Research - UVA Computational Biology PhD

Our program focuses on cutting-edge research at the intersection of computation and biology. Faculty in the Computational Biology program are engaged in cutting-edge research in a variety of areas, including computational genomics, systems biology, and bioinformatics. Explore opportunities with our world-class faculty across diverse research areas including genomics, AI in medicine, and more. Learn about our specialized training that prepares students for research excellence.

The best way to learn about the research being done by our faculty is to visit their websites and read their recent publications. You can find a list of faculty members and their websites on the faculty page. You can also browse papers from UVA COBI on PUBMED.

Recent Publications

1. Deciphering covalent kinase inhibitor binding landscape through structural kinome profiling.

2. Computational Modeling Identifies Protective Mechanisms of Estrogen and Testosterone Against Atrial Fibrosis.

3. Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics.

4. TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin in cancer cells.

5. Publisher Correction: Whole genome sequence analysis of pulmonary function and COPD in 44,287 multi-ancestry participants.

6. Performance of Age-Adjusted Whole Genome Sequencing Telomere Length in Idiopathic Pulmonary Fibrosis.

7. Tonotopic specialization of MYO7A isoforms in auditory hair cells.

8. Whole Genome Sequence Analysis of Weight Loss in 16 972 Participants With COPD Reveals Novel Risk Loci in DRAIC and RFX3.

9. eSIG-Net: an interaction language model that decodes the protein code of single mutations.

10. Plasma metabolomic profiles associated with cardiovascular disease in type 2 diabetes from the Trans-Omics for Precision Medicine (TOPMed) program.

11. Gene Expression Profiles at Early vs Late Stages After Cervical Artery Dissection.

12. Estimation of direct and indirect polygenic effects and gene-environment interactions using polygenic scores in case-parent trio studies.

13. RNAs anchoring replication complex control initiation and firing of DNA replication.

14. PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.

15. Co-occurring clonal hematopoiesis exhibits strong selection and high leukemia risk.

16. Respiratory viral infections prime accelerated lung cancer growth.

17. Sex-specific omics scores of sex hormones and associations with metabolic and sleep disorders.

18. Machine learning cross-platform proteomic imputation enables protein quality scoring and replication of epidemiological associations.

19. BART-spatial unravels biologically significant transcriptional regulators from spatial omics data.

20. Cell-o1 : training LLMs to solve single-cell reasoning puzzles with reinforcement learning.

21. Elevated levels of TNF and its targets characterize better-risk older acute myeloid leukemia patients.

22. Admixture-informed polygenic risk reporting using the ePRS framework.

23. The Common Fund Data Ecosystem (CFDE).

24. A diffusion-based framework for designing molecules in flexible protein pockets.

25. Enzyme-enhanced RNA isolation from biofilm-producing bacteria.

26. Multi-Organ Physiologic Deficits During Exercise Identify Clinical and Molecular Predisposition to Heart Failure with Preserved Ejection Fraction.

27. Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies.

28. CCAAT-enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia.

29. eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model.

30. Beyond gene length: Exon-intron architecture and isoform potential in the evolution of eukaryotic complexity.

31. An integrated germline and somatic genomic model for coronary artery disease.

32. ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.

33. Mosaic Loss of Y chromosome associates with lung function, emphysema and epigenetic aging.

34. Identifying Plasma Proteins Associated with Risk of Solid Cancers: A 25-Year Prospective Analysis of 4,712 Circulating Proteins in the ARIC Study.

35. Unified protein-small molecule graph neural networks for binding site prediction.

36. Relative maternal protection against type 1 diabetes: a combined analysis of five observational studies.

37. Governing real-world health data as a public utility.

38. A Common Missense Variant, W335S, in β2-Glycoprotein I (APOH) is Associated with Increased Autoantibody Levels but Reduced Venous Thromboembolism Risk.

39. Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.

40. Phase I/II clinical trial of a melanoma vaccine targeting shared non-mutated antigens and a shared mutated BRAF neoantigen with an agonistic CD40 antibody (CDX-1140) plus TLR3 agonist (poly-ICLC).

41. A Blue Start: A large-scale pairwise and higher-order social network dataset.

42. Gene-by-Sleep Duration Interaction for Glycemic Traits in over 480,000 Individuals.

43. Multi-ancestry genome-wide association study and meta-analysis of lung function decline.

44. BARTsc identifies key transcriptional regulators from single-cell omics data.

45. Differential analysis of image-based chromatin tracing data with Dory.

46. ATLAS: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions.

47. Mechanistic role of APOE lipidation in Alzheimer's disease pathogenesis.

48. Automated biomedical hypothesis generation with time-aware hypergraph contrastive learning.

49. IRIS: Interpretable Risk Clustering Intelligence for Survival Analysis.

50. Linear Optimal Transport Subspaces for Point Set Classification.