Research Scientist

Research Scientist

Position summary The Laboratory of Proteoform Medicine in the Department of Molecular Physiology and Biological Physics and the UVA Comprehensive Cancer Center is seeking a research scientist to lead a functional genomics program at the intersection of genetic screening, molecular biology, and multi-omics. The successful candidate will be a strong, versatile experimentalist and analyst who can design and run genetic perturbation screens, drive molecular biology and cell-based work, and generate and interpret omics data, particularly long-read RNA sequencing and mass spectrometry-based proteomics, alongside single-cell sequencing.

These efforts connect directly to the lab's proteogenomics platform and its goal of resolving and functionally interrogating protein isoforms and proteoforms. This role is suited to a scientist who is equally comfortable in the dry and wet lab domains, who wants substantial intellectual ownership over a program area, and who is excited to build technology at the boundary of functional genomics and proteoform biology.

Key responsibilities

• Design and execute pooled and arrayed CRISPR screens (Cas9, Cas
  13, CRISPRi/a as appropriate) including library design and cloning, lentiviral production, transduction, selection, and NGS readout.
• Develop and optimize gene perturbation approaches (knockout, knockdown, CRISPRi/a, and RNA-targeting Cas
  13 where isoform-level resolution is needed) in mammalian cell systems, including cancer cell lines and iPSC-derived models where applicable.
• Generate, process, and integrate multi-omics data - long-read RNA sequencing, mass spectrometry-based proteomics, and single-cell sequencing - and connect these readouts with screen and perturbation outputs through robust experimental and computational pipelines.
• Contribute to and lead molecular cloning workflows: guide library construction, vector design, plasmid prep, and verification by NGS.
• Partner with computational lab members on bioinformatic analysis (count matrices, hit calling, QC); independently perform first-pass analysis using established tools and scripting in Python and/or R.
• Mentor graduate students, postdocs, and research staff on functional genomics methods; help establish and document lab SOPs.
• Lead writing of methods, manuscripts, and contribute to grant applications (NIH, foundation); present at lab meetings, departmental seminars, and external conferences.
• Coordinate with collaborators across UVA and external partners on shared screening efforts.

Required qualifications

• Ph.D. in molecular biology, genetics, biochemistry, biomedical engineering, computational biology, or a related field, with 3+ years of postdoctoral or equivalent independent research experience for the senior level (adjust per UVA classification).
• Demonstrated, hands-on experience with genetic screening in mammalian cells - designing and executing pooled and/or arrayed CRISPR screens, or comparable functional-genomics screens - ideally evidenced by a first- or co-first-author publication or preprint.
• Strong, hands-on molecular biology and cloning skills: vector design, Gibson/Golden Gate assembly, library construction (including sgRNA libraries), and plasmid validation.
• Expertise in mammalian cell culture, including lentiviral packaging, titration, transduction, and stable line generation.
• Strong NGS skills: sample prep (amplicon, RNA-seq, scRNA-seq library prep), QC, and familiarity with Illumina platforms.
• Experience generating and/or analyzing omics data - for example bulk or single-cell RNA-seq - together with the aptitude and interest to work fluently with long-read RNA sequencing and mass spectrometry-based proteomics data.
• Solid bioinformatics ability - comfortable on an HPC, scripting in Python and/or R, running standard analysis pipelines (CRISPR screens, RNA-seq, and related omics workflows), and analyzing results independently rather than waiting on a bioinformatics collaborator.
• Strong written and verbal scientific communication; record of published peer-reviewed work.
• Ability to plan independently, manage parallel projects, and mentor more junior team members.

Preferred qualifications

• Direct experience with Cas
  13 (Cas
  13d, Rfx Cas
  13d, Cas
  13bt, etc.), including guide design for RNA targeting, knockdown validation, and trans-cleavage considerations.
• Hands-on experience with single-cell genomics and perturbation platforms (e.g., 10x Genomics scRNA-seq, Perturb-seq, CROP-seq, ECCITE-seq) - including sample prep, library construction, and downstream demultiplexing/analysis using established frameworks. Single-cell is the primary readout for our screens, so prior experience here will accelerate ramp-up significantly.
• Familiarity with iPSC culture and differentiation, or with primary patient-derived models.
• A strong plus: knowledge of alternative splicing and genetics, and a background or active interest in isoform biology, proteogenomics, or protein/proteoform-level biology - including any experience with mass…