Sinem Beyhan is an associate professor working in the Infectious Disease group. She is also an adjunct professor at UC San Diego and San Diego State University.

Dr. Beyhan’s research focuses on microbe-host interactions. She is particularly interested in the discovery of anti-fungal molecules, elucidation of gene pathways in Burkholderia and discovery of anti-Burkholderia drugs, and fungal genome assembly and annotation. Prior to her appointment at JCVI, Dr. Beyhan was a post-doctoral fellow at the University of California, San Francisco, where she was awarded American Lung Association Senior Research Training Fellowship, American Cancer Society Postdoctoral Fellowship and NIH-NIAID Pathway to Independence Award (K99/R00).

She received her PhD in Microbiology and Environmental Toxicology from the University of California, Santa Cruz, and her BS in Molecular Biology and Genetics from the Middle East Technical University, Ankara, Turkey.

Research Priorities

Mapping genetic networks that control cell morphology and virulence in the fungal pathogen Histoplasma capsulatum
  • Identification and characterization of regulatory factors that control the parasitic yeast form of H. capsulatum
  • Identification and characterization of sensory proteins that are important for sensing and responding to host signals
  • Identification and characterization of H. capsulatum virulence factors
Characterization of the factors that contribute to environmental and intracellular survival of the bacterial pathogen Burkholderia pseudomallei
  • Determining the molecular mechanism of biofilm formation in B. pseudomallei
  • Development of novel combination drug therapies to combat persistent B. pseudomallei infections
Characterization of the interactions between human gut microbiota and gut epithelial cells
  • Characterization of secreted factors of Bacteroides species for their roles in interacting with human gut epithelial cells


Coccidioides Species: A Review of Basic Research: 2022.
Journal of fungi (Basel, Switzerland). 2022-08-16; 8.8:
PMID: 36012847
Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA.
mSystems. 2022-02-22; 7.1: e0140421.
PMID: 35076277
Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species.
mBio. 2022-01-04; e0257421.
PMID: 35089059
Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing.
Journal of fungi (Basel, Switzerland). 2021-05-07; 7.5:
PMID: 34067070
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
PLoS computational biology. 2021-03-29; 17.3: e1008857.
PMID: 33780444
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients.
Microbial genomics. 2020-12-01; 6.12:
PMID: 33245689
Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes.
ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.
PMID: 32673475
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes.
mSystems. 2020-07-28; 5.4:
PMID: 32723799
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
PMID: 31907190
Sensing the heat and the host: Virulence determinants of Histoplasma capsulatum.
Virulence. 2019-12-01; 10.1: 793-800.
PMID: 31560240
Secondary Metabolites of Onygenales Fungi Exemplified by Aioliomyces pyridodomos.
Journal of natural products. 2019-06-28; 82.6: 1616-1626.
PMID: 31155876
The Vibrio cholerae virulence regulatory cascade controls glucose uptake through activation of TarA, a small regulatory RNA.
Molecular microbiology. 2010-12-01; 78.5: 1171-81.
PMID: 21091503
Identification and characterization of a phosphodiesterase that inversely regulates motility and biofilm formation in Vibrio cholerae.
Journal of bacteriology. 2010-09-01; 192.18: 4541-52.
PMID: 20622061
Cell envelope perturbation induces oxidative stress and changes in iron homeostasis in Vibrio cholerae.
Journal of bacteriology. 2009-09-01; 191.17: 5398-408.
PMID: 19542276
Indole acts as an extracellular cue regulating gene expression in Vibrio cholerae.
Journal of bacteriology. 2009-06-01; 191.12: 3504-16.
PMID: 19329638
Identification and characterization of cyclic diguanylate signaling systems controlling rugosity in Vibrio cholerae.
Journal of bacteriology. 2008-11-01; 190.22: 7392-405.
PMID: 18790873
Smooth to rugose phase variation in Vibrio cholerae can be mediated by a single nucleotide change that targets c-di-GMP signalling pathway.
Molecular microbiology. 2007-02-01; 63.4: 995-1007.
PMID: 17233827
Regulation of Vibrio polysaccharide synthesis and virulence factor production by CdgC, a GGDEF-EAL domain protein, in Vibrio cholerae.
Journal of bacteriology. 2007-02-01; 189.3: 717-29.
PMID: 17122338
Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR.
Journal of bacteriology. 2007-01-01; 189.1: 388-402.
PMID: 17071756
Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1.
Infection and immunity. 2006-06-01; 74.6: 3633-42.
PMID: 16714595
Transcriptome and phenotypic responses of Vibrio cholerae to increased cyclic di-GMP level.
Journal of bacteriology. 2006-05-01; 188.9: 3600-13.
PMID: 16672614
Cyclic-diGMP signal transduction systems in Vibrio cholerae: modulation of rugosity and biofilm formation.
Molecular microbiology. 2006-04-01; 60.2: 331-48.
PMID: 16573684
Infectious Fungi