophisticated data visualizations to represent complex biological data and trends.

Candidates must also have impeccable ethics and integrity with a strong work ethic, strong interpersonal and written skills, and the ability to work well in a team environment.

Candidates are required to provide the following:

• ​A current Curriculum Vitae (CV) or Resume

• A cover letter expressing detailing the candidate’s interest in the role

The Pennsylvania State University is committed to and accountable for advancing diversity, equity, and inclusion in all its forms. We embrace individual uniqueness, foster a culture of inclusive excellence that supports both broad and specific diversity initiatives, leverage the educational and institutional benefits of diversity, and engage all individuals to help them thrive. We value inclusive excellence as a core strength and an essential element of our public service mission.

Penn State offers a generous benefits package that includes health insurance, dental and vision plans, retirement plans, a 75% tuition discount for full-time employees, their spouse, and children to attend any Penn State campus, and paid vacation and sick days. More information about benefits is available here: https://hr.psu.edu/benefits

The salary range for this position, including all possible grades is:

Salary Structure - additional information on Penn State's job and salary structure. 

CAMPUS SECURITY CRIME STATISTICS:

Pursuant to the Jeanne Clery Disclosure of Campus Security Policy and Campus Crime Statistics Act and the Pennsylvania Act of 1988, Penn State publishes a combined Annual Security and Annual Fire Safety Report (ASR). The ASR includes crime statistics and institutional policies concerning campus security, such as those concerning alcohol and drug use, crime prevention, the reporting of crimes, sexual assault, and other matters. The ASR is available for review here.

Employment with the University will require successful completion of background check(s) in accordance with University policies. 

EEO IS THE LAW

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. If you are unable to use our online application process due to an impairment or disability, please contact 814-865-1473.

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