Bibliography 2004 -
Savas S, Follett A, Bishop D, King J, Taylor-Cutting J, Bilash T, Etchegary H, Whitten C, Stuckless T. Designing and delivering public engagement activities together with patient partners: The experience of Public Conference on Cancer. Journal of Psychosocial Oncology Research and Practice. 2023 July 1; 5(31): 110. doi: 10.1097/OR9.0000000000000110.
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Curtis AA, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer. Frontiers in Oncology. 2023 Mar 14; 13:1122229. doi: 10.3389/fonc.2023.1122229.
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Savas S, Winsor M, Tenkorang EY, Simmonds C, Stuckless T. Social stigma associated with cancer in the Newfoundland and Labrador population: An exploratory study. Journal of Psychosocial Oncology Research and Practice. 2023 April 1; 5(2). doi:10.1097/OR9.0000000000000100.
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Etchegary H, Pike A, Puddester R, Watkins K, Warren M, Francis V, Woods M, Green J, Savas S, Seal M, Gao Z, Avery S, Curtis F, McGrath J, MacDonald D, Burry TN, Dawson L. Cancer prevention in cancer predisposition syndromes: A protocol for testing the feasibility of building a hereditary cancer research registry and nurse navigator follow up model. PLoS One. 2022 Dec 22; 17(12):e0279317. doi: 10.1371/journal.pone.0279317.
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Curtis A, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods. Frontiers in Genetics. 2022 Aug 3; 13:902217. doi: 10.3389/fgene.2022.902217.
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Labadie JD, Savas S, Harrison TA, Banbury B, Huang Y, Buchanan DD, Campbell PT, Gallinger SJ, Giles GG, Gunter MJ, Hoffmeister M, Hsu L, Jenkins MA, Lin Y, Ogino S, Phipps AI, Slattery ML, Steinfelder RS, Sun W, Van Guelpen B, Hua X, Figuieredo JC, Pai RK, Nassir R, Qi L, Chan AT, Peters U, Newcomb PA. Genome-wide association study identifies tumor anatomical site-specific risk variants for colorectal cancer survival. Scientific Reports. 2022 Jan 7; 12(1):127. doi: 10.1038/s41598-021-03945-x.
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Savas S, Etchegary H, Stuckless T, Whitten C, Wiseman J, Bishop D, King J, Cutting J, Peddle D. Public interest group on cancer research: a successful patient-researcher partnership in Newfoundland and Labrador. Research Involvement and Engagement. 2022 Sep 3; 8(1):46. doi: 10.1186/s40900-022-00380-8.
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Molecular Oncology. 2021 Jul 26. doi: 10.1002/1878-0261.13067.
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Afzaljavan F, Sadr AS, Savas S, Pasdar A. GATA3 somatic mutations are associated with clinicopathological features and expression profile in TCGA breast cancer patients. Scientific Reports. 2021 Jan 18; 11(1):1679. doi: 10.1038/s41598-020-80680-9.
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10  Penney ME, Parfrey PS, Savas S, Yilmaz YE. A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. BMC Cancer. 2019 Feb 9; 19(1):133. doi: 10.1186/s12885-019-5346-5.
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11  Penney ME, Parfrey PS, Savas S, Yilmaz YE. Correction to: A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. BMC Cancer. 2019 May 10; 19(1):437. doi: 10.1186/s12885-019-5672-7.
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12  Yu Y, Carey M, Pollett W, Green J, Dicks E, Parfrey P, Yilmaz YE, Savas S. The long-term survival characteristics of a cohort of colorectal cancer patients and baseline variables associated with survival outcomes with or without time-varying effects. BMC Medicine. 2019 Jul 29; 17(1):150. doi: 10.1186/s12916-019-1379-5.
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13  Zhu Y, Wang PP, Zhai G, Bapat B, Savas S, Woodrow JR, Campbell PT, Li Y, Yang N, Zhou X, Dicks E, Mclaughlin JR, Parfrey PS. Association of rs2282679 A>C polymorphism in vitamin D binding protein gene with colorectal cancer risk and survival: effect modification by dietary vitamin D intake. BMC Cancer. 2018 Feb 6; 18(1):155. doi: 10.1186/s12885-018-4026-1.
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14  Penney ME, Parfrey PS, Savas S, Yilmaz YE. Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses. Biomarker Research. 2018 Jun 13; 6:17. doi: 10.1186/s40364-018-0133-z.
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15  Savas S, Skardasi G. The SWI/SNF complex subunit genes: Their functions, variations, and links to risk and survival outcomes in human cancers. Critical Reviews in Oncology / Hematology. 2018 Mar; 123:114-131. doi: 10.1016/j.critrevonc.2018.01.009.
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16  Yu Y, Cheng D, Parfrey P, Liu G, Savas S. Two functional indel polymorphisms in the promoter region of the Brahma gene (BRM) and disease risk and progression-free survival in colorectal cancer. PLoS One. 2018 Jun 12; 13(6):e0198873. doi: 10.1371/journal.pone.0198873.
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17  He Y, Penney ME, Negandhi AA, Parfrey PS, Savas S, Yilmaz YE. XRCC3 Thr241Met and TYMS variable number tandem repeat polymorphisms are associated with time-to-metastasis in colorectal cancer. PLoS One. 2018 Feb 2; 13(2):e0192316. doi: 10.1371/journal.pone.0192316.
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18  Werdyani S, Yu Y, Skardasi G, Xu J, Shestopaloff K, Xu W, Dicks E, Green J, Parfrey P, Yilmaz YE, Savas S. Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse. Cancer Medicine. 2017 Jun; 6(6):1220-1232. doi: 10.1002/cam4.1074.
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19  Briollais L, Ozcelik H, Xu J, Kwiatkowski M, Lalonde E, Sendorek DH, Fleshner NE, Recker F, Kuk C, Olkhov-Mitsel E, Savas S, Hanna S, Juvet T, Hunter GA, Friedlander M, Li H, Chadwick K, Prassas I, Soosaipillai A, Randazzo M, Trachtenberg J, Toi A, Shiah YJ, Fraser M, van der Kwast T, Bristow RG, Bapat B, Diamandis EP, Boutros PC, Zlotta AR. Germline mutations in the Kallikrein 6 region and predisposition for aggressive prostate cancer. Journal of the National Cancer Institute. 2017 Apr 1; 109(4). doi: 10.1093/jnci/djw258.
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20  Faluyi OO, Eng L, Qiu X, Che J, Zhang Q, Cheng D, Ying N, Tse A, Kuang Q, Dodbiba L, Renouf DJ, Marsh S, Savas S, Mackay HJ, Knox JJ, Darling GE, Wong RK, Xu W, Azad AK, Liu G. Validation of microRNA pathway polymorphisms in esophageal adenocarcinoma survival. Cancer Medicine. 2017 Feb; 6(2):361-373. doi: 10.1002/cam4.989.
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21  Zhu Y, Wang PP, Zhai G, Bapat B, Savas S, Woodrow JR, Sharma I, Li Y, Zhou X, Yang N, Campbell PT, Dicks E, Parfrey PS, Mclaughlin JR. Vitamin D receptor and calcium-sensing receptor polymorphisms and colorectal cancer survival in the Newfoundland population. British Journal of Cancer. 2017 Sep 5; 117(6):898-906. doi: 10.1038/bjc.2017.242.
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22  Cuffe S, Azad AK, Qiu X, Qiu X, Brhane Y, Kuang Q, Marsh S, Savas S, Chen Z, Cheng D, Leighl NB, Goss G, Laurie SA, Seymour L, Bradbury PA, Shepherd FA, Tsao MS, Chen BE, Xu W, Liu G. ABCC2 polymorphisms and survival in the Princess Margaret cohort study and the NCIC clinical trials group BR.24 trial of platinum-treated advanced stage non-small cell lung cancer patients. Cancer Epidemiology. 2016 Jan 24; 41:50-56. doi: 10.1016/j.canep.2015.12.012.
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23  Barras D, Savas S. Biomarkers for colon cancer. Biomarkers in Cancer. 2016 Apr 20; 7(Suppl 1):49-50. doi: 10.4137/BIC.S39882.
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24  Dan LA, Werdyani S, Xu J, Shestopaloff K, Hyde A, Dicks E, Younghusband B, Green J, Parfrey P, Xu W, Savas S. No associations of a set of SNPs in the Vascular Endothelial Growth Factor (VEGF) and Matrix Metalloproteinase (MMP) genes with survival of colorectal cancer patients. Cancer Medicine. 2016 Sep; 5(9):2221-31. doi: 10.1002/cam4.796.
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25  Xu W, Xu J, Shestopaloff K, Dicks E, Green J, Parfrey P, Green R, Savas S. A genome wide association study on Newfoundland colorectal cancer patients' survival outcomes. Biomarker Research. 2015 Mar 19; 3:6. doi: 10.1186/s40364-015-0031-6.
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26  Savas S, Xu J, Werdyani S, Shestopaloff K, Dicks E, Green J, Parfrey P, Green R, Xu W. A survival association study of 102 polymorphisms previously associated with survival outcomes in colorectal cancer. BioMed Research International. 2015; 2015:968743. doi: 10.1155/2015/968743.
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27  Eng L, Azad AK, Qiu X, Kong QQ, Cheng D, Ying N, Tse A, Kuang Q, Dodbiba L, Renouf DJ, Marsh S, Savas S, Mackay HJ, Knox JJ, Darling GE, Wong RK, Xu W, Liu G, Faluyi OO. Discovery and validation of Vascular Endothelial Growth Factor (VEGF) pathway polymorphisms in esophageal adenocarcinoma outcome. Carcinogenesis. 2015 Sep; 36(9):956-62. doi: 10.1093/carcin/bgv073.
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28  Haja Mohideen AM, Dicks E, Parfrey P, Green R, Savas S. Mitochondrial DNA polymorphisms, its copy number change and outcome in colorectal cancer. BMC Research Notes. 2015 Jun 27; 8:272. doi: 10.1186/s13104-015-1250-5.
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29  Haja Mohideen AM, Hyde A, Squires J, Wang J, Dicks E, Younghusband B, Parfrey P, Green R, Savas S. Examining the polymorphisms in the hypoxia pathway genes in relation to outcome in colorectal cancer. PLoS One. 2014 Nov 18; 9(11):e113513. doi: 10.1371/journal.pone.0113513.
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30  Zhu Y, Yang SR, Wang PP, Savas S, Wish T, Zhao J, Green R, Woods M, Sun Z, Roebothan B, Squires J, Buehler S, Dicks E, Zhao J, McLaughlin JR, Parfrey PS, Campbell PT. Influence of pre-diagnostic cigarette smoking on colorectal cancer survival: overall and by tumour molecular phenotype. British Journal of Cancer. 2014 Mar 4; 110(5):1359-66. doi: 10.1038/bjc.2014.6.
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31  Zhu Y, Wu H, Wang PP, Savas S, Woodrow J, Wish T, Jin R, Green R, Woods M, Roebothan B, Buehler S, Dicks E, McLaughlin JR, Campbell PT, Parfrey PS. Dietary patterns and colorectal cancer recurrence and survival: a cohort study. BMJ Open. 2013 Feb 7; 3(2). doi: 10.1136/bmjopen-2012-002270.
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32  Negandhi AA, Hyde A, Dicks E, Pollett W, Younghusband BH, Parfrey P, Green RC, Savas S. MTHFR Glu429Ala and ERCC5 His46His polymorphisms are associated with prognosis in colorectal cancer patients: Analysis of two independent cohorts from Newfoundland. PLoS One. 2013 Apr 23; 8(4):e61469. doi: 10.1371/journal.pone.0061469.
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33  Savas S, Liu G, Xu W. Special considerations in prognostic research in cancer involving genetic polymorphisms. BMC Medicine. 2013 Jun 17; 11:149. doi: 10.1186/1741-7015-11-149.
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34  Savas S. A curated database of genetic markers from the angiogenesis/VEGF pathway and their relation to clinical outcome in human cancers. Acta Oncologica. 2012 Feb; 51(2):243-6. doi: 10.3109/0284186X.2011.636758.
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35  Azad AK, Bairati I, Samson E, Cheng D, Cheng L, Mirshams M, Savas S, Waldron J, Changshu W, Goldstein D, Xu W, Meyer F, Liu G . Genetic sequence variants and the development of secondary primary cancers in patients with head and neck cancers. Cancer. 2012 Mar 15; 118(6):1554-65. doi: 10.1002/cncr.26446.
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36  Savas S, Hyde A, Stuckless SN, Parfrey P, Younghusband HB, Green R. Serotonin transporter gene (SLC6A4) variations are associated with poor survival in colorectal cancer patients. PLoS One. 2012; 7(7):e38953. doi: 10.1371/journal.pone.0038953.
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37  Azad AK, Bairati I, Samson E, Cheng D, Mirshams M, Qiu X, Savas S, Waldron J, Wang C, Goldstein D, Xu W, Meyer F, Liu G. Validation of genetic sequence variants as prognostic factors in early-stage head and neck squamous cell cancer survival. Clinical Cancer Research. 2012 Jan 1; 18(1):196-206. doi: 10.1158/1078-0432.CCR-11-1759.
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38  Eng L, Azad AK, Habbous S, Pang V, Xu W, Maitland-van der Zee AH, Savas S, Mackay HJ, Amir E, Liu G. Vascular endothelial growth factor pathway polymorphisms as prognostic and pharmacogenetic factors in aancer: A systematic review and meta-analysis. Clinical Cancer Research. 2012 Sep 1; 18(17):4526-4537. doi: 10.1158/1078-0432.CCR-12-1315.
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39  Eng L, Ibrahim-zada I, Jarjanazi H, Savas S, Meschian M, Pritchard KI, Ozcelik H. Bioinformatic analyses identifies novel protein-coding pharmacogenomic markers associated with paclitaxel sensitivity in NCI60 cancer cell lines. BMC Medical Genomics. 2011 Feb 11; 4:18. doi: 10.1186/1755-8794-4-18.
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40  Savas S, Azorsa DO, Jarjanazi H, Ibrahim-Zada I, Gonzales IM, Arora S, Henderson MC, Choi YH, Briollais L, Ozcelik H, Tuzmen S. NCI60 cancer cell line panel data and RNAi analysis help identify EAF2 as a modulator of simvastatin and lovastatin response in HCT-116 cells. PLoS One. 2011 Apr 4; 6(4):e18306. doi: 10.1371/journal.pone.0018306 .
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41  Savas S, Briollais L, Ibrahim-zada I, Jarjanazi H, Choi YH, Musquera M, Fleshner N, Venkateswaran V, Ozcelik H. A whole-genome SNP association study of NCI60 cell line panel indicates a role of Ca2+ signaling in selenium resistance. PLoS One. 2010 Sep 7; 5(9):e12601. doi: 10.1371/journal.pone.0012601.
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42  Savas S, Younghusband HB. dbCPCO: a database of genetic markers tested for their predictive and prognostic value in colorectal cancer. Human Mutation. 2010 Aug; 31(8):901-7. doi: 10.1002/humu.21285.
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43  Savas S. Useful genetic variation databases for oncologists investigating the genetic basis of variable treatment response and survival in cancer. Acta Oncologica. 2010 Nov; 49(8):1217-26. doi: 10.3109/0284186X.2010.500297.
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44  Savas S, Geraci J, Jurisica I, Liu G. A comprehensive catalogue of functional genetic variations in the EGFR pathway: protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research. International Journal of Cancer. 2009 Sep 15; 125(6):1257-65. doi: 10.1002/ijc.24535.
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45  Savas S, Liu G. Genetic variations as cancer prognostic factors: review and update. Human Mutation. 2009 Oct; 30(10):1369-77. doi: 10.1002/humu.21078.
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46  Savas S, Liu G. Studying genetic variations in cancer prognosis (and risk): a primer for clinicians. Oncologist, 2009 Jul; 14(7):657-66. doi: 10.1634/theoncologist.2009-0042.
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47  Jarjanazi H, Savas S, Pabalan N, Dennis JW, Ozcelik H. Biological implications of SNPs in signal peptide domains of human proteins. Proteins. 2008 Feb 1; 70(2):394-403. doi: 10.1002/prot.21548.
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48  Jarjanazi H, Kiefer J, Savas S, Briollais L, Tuzmen S, Pabalan N, Ibrahim-Zada I, Mousses S, Ozcelik H. Discovery of genetic profiles impacting response to chemotherapy: application to gemcitabine. Human Mutation. 2008 Apr; 29(4):461-7. doi: 10.1002/humu.20732.
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49  Savas S, Taylor IW, Wrana JL, Ozcelik H. Functional nonsynonymous single nucleotide polymorphisms from the TGF-beta protein interaction network. Physiological Genomics. 2007 Apr 24; 29(2):109-17. doi: 10.1152/physiolgenomics.00226.2006.
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50  Savas S, Shariff M, Taylor IW, Ozcelik H. Human non-synonymous single nucleotide polymorphisms can influence ubiquitin-mediated protein degradation. OMICS: A Journal of Integrative Biology. 2007 Summer; 11(2):200-8. doi: 10.1089/omi.2007.4324.
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51  Figueiredo JC, Knight JA, Cho S, Savas S, Onay UV, Briollais L, Goodwin PJ, McLaughlin JR, Andrulis IL, Ozcelik H. Polymorphisms cMyc-N11S and p27-V109G and breast cancer risk and prognosis. BMC Cancer. 2007 Jun 14; 7:99. doi: 10.1186/1471-2407-7-99.
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52  Savas S, Schmidt S, Jarjanazi H, Ozcelik H. Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations. Human Genomics. 2006 Mar; 2(5):287-96. doi: 10.1186/1479-7364-2-5-287.
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53  Cho S, Savas S, Ozcelik H. Genetic variation and the mitogen-activated protein kinase (MAPK) signaling pathway. OMICS: A Journal of Integrative Biology. 2006 Spring; 10(1):66-81. doi: 10.1089/omi.2006.10.66.
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54  Prigoda NL, Savas S, Abdalla SA, Piovesan B, Rushlow D, Vandezande K, Zhang E, Ozcelik H, Gallie BL, Letarte M. Hereditary haemorrhagic telangiectasia: mutation detection, test sensitivity and novel mutations. Journal of Medical Genetics. 2006 Sep; 43(9):722-8. doi: 10.1136/jmg.2006.042606.
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55  Savas S, Tuzmen S, Ozcelik H. Human SNPs resulting in premature stop codons and protein truncation. Human Genomics. 2006 Mar; 2(5):274-86. doi: 10.1186/1479-7364-2-5-274.
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56  Savas S, Ahmad MF, Shariff M, Kim DY, Ozcelik H. Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins. Proteins. 2005 Feb 15; 58(3):697-705. doi: 10.1002/prot.20367.
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57  Savas S, Ozcelik H. Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. BMC Cancer 2005 Aug 19; 5:107. doi: 10.1186/1471-2407-5-107.
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58  Lentz J, Savas S, Ng SS, Athas G, Deininger P, Keats B. The USH1C 216G-->A splice-site mutation results in a 35-base-pair deletion. Human Genetics. 2005 Feb; 116(3):225-7. doi: 10.1007/s00439-004-1217-4.
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59  Keats BJ, Savas S. Genetic heterogeneity in Usher syndrome. American Journal of Medical Genetics Part A. 2004 Sep 15; 130A(1):13-6. doi: 10.1002/ajmg.a.30052.
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60  Savas S, Kim DY, Ahmad MF, Shariff M, Ozcelik H. Identifying functional genetic variants in DNA repair pathway using protein conservation analysis. Cancer Epidemiology, Biomarkers & Prevention. 2004 May; 13(5):801-7. doi: 10.1158/1055-9965.801.13.5.
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61  Savas S, Frischhertz B, Batzer MA, Deininger PL, Keats BJ. Structure, diversity, and evolution of the 45-bp VNTR in intron 5 of the USH1C gene. Genomics. 2004 Mar; 83(3):439-44. doi: 10.1016/j.ygeno.2003.09.006.
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