Prof. Dr. Süleyman Yıldırım
[email protected]Selected Publications;
Functional neural networks stratify Parkinson's disease patients across the spectrum of cognitive impairment
Hajebrahimi F, Budak M, Saricaoglu M, Temel Z, Demir TK, Hanoglu L, Yildirim S, Bayraktaroglu Z. Functional neural networks stratify Parkinson's disease patients across the spectrum of cognitive impairment. Brain Behav. 2024 Jan;14(1):e3395. doi: 10.1002/brb3.3395. PMID: 38376051; PMCID: PMC10808882.
[Investigation of the Relationship Between Akkermansia Genomic Diversity in Gut Microbiota and Parkinson's Disease Dementia]
Arıkan M, Kahraman Demir T, Yıldız Z, Helvacı Yılmaz N, Şen A, Hanoğlu L, Yıldırım S. Parkinson Hastalığı Demansı ile Bağırsak Mikrobiyotasındaki Akkermansia Genomik Çeşitliliği Arasındaki İlişkinin İncelenmesi [Investigation of the Relationship Between Akkermansia Genomic Diversity in Gut Microbiota and Parkinson's Disease Dementia]. Mikrobiyol Bul. 2024 Jan;58(1):13-28. Turkish. doi: 10.5578/mb.20249951. PMID: 38263937.
Functional neural networks stratify Parkinson's disease patients across the spectrum of cognitive impairment
Hajebrahimi F, Budak M, Saricaoglu M, Temel Z, Demir TK, Hanoglu L, Yildirim S, Bayraktaroglu Z. Functional neural networks stratify Parkinson's disease patients across the spectrum of cognitive impairment. Brain Behav. 2024 Jan;14(1):e3395. doi: 10.1002/brb3.3395. PMID: 38376051; PMCID: PMC10808882.
Axillary Microbiota Is Associated with Cognitive Impairment in Parkinson's Disease Patients
Arikan M, Yildiz Z, Kahraman Demir T, Yilmaz NH, Sen A, Hanoglu L, Yildirim S. Axillary Microbiota Is Associated with Cognitive Impairment in Parkinson's Disease Patients. Microbiol Spectr. 2022 Feb 23;10(1):e0235821. doi: 10.1128/spectrum.02358-21. Epub 2022 Feb 9. PMID: 35138147; PMCID: PMC8826741.
Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort
Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, Ercan FB, Gündoğdu A, Velioğlu HA, Göl MF, Soylu AE, Koç F, Gülpınar EA, Kadak KS, Arıkan M, Mardinoğlu A, Koçak M, Köseoğlu E, Hanoğlu L. Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort. mSystems. 2022 Feb 22;7(1):e0000422. doi: 10.1128/msystems.00004-22. Epub 2022 Feb 8. PMID: 35133187; PMCID: PMC8823292.
Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity?
Yıldırım S, Shoskes D, Kulkarni S, Laguna P. Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity? World J Urol. 2020 Nov;38(11):2721-2731. doi: 10.1007/s00345-020-03099-x. Epub 2020 Jan 31. PMID: 32006175.
Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum
Demircan T, İlhan AE, Ovezmyradov G, Öztürk G, Yıldırım S. Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum. Sci Data. 2019 May 23;6(1):70. doi: 10.1038/s41597-019-0077-7. PMID: 31123261; PMCID: PMC6533342.
Experimentally Induced Metamorphosis in Axolotl (Ambystoma mexicanum) Under Constant Diet Restructures Microbiota Accompanied by Reduced Limb Regenerative Capacity
Demircan T, Ovezmyradov G, Yıldırım B, Keskin İ, İlhan AE, Fesçioğlu EC, Öztürk G, Yıldırım S. Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota. Sci Rep. 2018 Jul 20;8(1):10974. doi: 10.1038/s41598-018-29373-y. PMID: 30030457; PMCID: PMC6054665.
Association of enteric protist blastocystis spp. And gut microbiota with hepatic encephalopathy
Yildiz S, Doğan İ, Doğruman-Al F, Nalbantoğlu U, Üstek D, Sarzhanov F, Yildirim S. Association of Enteric Protist Blastocystis spp. and Gut Microbiota with Hepatic Encephalopathy. J Gastrointestin Liver Dis. 2016 Dec;25(4):489-497. doi: 10.15403/jgld.2014.1121.254.yiz. PMID: 27981305.
Evaluation of Parameters for High Efficiency Transformation of Acinetobacter baumannii
Yildirim S, Thompson MG, Jacobs AC, Zurawski DV, Kirkup BC. Evaluation of Parameters for High Efficiency Transformation of Acinetobacter baumannii. Sci Rep. 2016 Feb 25;6:22110. doi: 10.1038/srep22110. PMID: 26911658; PMCID: PMC4766488.
Terrestrial Vertebrate Animal Metagenomics: Non-domesticated Primates, Prosimians
Yildirim, S. (2014). Terrestrial Vertebrate Animal Metagenomics: Non-domesticated Primates, Prosimians. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_108-7
Validation of a novel murine wound model of Acinetobacter baumannii infection
Thompson MG, Black CC, Pavlicek RL, Honnold CL, Wise MC, Alamneh YA, Moon JK, Kessler JL, Si Y, Williams R, Yildirim S, Kirkup BC Jr, Green RK, Hall ER, Palys TJ, Zurawski DV. Validation of a novel murine wound model of Acinetobacter baumannii infection. Antimicrob Agents Chemother. 2014;58(3):1332-42. doi: 10.1128/AAC.01944-13. Epub 2013 Dec 16. PMID: 24342634; PMCID: PMC3957858.
Genetic Manipulation of Acinetobacter baumannii
Jacobs AC, Thompson MG, Gebhardt M, Corey BW, Yildirim S, Shuman HA, Zurawski DV. Genetic Manipulation of Acinetobacter baumannii. Curr Protoc Microbiol. 2014 Nov 3;35:6G.2.1-11. doi: 10.1002/9780471729259.mc06g02s35. PMID: 25367274.
Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance
Yildirim S, Yeoman CJ, Janga SC, Thomas SM, Ho M, Leigh SR; Primate Microbiome Consortium; White BA, Wilson BA, Stumpf RM. Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance. ISME J. 2014 Dec;8(12):2431-44. doi: 10.1038/ismej.2014.90. Epub 2014 Jul 18. PMID: 25036926; PMCID: PMC4260710.
Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes
Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 2013 Jul;7(7):1344-53. doi: 10.1038/ismej.2013.16. Epub 2013 Mar 14. PMID: 23486247; PMCID: PMC3695285.
Pilus gene pool variation and the virulence of Corynebacterium diphtheriae clinical isolates during infection of a nematode
Broadway MM, Rogers EA, Chang C, Huang IH, Dwivedi P, Yildirim S, Schmitt MP, Das A, Ton-That H. Pilus gene pool variation and the virulence of Corynebacterium diphtheriae clinical isolates during infection of a nematode. J Bacteriol. 2013 Aug;195(16):3774-83. doi: 10.1128/JB.00500-13. Epub 2013 Jun 14. PMID: 23772071; PMCID: PMC3754579.
The primate vaginal microbiome: comparative context and implications for human health and disease
Stumpf RM, Wilson BA, Rivera A, Yildirim S, Yeoman CJ, Polk JD, White BA, Leigh SR. The primate vaginal microbiome: comparative context and implications for human health and disease. Am J Phys Anthropol. 2013 Dec;152 Suppl 57:119-34. doi: 10.1002/ajpa.22395. Epub 2013 Oct 28. PMID: 24166771.
Heavy metal and disinfectant resistance of Listeria monocytogenes from foods and food processing plants
Ratani SS, Siletzky RM, Dutta V, Yildirim S, Osborne JA, Lin W, Hitchins AD, Ward TJ, Kathariou S. Heavy metal and disinfectant resistance of Listeria monocytogenes from foods and food processing plants. Appl Environ Microbiol. 2012 Oct;78(19):6938-45. doi: 10.1128/AEM.01553-12. Epub 2012 Jul 27. PMID: 22843526; PMCID: PMC3457492.
Comparative analysis of the vaginal microbiome in health and disease
White, B.A., Gomez, A.M., Ho, M. et al. Comparative analysis of the vaginal microbiome in health and disease. Genome Biol 12 (Suppl 1), I17 (2011). https://doi.org/10.1186/gb-2011-12-s1-i17
Towards an Evolutionary Model of Animal-Associated Microbiomes
Yeoman, C.J.; Chia, N.; Yildirim, S.; Miller, M.E.B.; Kent, A.; Stumpf, R.; Leigh, S.R.; Nelson, K.E.; White, B.A.; Wilson, B.A. Towards an Evolutionary Model of Animal-Associated Microbiomes. Entropy 2011, 13, 570-594. https://doi.org/10.3390/e13030570
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential
Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA. Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. PLoS One. 2010 Aug 26;5(8):e12411. doi: 10.1371/journal.pone.0012411. PMID: 20865041; PMCID: PMC2928729.
Conservation of genomic localization and sequence content of Sau3AI-like restriction-modification gene cassettes among listeria monocytogenes epidemic clone I and selected strains of serotype 1/2a
Yildirim SElhanafi DLin WHitchins AD, Siletzky RM, Kathariou S 2010. Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a. Appl Environ Microbiol 76:.
https://doi.org/10.1128/AEM.00648-10
Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities
Yildirim S, Yeoman CJ, Sipos M, Torralba M, Wilson BA, Goldberg TL, Stumpf RM, Leigh SR, White BA, Nelson KE. Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities. PLoS One. 2010 Nov 12;5(11):e13963. doi: 10.1371/journal.pone.0013963. PMID: 21103066; PMCID: PMC2980488.
Analysis of milk gland structure and function in Glossina morsitans: Milk protein production, symbiont populations and fecundity
Attardo GM, Lohs C, Heddi A, Alam UH, Yildirim S, Aksoy S. Analysis of milk gland structure and function in Glossina morsitans: milk protein production, symbiont populations and fecundity. J Insect Physiol. 2008 Aug;54(8):1236-42. doi: 10.1016/j.jinsphys.2008.06.008. Epub 2008 Jul 4. PMID: 18647605; PMCID: PMC2613686.
Epidemic Clone I-Specific Genetic Markers in Strains of Listeria monocytogenes Serotype 4b from Foods
Yildirim S, Lin W, Hitchins AD, Jaykus L, Altermann E, Klaenhammer TR, Kathariou S 2004. Epidemic Clone I-Specific Genetic Markers in Strains of Listeria monocytogenes Serotype 4b from Foods. Appl Environ Microbiol 70:.
https://doi.org/10.1128/AEM.70.7.4158-4164.2004
Natural atypical Listeria innocua strains with Listeria monocytogenes pathogenicity island 1 genes
Johnson J, Jinneman K, Stelma G, Smith BG, Lye D, Messer J, Ulaszek J, Evsen L, Gendel S, Bennett RW, Swaminathan B, Pruckler J, Steigerwalt A, Kathariou S, Yildirim S, Volokhov D, Rasooly A, Chizhikov V, Wiedmann M, Fortes E, Duvall RE, Hitchins AD 2004. Natural Atypical Listeria innocua Strains with Listeria monocytogenes Pathogenicity Island 1 Genes. Appl Environ Microbiol 70:.
https://doi.org/10.1128/AEM.70.7.4256-4266.2004