Publications

Peer-reviewed journal publications

• Huang W, Li H, Tsourkas PK, McIlwain SJ, Ong I, Kyriakopoulos CE, Johnson B, Cho SY, Wells SA, Alzate AR, Jarrard DF, Heninger E, Lang JM (2025 Nov) Quantifying partial pathological response rate in prostate cancer patients who underwent neoadjuvant chemotherapy using a novel morphometric approach. J Pathology Informatics 100528.

• Jiang K, Fu Z, Tsourkas PK, Kothandapani A, Kearse T,McIlwain SJ, Mayere C, Nef S, Jorgensen J (2025 Jun) Single-Cell Resolution Uncovers Neighboring Cell Subtypes That Share Steroidogenic Capacity During Fetal Testis Development. PNAS 122(23):e2501392122.

• Kok DN, Gosselin SP, Howard B, Cresawn SG, Tsourkas PK, Hendrickson HL (2025 Jan) Genomic Analysis of 96 Paenibacillus larvae Bacteriophages Including 26 from Aotearoa, New Zealand. Viruses 17(2):137.

• Zheng C, Allen KO, Liu T, Solodin NM, Meyer MB, Salem K, Tsourkas PK, McIlwain SJ, Vera JM, Cromwell ER, Ozers MS, Fowler AM, Alarid ET (2024 Aug) Elevated GRHL2 Imparts Plasticity in ER-Positive Breast Cancer Cells. Cancers (Basel). 16(16):2906.

• Kim J, Herrera C, Aung WY, Gonzales Boyles GP, Chavez C, Cibulka M, Foley E, Guerra J, Kumar DBM, Levrant W, Lim L, Llanes J, O’Brien ZK, Pagaduan A, Richardson JA, Rosales K, Schrecengost J, Shin T, Strong-Lundquist G, Tat W, Vanderford F, Vrinceanu I, Wang V, Yang S, Strong C, Tsourkas PK, Regner K (2024 Jan) Complete genome sequences of cluster F1 and cluster B1 Mycobacterium smegmatis phages Karhdo and Basato. Microbiol. Resour. Announc. 17;13(1):e0093823.

• Sali O, Patel DM, Ortega MC, Han S, Esperanza Gonzales HG, et al. (2023 October) Complete genome sequences of cluster G1 and cluster K4 Mycobacterium smegmatis phages Omnicritical and Barkley26. Microbiol Resour Announc. 12(10):e0027423.

• Kok DN, Zhou D, Tsourkas PK, Hendrickson HL (2023 Aug). Paenibacillus larvae and their phages; a community science approach to discovery and initial testing of prophylactic phage cocktails against American Foulbrood in New Zealand. Microbiome Res. Rep. 2(4):30.

• Kok DN, Turnbull J, Takeuchi N, Tsourkas P, Hendrickson HL. (2023 Jun) In Vitro Evolution to Increase the Titers of Difficult Bacteriophages: RAMP-UP Protocol. PHAGE: Therapy, Applications & Research. 4(2):68-81.

• Unterberger CJ, McIlwain SJ, Tsourkas P, Maklakova VI, Prince JL, Onesti A, et al. (2023 Apr) Conditional gene regulation models demonstrate a pro-proliferative role for growth hormone receptor in prostate cancer. Prostate. 83(5):416-429.

• Unterberger CJ, Maklakova VI, Lazar M, Arneson PD, McIlwain SJ, Tsourkas P, et al. (2022) GH action in prostate cancer cells promotes proliferation, limits apoptosis, and regulates cancer-related gene expression. Endocrinology. 163(5):bqac031.

• Hanauer DI, Graham MJ, Arnold RJ, Ayuk MA, Balish MF, Beyer AR, et al. (2022) Instructional models for course-based research experience (CRE) teaching. Life Sci Ed. 21(ar8):1-14.

• Lazeroff M, Ryder G, Harris S, Tsourkas P (2021) Phage Commander, a software tool for rapid gene identification of genes in bacteriophage genomes using multiple programs. PHAGE: Therapy, Applications & Research. 2(4):204-213.

• Thompson J, Ozdemir A, Topchyan AM, Torosian M, Thymianos VZ, Eagle A, McCormick J, Boyles LKG, Benito AA, Regner K, Strong C, Tsourkas P (2021) Complete genome sequences of cluster A6 and cluster G1 Mycobacterium smegmatis phages Hoot and Jolene. 10(42):e00578-21.

• Stamereilers C, Wong S, Tsourkas P (2021) Characterization of CRISPR spacer and protospacer sequences in Paenibacillus larvae and its bacteriophages. Viruses 13(3):459-473.

• Palmer M, Hedlund BP, Roux S, Tsourkas P, et al. (2020) Diversity and distribution of a novel genus of hyperthermophilic Aquificae viruses encoding a proofreading family A DNA polymerase. Frontiers Env Microbiol. 11:2809. doi: 10.3389/fmicb.2020.583361.

• Van R, Nie W, Abdela F, Eivazi B, Kickbusch D, Finkle M, Cris C, Rubinstein M, Akavan B, Raja M, Vergara J, Andrade W, Barajas A, Sanchez J, Duenas M, Regner K, Strong C, Tsourkas P (2020) Complete genome sequences of a cluster P1 and cluster C1 Mycobacterium smegmatis phages Jung and Ronan. Microbiol Resource Announc. 9(999):e00678-20. doi: 10.1128/MRA.00678-20.

• Jacobs-Sera D, et al. (2020) Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One. 15(6):e0234636. doi: 10.1371/journal.pone.0234636.

• Tsourkas P (2020) Paenibacillus larvae bacteriophages: obscure past, promising future. Microb. Genomics. doi: 10.1099/mgen.0.000329 .

• Salisbury A, Doss R, Mehta A, Bhatti K, Dapra C, Huntsinger A, Rodriguez S, Yacek S, Sandberg R, Gildore A, Knudtson J, Tibayan F, Ohta T, Zafar N, Mercado G, Le A, Mekhaeel N, Willer J, Rodrich E, McFarland M, Regner K, Strong C, Tsourkas P (2019) Complete genome sequences of Mycobacterium smegmatis phages NihilNomen and Carlyle, isolated in Las Vegas, Nevada. Microbiol Resource Announc 8(38):e00677-19. doi: 10.1128/MRA.00677-19.

• Salisbury A, Tsourkas P. (2019) A method for improving the accuracy and efficiency of bacteriophage genome annotations. Int J Mol Sci. 20;3391. doi: 10.3390/ijms20143391.

• Faramarzi N, Dadkhah S, Sohal S, Al Azzam B, Tsourkas P, Pilla SV (2019) In hospital outcome of fall in the elderly population treated with direct oral coagulants versus warfarin. J Med & Clin Case Rep 3(2):1-6.

• Salisbury A, Cassin E, Ayala-Pineda K, Barroga N, Cadiz V, Cisneros R, Fersini J, Jeanite T, Juste J, Ines J, Leyva G, Macalinao D, Muscelli S, Nhan S, Reyes G, Rhoden H, Tan R, Torres E, Tran K, Uriarte-Valle G, Wallace C, Wong S, Regner K, Strong C, Tsourkas P (2019) Complete genome sequences of Mycobacterium smegmatis phages Chewbacca, Reptar3000, and Riparian, isolated in Las Vegas, Nevada. Microbiol Resource Announc 8(999):e01558-18. doi: 10.1128/MRA.01558-18.

•  Dadkhah S, Shrestha E, Kansakar AR, Faramarzi N, Parekh A, Dacenko-Grawe L, Sohal S, Abdalla MOA, Macchi Cattoni HJ, Al-azzam B, Tsourkas P (2018) Effect of modified early warning system on rapid response team call outcome. J Cardio Case Reports 1(1):1-3. doi: 10.15761/JCCR1000104.

• Merrill BD, Fajardo CP, Hilton JA, Payne AM, Ward AT, Walker JK, Dhalai A, Imahara C, Mangohig J, Monk J, Rai P, Pascacio C, Salisbury A, Velez K, Bloomfield TJ, Buhler B, Duncan SG, Furiman DA, George J, Graves K, Heaton KE, Hill HL, Kim M, Knabe BK, Ririe DB, Rogers SL, Stamereilers C, Stevenson MB, Ward CS, Wright CK, Withers JM, Usher BK, Breakwell DP, Grose JH, Hope S, and Tsourkas P (2018) Complete genome sequences of 18 Paenibacillus larvae phages from the Western United States. Microbiol Resource Announc 7(13):e00966-18. doi: 10.1128/MRA00966-18.

• Yost D, Chang C, LeBlanc L, Cassin E, Peterman C, Rai P, Salisbury A, Barroga N, Cisneros R, Fersini, J, Juste J, Ines J, Leyva G, Macalinao D, Muscelli S, Reyes S, Rhoden H, Tan R, Torres E, Tran K, Uriarte-Valle G, Wallace C, Wong S, Ayala Pineda K, Cadiz VM, Jeanite T, Nhan S, Strong C, Grose JH, Amy PS, Tsourkas P (2018) Complete genome sequences of Paenibacillus larvae phages Halcyone, Heath, Scottie, and Unity from the Las Vegas area. Microbiol Resource Announc 7(12):e00877-18. doi: 10.1128/MRA00977-18.

• Stamereilers C, Fajardo C, Walker J, Grose JH, Hope S, Tsourkas P (2018) Genomic analysis of 48 Paenibacillus larvae bacteriophage genomes. Viruses 10(7):377. doi: 10.3390/v10070377.

• Walker JK, Merrill BD, Berg JA, Dhalai A, Dingman DW, Fajardo CP, Graves K, Hill HL, Hilton JA, Imahara C, Knabe BK, Mangohig J, Monk J, Mun H, Payne AM, Salisbury A,  Stamereilers C, Velez K, Ward AT, Breakwell DP, Grose JH, Hope S, Tsourkas P (2018) Complete genome sequences of Paenibacillus larvae phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana. Microbiol. Resource Announc 6(4):e01601-17. doi: 10.1128/genomeA.01602-17.

• Stamereilers C, LeBlanc L, Yost DG, Amy PS, Tsourkas P (2016) Comparative genomics of 9 novel Paenibacillus larvae bacteriophages. Bacteriophage 6(3):e1220349. doi: 10.1080/21597081.2016.1220349.

• Yost DG, Tsourkas P, Amy PS (2016) Experimental bacteriophage treatment of honeybees (Apis mellifera) infected with Paenibacillus larvae, the causative agent of American Foulbrood Disease. Bacteriophage 6(1):e1122698. doi: 10.1080/21597081.2015.1122698.

• Tsourkas P, Yost D, Krohn A, Leblanc L, Zhang A, Stamereilers C, Amy PS (2015) Complete genome sequences of nine phages capable of infecting Paenibacillus larvae, the causative agent of American Foulbrood disease of honeybees. Microbiol. Resource Announc 3(5):e01120-15. doi: 10.1128/genomeA.01120-15. 

• LeBlanc L, Nezami S, Yost D, Tsourkas P, Amy PS (2015) Isolation and characterization of a novel phage lysin active against Paenibacillus larvae, a Honeybee pathogen. Bacteriophage 5(4):e1080787. doi: 10.1080/21597081.2015.1080787.

• Tsourkas P, Yu-Yang P, Liu W, Pierce SK, Raychaudhuri S (2012) Formation of BCR oligomers provides a mechanism for B cell affinity discrimination. J. Theor. Biol. 307:174-182. doi: 10.1016/j.jtbi.2012.05.008.

• Cooke DF, Goldring AB, Yamakyoshi I, Tsourkas P, et al. (2012) Fabrication of an inexpensive, implantable cooling device for reversible brain deactivation in animals ranging from rodents to primates. J. Neurophysiol. 107:3543-3558. doi: 10.1152/jn.01101.2011.

• Tsourkas P, Liu W, Das S, Pierce SK, Raychaudhuri S (2012) Affinity discrimination in response to membrane antigen in B cells requires that kinetic proofreading predominate over serial engagement. Cell. & Mol Immunol. 9:62-74. doi: 10.1038/cmi.2011.29.

• Alla SR, Tsourkas P, Raychaudhuri S (2011) Monte Carlo study of B-cell receptor clustering mediated by antigen cross-linking and directed transport. Cell. & Mol. Immunol. 8(3):255-264. doi: 10.1038/cmi.2011.3.

• Tsourkas P, Raychaudhuri S (2011) Monte Carlo investigation of diffusion of receptors and ligands that bind across opposing surfaces. Ann. Biomed. Engr. 39 (1):427-442. doi: 10.1007/s10439-010-0143-y.  
• Tsourkas P, Raychaudhuri S (2010) Modeling of B cell synapse formation by Monte Carlo simulation shows that directed transport of receptor molecules is a potential formation mechanism. Cell. & Mol.Bioeng. 3(3):256-268. doi: 10.1007/s12195-010-0123-1.

• Tsourkas P, Longo ML, Raychaudhuri S (2008) Monte Carlo study of single molecule diffusion can elucidate the mechanism of B cell synapse formation. Biophysical Journal 95:1118-1125. doi: 10.1529/biophysj.107.122564.

• Tsourkas P, Baumgarth N, Simon SI, and Raychaudhuri S (2007) Mechanisms of B cell synapse formation predicted by Monte Carlo simulation. Biophysical Journal 92:4196-4208. doi: 10.1529/biophysj.106.094995.

• Tsourkas P, Rubinsky B (2005) A parallel genetic algorithm for heat conduction problems. Numerical Heat Transfer B: Fundamentals 47:97-110. doi: 10.1080/10407790490515774.
• Tsourkas P, Rubinsky B (2003) An evolutionary-genetic algorithm for solving 2-D steady-state heat conduction problems. Numerical Heat Transfer B: Fundamentals 43:99-115. doi: 10.1080/713836171.

Selected Conference Abstracts

• Heninger E, Sperger JM, Weinstein K, Johnson BP, Geiger PG, Wells SA, Cho SY, Huang W, Tsourkas P, McIlwain S (2026) Differential Patterns of Immune Infiltration in the Tumor Immune Microenvironment Associate with Therapeutic Response in Primary Prostate Cancer Following Chemohormonal Therapy. Cancer Res 86 (Supplement 2): A023.
• Zheng C, Allen KO, Liu T, Solodin NM, Salem K, Fowler AM, Vera J, Tsourkas PK, McIlwain SJ, Ozers Mary S (2024) EMT Plasticity Induced By GRHL2 Overexpression Stimulates Dormancy And Enriches Stem Cell Characteristics In ER+ Breast Cancer Cells. J Endocr Soc 8 (Supplement 1):bvae163. 2158
• Shin M, Tsourkas P, Bradshaw T, Kyriakopoulos C, Huang W, Jarrard D, Lang J, Mcilwain SJ, Ong I, Wells S (2023) Predictive Features of 18F-DCFPyL PSMA PET/MRI in High-Risk Prostate Cancer Patients Treated with Neoadjuvant Chemohormonal Therapy Prior to Radical Prostatectomy. J Nucl Med 64 (Supplement 1): P1354-P1354.

Book Chapters                     

• Raychaudhuri S, Tsourkas P, Willgohs E (2009) Computational modeling of receptor-ligand binding and cellular signaling processes. In Handbook of Modern Biophysics, Volume I Fundamentals, T. Jue, editor. Humana Press, Springer, New York.

• Tsourkas P, Rubinsky B (2005) Principles of energy conservation in evolutionary genetics analysis. Annual Review of Heat Transfer 14:277-294.    

Ratified Taxonomy Proposals (peer-reviewed)

• Amy P, Kropinski AM, Adriaenssens EM, Kuhn JH, Tsourkas PK (2016). ICTV Taxonomic Proposal 2016.017a-dB.A.v1.Harrisonvirus. Create genus Harrisonvirus in the family Siphoviridae, order Caudovirales. 

• Amy P, Kropinski AM, Adriaenssens EM, Kuhn JH, Tsourkas PK (2016). ICTV Taxonomic Proposal 2016.052a-dB.A.v1.Vegasvirus. Create genus Vegasvirus in the family Siphoviridae, order Caudovirales.