Sinem Beyhan, PhD

Associate Professor

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

Publications

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

Molecular microbiology. 2007-02-01; 63.4: 995-1007.

Smooth to rugose phase variation in Vibrio cholerae can be mediated by a single nucleotide change that targets c-di-GMP signalling pathway

Beyhan S, Yildiz FH

PMID: 17233827

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