Bioinformatics Programmer I - 138676

UCSD Health Sciences is a $1 billion dollar plus organization encompassing 16 academic departments (14 clinical, 2 basic sciences), 2 pre-academic/hospital departments, 2 professional schools (School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences), 2 hospitals, and various other programs and units all dedicated towards fulfilling the Health Sciences missions. The UCSD Department of Cellular and Molecular Medicine (CMM) is one of two basic science units in the School of Medicine where world-class researchers study fundamental cellular processes and pathways using a variety of techniques from classical genetics and fluorescence microscopy to high-throughput genomics, systems biology, and crystallography. Our 36 faculty and over 200 postdoctoral scholars, graduate students, and research staff work on the cutting edge of biology, cutting across fields from basic biochemistry and genetics to genomics, systems biology and stem cell biology. The faculty also play a major role in medical and graduate student training, providing educational and programmatic offerings that span several disciplines and provide diversity to meet the interests of a broad spectrum of students and scholars. The diverse mix of ages, backgrounds, and talents creates a robust work environment with challenging career opportunities and a commitment to continued growth potential. We constantly seek to recruit highly motivated, technologically advanced, and deeply interested individuals who are ready to become a part of our dynamic research and educational environment.

The Center for Network Medicine [www.cnetmed.ucsd.edu] is striving towards a goal of understanding the fundamental principles that allow eukaryotic cells to do their business, i.e., iteratively sense, decide, act, and learn/adapt. We hypothesize that they do so through an ad hoc molecular interaction network whose architectural principles and computational rules are like those used in the layered communication systems in the engineering world. These rules enable noise reduction, error minimization, shielding and encapsulation of breakdowns, control of delays and state explosion, etc. Success in decoding these fundamental rules should not only enable us to complete and 'clean up' the existing incomplete and messy biological networks but also use these networks for simulating and predicting cell behavior. This will usher a new era in network-based diagnostic tools and network-resetting therapeutics for major diseases. On the flip side, knowing how a cell autonomously carries out its business will provide insights into designing new kind s of self- organizing networks (SON) and provide a novel paradigm (beyond artificial neural networks) for developing Artificial Intelligence (AI).

The Ghosh lab is an active member of CNetMed, which specializes in cell biology, molecular biology, and translational medicine. More specifically, the Ghosh lab strives to study the cell biology of signal transduction, with a focus on heterotrimeric G-proteins (trimericGTPases) and monomeric GTPases, both are switches for signal flow in cells. All standard cell and molecular biology techniques are routinely used in the lab.

Under direct supervision, applies professional bioinformatics concepts and computational procedures to complete small projects or portions of projects. Works on assignments of limited scope and complexity. Follows standard programming procedures to analyze situations and data from which answers can be readily obtained.

The incumbent will use standard bioinformatics and statistical software to process, analyze, and interpret omics datasets (bulk RNA-seq, single-cell RNA-seq, proteomics), including QC, normalization, differential analysis, and visualization.. Performs other duties as assigned.

• Bachelor's degree in Bioinformatics, Computational Biology, Genetics/Genomics, Biostatistics, Computer Science, Biomedical Engineering, or related area.

• Basic knowledge of bioinformatics methods and data structures. This includes standard file formats such as FASTQ, BAM, VCF, GTF, BED.

• Basic knowledge of applications programming and web development.

• Basic knowledge of databases.

• Basic project management skills.

• Basic knowledge of modern biology and applicable field of research. Basic knowledge of molecular and cellular biology and core "omics" concepts (gene expression, pathways, experimental design, QC/controls).

• Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization.

• Ability to communicate technical information in a clear and concise manner.

• Self motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.

• Basic knowledge of application and data security concepts.

• Familiarity with R and or Python for data analysis, visualization, automation, and reproducible reporting (R Markdown, Quarto, or Jupyter). Ability to work comfortably in a Linux and HPC environment.

• Basic knowledge of genomics and proteomics databases and resources (GEO, SRA, Ensembl, UniProt) and ability to query data using basic SQL or API based tools.

• Basic project management skills.

• Familiarity with Git and a code hosting platform (GitHub or similar) for version control, code review, issue tracking, and collaboration.

• Interpersonal skills to work with both technical and non-technical personnel at various levels in the organization.

• Ability to communicate technical information in a clear and concise manner.

• Self-motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.

• Basic knowledge of application and data security concepts.

• Demonstrated ability to maintain high level of confidentiality in handling files and data and clear understanding of the Universities data privacy and acceptable use policies and procedures.

• Basic knowledge of molecular dynamics simulation and docking concepts and workflows.

• Basic knowledge of machine learning concepts and common algorithms used in bioinformatics.

• Employment is subject to a criminal background check.