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


Journal of fungi (Basel, Switzerland). 2024-02-25; 10.3:
The Host Response to Coccidioidomycosis
Kirkland TN, Hung CY, Shubitz LF, Beyhan S, Fierer J
PMID: 38535182
Journal of fungi (Basel, Switzerland). 2023-11-09; 9.11:
Evaluation of Different Gene Prediction Tools in Coccidioides immitis
Kirkland TN, Beyhan S, Stajich JE
PMID: 37998899
Current clinical microbiology reports. 2023-06-01; 10.2: 17-28.
Genetic Diversity of Human Fungal Pathogens
Freese J, Beyhan S
PMID: 37388463
PLoS biology. 2023-03-21; 21.3: e3002060.
Retraction: Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum
Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A
PMID: 36944162
Biosensors & bioelectronics. 2023-02-15; 222.114986.
A novel biosensor for ultrasensitive detection of fungal genes
Rana M, Yilmaz T, Cohen S, Beyhan S, Argun AA
PMID: 36508932
Journal of fungi (Basel, Switzerland). 2022-08-16; 8.8:
Coccidioides Species: A Review of Basic Research: 2022
Kirkland TN, Stevens DA, Hung CY, Beyhan S, Taylor JW, Shubitz LF, Duttke SH, Heidari A, Johnson RH, Deresinski SC, Lauer A, Fierer J
PMID: 36012847
PLoS pathogens. 2022-04-06; 18.4: e1009832.
The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii
Mandel MA, Beyhan S, Voorhies M, Shubitz LF, Galgiani JN, Orbach MJ, Sil A
PMID: 35385558
mSystems. 2022-02-22; 7.1: e0140421.
Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA
Duttke SH, Beyhan S, Singh R, Neal S, Viriyakosol S, Fierer J, Kirkland TN, Stajich JE, Benner C, Carlin AF
PMID: 35076277
mBio. 2022-02-22; 13.1: e0257421.
Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species
Voorhies M, Cohen S, Shea TP, Petrus S, Muñoz JF, Poplawski S, Goldman WE, Michael TP, Cuomo CA, Sil A, Beyhan S
PMID: 35089059
Journal of fungi (Basel, Switzerland). 2021-05-07; 7.5:
Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing
Carlin AF, Beyhan S, Peña JF, Stajich JE, Viriyakosol S, Fierer J, Kirkland TN
PMID: 34067070
PLoS computational biology. 2021-03-29; 17.3: e1008857.
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
Espinoza JL, Dupont CL, O'Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE
PMID: 33780444
Microbial genomics. 2020-12-01; 6.12:
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
Nguyen MH, Kaul D, Muto C, Cheng SJ, Richter RA, Bruno VM, Liu G, Beyhan S, Sundermann AJ, Mounaud S, Pasculle AW, Nierman WC, Driscoll E, Cumbie R, Clancy CJ, Dupont CL
PMID: 33245689
ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.
Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes
Yu Y, O'Rourke A, Lin YH, Singh H, Eguez RV, Beyhan S, Nelson KE
PMID: 32673475
mSystems. 2020-07-28; 5.4:
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
Rojas MI, Cavalcanti GS, McNair K, Benler S, Alker AT, Cobián-Güemes AG, Giluso M, Levi K, Rohwer F, Bailey BA, Beyhan S, Edwards RA, Shikuma NJ
PMID: 32723799
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling
O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE
PMID: 31907190
Frontiers in microbiology. 2020-02-19; 11.136.
Emerging Priorities for Microbiome Research
Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL
PMID: 32140140
Virulence. 2019-12-01; 10.1: 793-800.
Sensing the heat and the host: Virulence determinants of Histoplasma capsulatum
Beyhan S, Sil A
PMID: 31560240
Journal of natural products. 2019-06-28; 82.6: 1616-1626.
Secondary Metabolites of Onygenales Fungi Exemplified by Aioliomyces pyridodomos
Lin Z, Kakule TB, Reilly CA, Beyhan S, Schmidt EW
PMID: 31155876
Molecular microbiology. 2010-12-01; 78.5: 1171-81.
The Vibrio cholerae virulence regulatory cascade controls glucose uptake through activation of TarA, a small regulatory RNA
Richard AL, Withey JH, Beyhan S, Yildiz F, DiRita VJ
PMID: 21091503
Journal of bacteriology. 2010-09-01; 192.18: 4541-52.
Identification and characterization of a phosphodiesterase that inversely regulates motility and biofilm formation in Vibrio cholerae
Liu X, Beyhan S, Lim B, Linington RG, Yildiz FH
PMID: 20622061
Journal of bacteriology. 2009-09-01; 191.17: 5398-408.
Cell envelope perturbation induces oxidative stress and changes in iron homeostasis in Vibrio cholerae
Sikora AE, Beyhan S, Bagdasarian M, Yildiz FH, Sandkvist M
PMID: 19542276
Journal of bacteriology. 2009-06-01; 191.12: 3504-16.
Indole acts as an extracellular cue regulating gene expression in Vibrio cholerae
Mueller RS, Beyhan S, Saini SG, Yildiz FH, Bartlett DH
PMID: 19329638
Journal of bacteriology. 2008-11-01; 190.22: 7392-405.
Identification and characterization of cyclic diguanylate signaling systems controlling rugosity in Vibrio cholerae
Beyhan S, Odell LS, Yildiz FH
PMID: 18790873
Journal of bacteriology. 2007-02-01; 189.3: 717-29.
Regulation of Vibrio polysaccharide synthesis and virulence factor production by CdgC, a GGDEF-EAL domain protein, in Vibrio cholerae
Lim B, Beyhan S, Yildiz FH
PMID: 17122338
Journal of bacteriology. 2007-01-01; 189.1: 388-402.
Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR
Beyhan S, Bilecen K, Salama SR, Casper-Lindley C, Yildiz FH
PMID: 17071756
Infection and immunity. 2006-06-01; 74.6: 3633-42.
Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1
Beyhan S, Tischler AD, Camilli A, Yildiz FH
PMID: 16714595
Journal of bacteriology. 2006-05-01; 188.9: 3600-13.
Transcriptome and phenotypic responses of Vibrio cholerae to increased cyclic di-GMP level
Beyhan S, Tischler AD, Camilli A, Yildiz FH
PMID: 16672614
Molecular microbiology. 2006-04-01; 60.2: 331-48.
Cyclic-diGMP signal transduction systems in Vibrio cholerae: modulation of rugosity and biofilm formation
Lim B, Beyhan S, Meir J, Yildiz FH
PMID: 16573684
Infectious Fungi