1. Li J, Yang A, Carneiro BA, Gamsiz Uzun ED, Massingham L, Uzun A. Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants. BMC Bioinformatics. 2024 Sep 3;25(1):288. doi: 10.1186/s12859-024-05875-7. PubMed PMID: 39227781.
  2. Underhill LA, Mennella JM, Tollefson GA, Uzun A, Lechner BE. Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes. BMC Med Genomics. 2024 Mar 5;17(1):72. doi: 10.1186/s12920-024-01841-7. PMID: 38443884;
  3. Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc. 2024 Jan 18;31(2):536-541. doi: 10.1093/jamia/ocad211. PMID: 38037121;
  4. Hacking S, Chou C, Baykara Y, Wang Y, Uzun A, Gamsiz Uzun ED. MMR Deficiency Defines Distinct Molecular Subtype of Breast Cancer with Histone Proteomic Networks. Int J Mol Sci. 2023 Mar 10;24(6):5327. doi: 10.3390/ijms24065327. PMID: 36982402; PMCID: PMC10049366.
  5. De Souza AL, Mega AE, Douglass J, Olszewski AJ, Gamsiz Uzun ED, Uzun A, Chou C, Duan F, Wang J, Ali A, Golijanin DJ, Holder SL, Lagos GG, Safran H, El-Deiry WS, Carneiro BA. Clinical features of patients with MTAP-deleted bladder cancer. Am J Cancer Res. 2023;13(1):326-339. eCollection 2023. PubMed PMID: 36777505; PubMed Central PMCID: PMC9906077.
  6. Scaffa A, Tollefson GA, Yao H, Rizal S, Wallace J, Oulhen N, Carr JF, Hegarty K, Uzun A, Dennery PA. Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein. Antioxidants (Basel). 2022 Oct 28;11(11):2135. doi: 10.3390/antiox11112135. PMID: 36358506; PMCID: PMC9686683.
  7. Jessica Schuster, George A Tollefson, Valeria Zarate, Anthony Agudelo, Joan Stabila, Ashok Ragavendran, James Padbury and Alper Uzun. Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia. Frontiers in Genetics Computational Genomics. June 2, 2022.
  8. Uzun A, Schuster JS, Stabila J, Zarate V, Tollefson GA, Agudelo A, Kothiyal P, Wong WSW, Padbury J. Protein interaction networks define the genetic architecture of preterm birth. Sci Rep. 2022 Jan 10;12(1):438. doi: 10.1038/s41598-021-03427-0. PMID: 35013336.
  9. Najrana T, Ahsan N, Abu-Eid R, Uzun A, Noble L, Tollefson G, Sanchez-Esteban J. Proteomic analysis of a murine model of lung hypoplasia induced by oligohydramnios. Pediatr Pulmonol. 2021 Jun 8. doi: 10.1002/ppul.25525. Epub ahead of print. PMID: 34102042.
  10. Bliss JM, Tollefson GA, Cuevas A, Longley SJ, Neale MN, Uzun A, Shaw SK. Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis. mSphere. 2021 Feb 10;6(1):e01071-20. doi: 10.1128/mSphere.01071-20. PMID: 33568454.
  11. Armanious D, Schuster J, Tollefson GA, Agudelo A, DeWan AT, Istrail S, Padbury J, Uzun A. Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool. Genomics. 2020 Jul 20:S0888-7543(20)30305-0. doi: 10.1016/j.ygeno.2020.07.028. Epub ahead of print. PMID: 32702417.
  12. Najrana T, Mahadeo A, Abu-Eid R, Kreienberg E, Schulte V, Uzun A, Schorl C, Goldberg L, Quesenberry P, Sanchez-Esteban J. Mechanical stretch regulates the expression of specific miRNA in extracellular vesicles released from lung epithelial cells. J Cell Physiol. 2020 Nov;235(11):8210-8223. doi: 10.1002/jcp.29476. Epub 2020 Jan 22. PMID: 31970782; PMCID: PMC7374064.
  13. Tollefson GA, Schuster J, Gelin F, Agudelo A, Ragavendran A, Restrepo I, Stey P, Padbury J, Uzun A. VIVA (VIsualization of VAriants): A VCF File Visualization Tool. Sci Rep. 2019 Sep 2;9(1):12648. doi: 10.1038/s41598-019-49114-z. PMID: 31477778; PMCID: PMC6718772.
  14. Ugur MR, Kutchy NA, de Menezes EB, Ul-Husna A, Haynes BP, Uzun A, Kaya A, Topper E, Moura A, Memili E. Retained Acetylated Histone Four in Bull Sperm Associated With Fertility. Front Vet Sci. 2019 Jul 31;6:223. doi: 10.3389/fvets.2019.00223. PMID: 31417913; PMCID: PMC6685445.
  15. Schuster J, Uzun A, Stablia J, Schorl C, Mori M, Padbury JF. Effect of prematurity on genome wide methylation in the placenta. BMC Med Genet. 2019 Jun 28;20(1):116. doi: 10.1186/s12881-019-0835-6. PubMed PMID: 31253109; PubMed Central PMCID: PMC6599230.
  16. Schuster J, Superdock M, Agudelo A, Stey P, Padbury J, Sarkar IN, Uzun A. Machine learning approach to literature mining for the genetics of complex diseases. Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz124. PubMed PMID: 31768545; PubMed Central PMCID: PMC6877776.
  17. Xu Y, Gray A, Hardie DG, Uzun A, Shaw S, Padbury J, Phornphutkul C, Tseng YT. A novel, de novo mutation in the PRKAG2 gene: infantile-onset phenotype and the signaling pathway involved. Am J Physiol Heart Circ Physiol. 2017 Aug 1;313(2):H283-H292. doi: 10.1152/ajpheart.00813.2016. Epub 2017 May 26. PubMed PMID: 28550180; PubMed Central PMCID: PMC5582920.
  18. Giarraputo J, DeLoach J, Padbury J, Uzun A, Marsit C, Hawes K, Lester B. Medical morbidities and DNA methylation of NR3C1 in preterm infants. Pediatr Res. 2017 Jan;81(1-1):68-74. doi: 10.1038/pr.2016.185. Epub 2016 Sep 21. PubMed PMID: 27653086; PubMed Central PMCID: PMC5313510.
  19. Uzun A, Sahin Y, Schuster JS, Zheng X, Ryckman K, Feingold E, Padbury J. Structural and genomic variation in preterm birth. Pediatr Res. 2016 Dec;80(6):829-836. doi: 10.1038/pr.2016.152. Epub 2016 Jul 24. PubMed PMID: 27466897; PubMed Central PMCID: PMC5112111.
  20. Uzun A, Schuster J, McGonnigal B, Schorl C, Dewan A, Padbury J. Targeted Sequencing and Meta-Analysis of Preterm Birth. PLoS One. 2016;11(5):e0155021. doi: 10.1371/journal.pone.0155021. eCollection 2016. PubMed PMID: 27163930; PubMed Central PMCID: PMC4862658.
  21. Saunders AC, McGonnigal B, Uzun A, Padbury J. The developmental expression of the CDK inhibitor p57(kip2) (Cdkn1c) in the early mouse placenta. Mol Reprod Dev. 2016 May;83(5):405-12. doi: 10.1002/mrd.22637. Epub 2016 Apr 28. PubMed PMID: 26988311.
  22. Uzun A, Triche EW, Schuster J, Dewan AT, Padbury JF. dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes. Database (Oxford). 2016;2016. doi: 10.1093/database/baw006. Print 2016. PubMed PMID: 26946289; PubMed Central PMCID: PMC4779341.
  23. Triche EW, Uzun A, DeWan AT, Kurihara I, Liu J, Occhiogrosso R, Shen B, Parker J, Padbury JF. Bioinformatic approach to the genetics of preeclampsia. Obstet Gynecol. 2014 Jun;123(6):1155-61. doi: 10.1097/AOG.0000000000000293. PubMed PMID: 24807322; PubMed Central PMCID: PMC4409136.
  24. Kawar N, Maclaughlan S, Horan TC, Uzun A, Lange TS, Kim KK, Hopson R, Singh AP, Sidhu PS, Glass KA, Shaw S, Padbury JF, Vorsa N, Arnold LA, Moore RG, Brard L, Singh RK. PT19c, Another Nonhypercalcemic Vitamin D2 Derivative, Demonstrates Antitumor Efficacy in Epithelial Ovarian and Endometrial Cancer Models. Genes Cancer. 2013 Nov;4(11-12):524-34. doi: 10.1177/1947601913507575. PubMed PMID: 24386512; PubMed Central PMCID: PMC3877664.
  25. Uzun A, Dewan AT, Istrail S, Padbury JF. Pathway-based genetic analysis of preterm birth. Genomics. 2013 Mar;101(3):163-70. doi: 10.1016/j.ygeno.2012.12.005. Epub 2013 Jan 6. PubMed PMID: 23298525; PubMed Central PMCID: PMC3570639.
  26. Govindaraju A, Uzun A, Robertson L, Atli MO, Kaya A, Topper E, Crate EA, Padbury J, Perkins A, Memili E. Dynamics of microRNAs in bull spermatozoa. Reprod Biol Endocrinol. 2012 Sep 14;10:82. doi: 10.1186/1477-7827-10-82. PubMed PMID: 22978562; PubMed Central PMCID: PMC3488333.
  27. Moore RG, Lange TS, Robinson K, Kim KK, Uzun A, Horan TC, Kawar N, Yano N, Chu SR, Mao Q, Brard L, DePaepe ME, Padbury JF, Arnold LA, Brodsky A, Shen TL, Singh RK. Efficacy of a non-hypercalcemic vitamin-D2 derived anti-cancer agent (MT19c) and inhibition of fatty acid synthesis in an ovarian cancer xenograft model. PLoS One. 2012;7(4):e34443. doi: 10.1371/journal.pone.0034443. Epub 2012 Apr 3. PubMed PMID: 22509304; PubMed Central PMCID: PMC3317945.
  28. Uzun A, Sharma S, Padbury J. A bioinformatics approach to preterm birth. Am J Reprod Immunol. 2012 Apr;67(4):273-7. doi: 10.1111/j.1600-0897.2012.01122.x. Epub 2012 Mar 5. Review. PubMed PMID: 22385126; PubMed Central PMCID: PMC3309125.
  29. Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. dbPTB: a database for preterm birth. Database (Oxford). 2012;2012:bar069. doi: 10.1093/database/bar069. Print 2012. PubMed PMID: 22323062; PubMed Central PMCID: PMC3275764.
  30. DeMaso CR, Kovacevic I, Uzun A, Cram EJ. Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2. PLoS One. 2011;6(7):e22428. doi: 10.1371/journal.pone.0022428. Epub 2011 Jul 25. PubMed PMID: 21799850; PubMed Central PMCID: PMC3143143.
  31. Uzun A, Rodriguez-Osorio N, Kaya A, Wang H, Parrish JJ, Ilyin VA, Memili E. Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis. BMC Genomics. 2009 Apr 24;10:183. doi: 10.1186/1471-2164-10-183. PubMed PMID: 19393058; PubMed Central PMCID: PMC2684548.
  32. Marziale F, Pucciarelli S, Ballarini P, Melki R, Uzun A, Ilyin VA, Detrich HW 3rd, Miceli C. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS J. 2008 Nov;275(21):5367-82. doi: 10.1111/j.1742-4658.2008.06666.x. PubMed PMID: 18959762.
  33. Abyzov A, Uzun A, Strauss PR, Ilyin VA. An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces. PLoS Comput Biol. 2008 Apr 25;4(4):e1000066. doi: 10.1371/journal.pcbi.1000066. PubMed PMID: 18437203; PubMed Central PMCID: PMC2289873.
  34. Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W384-92. doi: 10.1093/nar/gkm232. Epub 2007 May 30. PubMed PMID: 17537826; PubMed Central PMCID: PMC1933130.
  35. Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. Active site prediction for comparative model structures with thematics. J Bioinform Comput Biol. 2005 Feb;3(1):127-43. doi: 10.1142/s0219720005000916. PubMed PMID: 15751116.
  36. Hergenç G, Ozsüllü T, Uzun A. Coronary heart disease risk assessment in Kocaeli Region Turkey. Biochem Soc Trans. 1998 Feb;26(1):S20. doi: 10.1042/bst026s020. PubMed PMID: 10909778.

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