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. From data to wisdom: A new era of scientific inquiry.

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

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

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

5. ERIS2: A deep-learning platform for predicting mutation-induced protein stability changes.

6. Gene-by-Sleep Duration Interaction for Glycemic Traits in More Than 480,000 Individuals.

7. KinomeX: A Source-Linked, Evidence-Traceable Atlas of the Human Kinome.

8. Global Burden of Anorexia Nervosa and Bulimia Nervosa, 1990 to 2023, With Forecasts to 2050: A Global Burden of Disease Study 2023 Analysis.

9. Role of Plasma Proteins in the Association Between Socioeconomic Status and Cardiovascular Disease Events: Results From Trans-Omics for Precision Medicine Cohorts.

10. Network modeling predicts how DYRK1A inhibition promotes cardiomyocyte cycling after ischemia/reperfusion injury.

11. Host-like temperature unlocks glucose uptake and metabolism in pathogenic Leptospira.

12. Systems analysis reveals neuregulin-1 control of cardiomyocyte size and shape mediated by distinct PI3K and p38 pathways.

13. Longitudinal Proteomic Profiling of Blood Pressure in the Community.

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

15. RNAdex: graph-based 3D RNA Motif library incorporating non-Watson-Crick interactions.

16. Tumor suppressor-like mutations mark a dosage-constrained dependency in leukemia.

17. Integrated Risk Prediction of Kidney Failure: Clinical and Multi-Omic Approaches.

18. Mapping a genome-scale in vivo knockout screen to a mechanistic network model identifies VAV2, RASA1, and LEPR as regulators of cardiomyocyte hypertrophy.

19. Internal Grant Review: A Pre-Submission Program for Early-Career Clinical and Translational Researchers.

20. Dietary vitamin C intake and the risk of islet autoimmunity and type 1 diabetes: The Environmental Determinants of Diabetes in the Young (TEDDY) Study.

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

22. Biallelic DAW1 variants reveal a tissue-specific role in heterotaxy without primary ciliary dyskinesia.

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

24. PU.1 as a Master Regulator of Immune Cell Development and Function: Structural Basis, Gene Regulatory Networks, Disease Roles, and Therapeutic Targeting.

25. Assessing and refining a metabolite-based distress score for use in different populations within three US cohorts.

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

27. A Coding Single-Nucleotide Polymorphism in β(2)-Glycoprotein I (APOH) Is Associated With Increased Autoantibody Levels but Reduced Venous Thromboembolism Risk.

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

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

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

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

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

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

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

35. Benchmarking biochemical networks generated by large language models.

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

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

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

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

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

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

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

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

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

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

46. Reconstruction of septin higher-order nano-size structures in ovarian cancer cells uncover susceptibility to the septin-targeting small molecule UR214-9.

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

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

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

50. Bridge2AI recommendations for AI-ready genomic data.