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. Association of metabolomics measurements with blood cell phenotypes.

2. Patient-informed CRISPR Screen Identifies FLNB as a Congenital Heart Disease and Ciliopathy Gene.

3. Trimethylamine N-oxide and related metabolites may regulate DNA methylation and trigger cardiovascular disease.

4. Single-Cell Multimodal Profiling Highlights Persistent Aortic Smooth Muscle Cell Changes in Diabetic Mice Despite Glycemic Control.

5. Novel extracellular vesicle release pathway facilitated by toxic superoxide dismutase 1 oligomers.

6. Characterizing Spatiotemporal Expansion of Pseudomonas aeruginosa Communities in Polymer and Mucin Gel Environments.

7. Genetic Predictors of Response to Oral Insulin for Type 1 Diabetes Prevention.

8. Targeting IL-1/IRAK1/4 signaling in acute myeloid leukemia stem cells following treatment and relapse.

9. cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions.

10. The LMO2-LDB1-TAL1 complex regulates transcription networks in acute myeloid leukemia.

11. Compound heterozygous DAW1 variants reveal tissue-specific roles in left-right patterning and congenital heart disease without primary ciliary dyskinesia.

12. Multimodal Bond Reconstruction toward Generative Molecular Design.

13. Cross-ancestry comparison of aptamer and antibody protein measures.

14. Type 2 Diabetes Genetic Risk and Type 1 Diabetes Heterogeneity and Progression.

15. Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease.

16. Whole genome sequence analysis of pulmonary function and COPD in 44,287 multi-ancestry participants.

17. Circulating metabolites, genetics and lifestyle factors in relation to future risk of type 2 diabetes.

18. Peptide-based drug design using generative AI.

19. Large-scale blood pressure GWAS accounting for gene-depression interactions in 564,680 individuals from diverse populations.

20. Fibrinogen-associated plasma metabolites and implications for coagulation, inflammation, and vascular diseases.

21. Expanding Chemical Space of Nucleic Acid Nanoparticles for Tunable Antiviral-Like Immunomodulatory Responses and Potent Adjuvant Activity.

22. N-Palmitoyl Glutamine Is a Candidate Mediator of Cardiorespiratory Fitness.

23. Proteoform medicine: characterizing and targeting protein forms in human disease.

24. Development and Validation of a Type 1 Diabetes Multi-Ancestry Polygenic Score.

25. Genome-wide gene-sleep interaction study identifies novel lipid loci in 732,564 participants.

26. Predictive modeling of hematoma expansion from non-contrast computed tomography in spontaneous intracerebral hemorrhage patients.

27. Temporal single-cell analysis reveals age-associated delay in immune resolution after respiratory viral infection.

28. Correction: Development and recalibration of a multivariable type 1 diabetes prediction model for type 1 diabetes across multiple screening studies.

29. Elevated intracellular copper induces CTR1 monomerization and prevents copper uptake.

30. Proteome-wide association study of prostate cancer risk across populations.

31. Epigenome-wide association study of nuclear DNA methylation in relation to mitochondrial heteroplasmy.

32. Single-cell dynamics reveal a stress-induced decision between hypertrophy and apoptosis in neonatal rat cardiomyocytes.

33. Association of Epigenetic Age Acceleration and Mitochondrial DNA-Based Aging Metrics Provides Insights Into Mechanisms of Aging-Related Diseases.

34. Author Correction: Brahma safeguards canalization of cardiac mesoderm differentiation.

35. Dissecting Genetic and Environmental Determinants of Plasma Molecular Signatures and Their Link to Type 2 Diabetes Risk.

36. Human plasma proteomic profile of clonal hematopoiesis.

37. Metabolic network analysis of Crohn's disease reveals sex- and age-specific cellular phenotypes.

38. Quantifying the impact of early life growth adversity on later life health.

39. Flexible nanoelectronics reveal arrhythmogenesis in transplanted human cardiomyocytes.

40. Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data.

41. AI-powered programmable virtual humans toward human physiologically-based drug discovery.

42. ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation.

43. Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity.

44. Insights, opportunities, and challenges provided by large cell atlases.

45. Patient-informed CRISPR Screen Identifies FLNB as a Novel Congenital Heart Disease and Ciliopathy Gene.

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

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

48. PSP-0119: Targeted IRAK4 Degradation as a Novel Therapeutic Strategy for FLT3-Mutant AML.

49. Transcriptional Condensates: Epigenetic Reprogramming and Therapeutic Targets in Hematologic Malignancies.

50. Augmenting early stroke diagnosis with an eye-tracker.