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. Urine leukemia inhibitory factor predicts kidney function recovery in patients with acute interstitial nephritis.

2. Multiscale model calibrated with a Bayesian algorithm predicts long-term outcomes of treatments for mitral valve regurgitation in animal models.

3. Network modeling predicts how DYRK1A inhibition promotes cardiomyocyte cycling after ischemic/reperfusion injury.

4. Diabetes related genetics and outcomes after total pancreatectomy with islet autotransplantation.

5. International consensus guidance for general population screening for islet autoantibodies to diagnose early-stage type 1 diabetes: a nominal group technique process.

6. Longitudinal Repeated Protein Measurements in a Multiethnic Cohort Identify Novel Diabetes Biomarkers That Reveal Unique Disease Pathways.

7. A Coding Single Nucleotide Polymorphism in β2-Glycoprotein I (APOH) is Associated with Increased Autoantibody Levels but Reduced Venous Thromboembolism Risk.

8. Integrating multi-omics data with network modeling to characterize Pseudomonas aeruginosa persister cell metabolism.

9. Translational uncoupling of renin synthesis and activity reveals a mechanism of kidney vascular remodeling.

10. Genetic drivers of protein changes over time: Findings, considerations, and approaches in TOPMed cohorts and UK Biobank.

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

12. G-quadruplex structures as regulators of cellular processes and drivers of genome instability in cancer.

13. Computational modeling identifies protective mechanisms of estrogen and testosterone against atrial fibrosis.

14. Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted CD8(+) T cell fate.

15. Model Context Protocol: The unexpected catalyst of a bioinformatics interoperability revolution.

16. Benchmarking biochemical networks generated by large language models.

17. Taming the reference genome jungle: the refget sequence collection standard.

18. Genetic associations with pulmonary embolism among those with a deep vein thrombosis: the International Network Against Venous Thrombosis Consortium.

19. Tutorial: guidance on the use of large language models for medical research.

20. GeneKnow: An auditable AI framework for source-grounded biological evidence synthesis.

21. Environmental former Massilia group bacteria secrete metabolites that promote Leptospira growth.

22. Mucin-induced metabolic reprogramming in Pseudomonas aeruginosa clinical isolates.

23. Using Polygenic Risk Scores to Evaluate Definitions of Self-Reported Sleep Phenotypes Across Cohorts.

24. Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.

25. Mosaic loss of Y chromosome associates with lung function, emphysema, and epigenetic aging.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

44. The Common Fund Data Ecosystem (CFDE).

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

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

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

48. Editorial: The future of oncology: digital twins and precision cancer care.

49. Methods for modeling gene-environment interplay using polygenic risk scores.

50. Integrative genome-scale metabolic model of GABAergic neurons reveals metabolic signatures across the mild cognitive impairment - Alzheimer disease continuum.