Research Scientist

UVA Health•Charlottesville, VA

12d•Onsite

About The Position

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. For the scientific vision behind this role, see our recent review: Korchak et al., “Proteoform medicine: characterizing and targeting protein forms in human disease,” Nature Reviews Genetics 27, 271–291 (2026). This program builds out the vision of the map–perturb–predict framework described there.

Requirements

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.

Nice To Haves

Direct experience with Cas13 (Cas13d, RfxCas13d, Cas13bt, 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 spectrometry-based proteomics, long-read RNA sequencing (PacBio Iso-Seq/Kinnex, Oxford Nanopore), or top-down proteomics.
Experience with high-content imaging, flow cytometry-based screen readouts, or FACS sorting for screens.
Track record of mentorship, training, or formal teaching.
Experience contributing to grant applications, technical reports, or consortium-level deliverables.

Responsibilities

Design and execute pooled and arrayed CRISPR screens (Cas9, Cas13, 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 Cas13 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.