The Logsdon Lab at the University of Pennsylvania Perelman School of Medicine is looking for a highly skilled Bioinformatics Specialist to work full-time starting in Summer 2024. The Logsdon lab is interested in understanding how some of the most rapidly evolving regions of the human genome vary among the population and throughout evolution in both health and disease. We are particularly interested in the centromeres, which are found on every chromosome and are known to play an important role in infertility, cancer, and birth defects. More information about our research can be found on our lab website: logsdonlab.com

The Bioinformatics Specialist will collaborate with Dr. Logsdon, postdoctoral fellows, and graduate students to develop, implement, and execute computational methods and tools that assess the organization and evolution of human centromeres using long-read sequencing technologies. The successful candidate will focus on the discovery of genetic and epigenetic variation within human centromeres relevant to disease and their evolution through the primate phylogeny. They will also work as part of large sequencing consortia to develop methods to sequence and assemble high-quality reference genomes.

Position Complexities
The Logsdon Lab is involved in several different projects simultaneously, which requires skills in integrating data and systems. Familiarity with existing bioinformatics-specific software tools, especially data mining of whole-genome shotgun sequence data analysis, is required. Experience in genomics research is necessary for performance of this job. The ideal 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.

Duties and responsibilities

• Develop and maintain algorithms and computational tools to assess the sequence composition and organization of centromeres using data generated from genome sequencing projects. (40%)
• Create tools to create, manage, and analyze next-generation sequencing datasets using massively parallel computing infrastructure. (20%)
• Develop programs and/or scripts, including graphical visualization software, to facilitate large-scale data mining of the genome, genetic, epigenetic, 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:

• Supervise and manage massively parallel computing infrastructure, 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
Minimum requirements:

• Bachelor’s degree in Computer Science, Bioinformatics, or related field, or equivalent in education and experience.
• At least two years of experience developing computational methods and tools used in bioinformatics research.
• In-depth understanding of data structures, algorithm design, and software implementation.
• Extensive experience in two or more programming languages (Python, R, Java, C/C , Perl, etc.).
• 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 multitasking and project management skills.
• Ability to be flexible and effectively adapt to changing priorities

Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.

Desired experience:

• Master’s degree in Computer Science/Bioinformatics or related field, or equivalent in education and experience.
• At least one year of bioinformatics or related research experience in data analysis of next-generation sequencing or whole-genome shotgun data.
• Experience with long-read sequencing technologies, such as Pacific Bioscience (PacBio) or Oxford Nanopore Technologies (ONT).
• Proficient with integrating data and systems and existing bioinformatics tools (e.g., BWA, GATK, BLAST, CLUSTALW, MEGA), particularly data mining of whole-genome shotgun sequence data analysis.
• Experience with Python and its scientific libraries (NumPy, SciPy, Pandas, Snakemake).
• An understanding of common bioinformatics file formats (FASTQ, SAM/BAM, VCF, BED).

Contact
Interested individuals should email Dr. Glennis Logsdon (glogsdon@pennmedicine.upenn.edu) with a cover letter with a link to a recent code sample that demonstrates your programming ability and technique, as well as contact information of three references.

Job Type: Full-time

Benefits:

• 401(k)
• Dental insurance
• Health insurance
• Paid time off
• Vision insurance

Schedule:

• Monday to Friday

Application Question(s):

• Please provide a link to a recent code sample that demonstrates your programming ability and technique.

Experience:

• Python: 2 years (Preferred)
• bioinformatics: 1 year (Preferred)

Job-related location requirement:

• Candidates must be within a 25-mile radius.

Work Location: In person