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Jason A. Young, PhD

Jason A. Young, PhD

Assistant Professor

Contact Information

Department of Medicine
University of California, San Diego
220 Dickinson St, Suite A
San Diego, CA 92103

Email: jay007 at ucsd dot edu
Phone: 619-543-8073
Fax: 619-543-5066


  • BS, Molecular Biology/Botany, University of Wisconsin - Madison
  • PhD, Biology, The Scripps Research Institute
  • Open Source Biomedical Software Development
  • Clinical Research Data Management
  • Infectious Disease Functional Genomics

Manuscripts/Reviews/Book Chapters:

  1. Young JA, Winzeler EA. (2005) “Using expression information to discover new drug and vaccine targets in the malaria parasite Plasmodium falciparum.” Pharmacogenomics. Jan;6(1):17-26. PMID: 15723602
  2. Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, Winzeler EA. (2005) “In silico gene function prediction using ontology-based pattern identification.” Bioinformatics. Apr 1;21(7):1237-45. PMID: 15531612
  3. Jessani N, Young JA, Diaz SL, Patricelli MP, Varki A, Cravatt BF. (2005) “Class assignment of sequence-unrelated members of enzyme superfamilies by activity-based protein profiling.” Angewante Chemi International Edition English. Apr 15;44(16):2400-3. PMID: 15765498
  4. Young JA, Fivelman QL, Blair PL, de la Vega P, Le Roch KG, Zhou Y, Carucci DJ, Baker DA, Winzeler EA. (2005) “The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification.” Molecular Biochemical Parasitology. Sep;143(1):67-79. PMID: 16005087
  5. Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. (2008) “In silico dicovery of transcription regulatory elements in Plasmodium falciparum.”  BMC Genomics. Feb 7;9:70. PMID: 18257930
  6. Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA. (2008) “Evidence-based annotation of the malaria parasite’s genome using comparative expression profiling.” PLoS ONE. Feb 13;3(2):e1570. PMID: 18270564
  7. Garcia CRS, de Azevedo MF, Wunderlich G, Budu A, Young JA, Bannister L. (2008) “Plasmodium in the post-genomic era: New insights into the molecular cell biology of malaria parasites.” International Review of Cell and Molecular Biology, Chapter 3.
  8. Gianella S, Delport W, Pacold ME, Young JA, Choi JY, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM. (2011) “Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants.” Journal of Virology. Aug;85(16):8359-67. PMID: 21632754
  9. Mehta SR, Kosakovsky Pond SL, Young JA, Richman D, Little S, Smith DM. (2012) “Associations Between Phylogenetic Clustering and HLA Profile Among HIV-Infected Individuals in San Diego, California.” The Journal of Infectious Diseases. May 15;205(10):1529-33. PMID: 22448013
  10. Grönwall C, Kosakovsky Pond SL, Young JA, Silverman GJ. (2012) "In Vivo VL-Targeted Microbial Superantigen Induced Global Shifts in the B Cell Repertoire." The Journal of Immunology. Jul 15;189(2):850-9. PMID: 22696444
  11. Gianella S, Mehta SR, Strain MC, Young JA, Vargas MV, Little SJ, Richman DD, Pond SL, Smith DM. (2012) “Impact of Seminal Cytomegalovirus Replication on HIV-1 Dynamics between Blood and Semen.” Journal of Medical Virology. Nov; 84(11):1703-9. PMID: 22997072
  12. Gianella S, Mehta SR, Young JA, Vargas MV, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM. (2012) “Sexual Transmission of Predicted CXCR4-Tropic HIV-1 Likely Originating from the Source Partner’s Seminal Cells.” Virology. Dec 5;434(1):2-4 PMID: 23040890
  13. Gianella S, Morris SR, Vargas MV, Young JA, Callahan B, Richman DD, Little SJ, Smith DM. (2013) “Role of Seminal Shedding of Herpesviruses in HIV-1 Transmission.” The Journal of Infectious Diseases. Jan;207(2):257-61. PMID 23148284
  14. Gianella S, Morris SR, Anderson C, Spina CA, Vargas MV, Young JA, Richman DD, Little SJ, Smith DM. (2013) “Herpesviruses and HIV-1 Drug Resistance Mutations Influence the Virologic and Immunologic Milieu of the Male Genital Tract.” AIDS. Jan 2;27(1):39-47. PMID: 22739399
  15. Le T, Wright EJ, Smith DM, He W, Catano G, Okulicz JF, Young JA, Clark RA, Richman DD, Little SJ, Ahuja SK. (2013) “Enhanced CD4+ T-cell Recovery with Earlier HIV-1 Antiretroviral Therapy.” NEJM. Jan 17;368(3):218-30. PMID: 23323898
  16. Perez-Santiago J, Gianella S, Massanella M, Spina CA, Karris MY, Var SR, Patel D, Jordan PS, Young JA, Little SJ, Richman DD, Smith DM. (2013) “Gut Lactobacillales are Associated with Higher CD4 and Less Microbial Translocation during HIV Infection.” AIDS. Mar 18;27(12):1921-931. PMID: 24180001
  17. Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM. (2014) “Using HIV Networks to Inform Real Tim Prevention Interventions.” PLOS ONE. June;9(6):e98443. PMID: 24901437