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Deng X, Geng H, Ali H. Learning yeast gene functions from heterogeneous sources of data using hybrid weighted Bayesian networks. Proc IEEE Comput Syst Bioinform Conf. 2005;:25-34. doi: 10.1109/csb.2005.38. PubMed PMID: 16447959.
Deng X, Geng H, Ali H. EXAMINE: a computational approach to reconstructing gene regulatory networks. Biosystems. 2005 Aug;81(2):125-36. doi: 10.1016/j.biosystems.2005.02.007. PubMed PMID: 15951103.
Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 2006 Apr;4(2):217-39. doi: 10.1142/s0219720006001928. PubMed PMID: 16819781.
Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol. 2006 Sep;24(9):1162-9. doi: 10.1038/nbt1238. PubMed PMID: 17061323.
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep;24(9):1151-61. doi: 10.1038/nbt1239. PubMed PMID: 16964229; PubMed Central PMCID: PMC3272078.
Deng X, Geng H, Bastola DR, Ali HH. Link test--A statistical method for finding prostate cancer biomarkers. Comput Biol Chem. 2006 Dec;30(6):425-33. doi: 10.1016/j.compbiolchem.2006.09.002. PubMed PMID: 17126079; PubMed Central PMCID: PMC1941704.
Deng X, Geng H, Matache MT. Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes. Biosystems. 2007 Mar;88(1-2):16-34. doi: 10.1016/j.biosystems.2006.04.002. Epub 2006 Jul 25. PubMed PMID: 16870321.
Deng X, Geng H, Ali HH. Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data. Cancer Inform. 2007 Apr 29;3:183-202. PubMed PMID: 19455243; PubMed Central PMCID: PMC2675834.
Xu J, Deng X, Chan V, Kelley-Loughnane N, Harker BW, Shi L, Hussain SM, Frazier JM, Wang C. Variability of DNA microarray gene expression profiles in cultured rat primary hepatocytes. Gene Regul Syst Bio. 2007 Nov 18;1:235-49. PubMed PMID: 19936092; PubMed Central PMCID: PMC2759134.
Deng X, Geng H, Ali HH. A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data. Int J Bioinform Res Appl. 2008;4(3):263-73. doi: 10.1504/IJBRA.2008.019574. PubMed PMID: 18640903.
Geng H, Deng X, Ali HH. Message Passing Clustering (MPC): a knowledge-based framework for clustering under biological constraints. Int J Data Min Bioinform. 2008;2(2):95-120. doi: 10.1504/ijdmb.2008.019092. PubMed PMID: 18767349.
Xu J, Deng X, Demetriou AA, Farkas DL, Hui T, Wang C. Factors released from cholestatic rat livers possibly involved in inducing bone marrow hepatic stem cell priming. Stem Cells Dev. 2008 Feb;17(1):143-55. doi: 10.1089/scd.2007.0094. PubMed PMID: 18225978.
Deng X, Xu J, Wang C. Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S14. doi: 10.1186/1471-2105-9-S6-S14. PubMed PMID: 18541049; PubMed Central PMCID: PMC2423437.
Deng X, Xu J, Hui J, Wang C. Probability fold change: a robust computational approach for identifying differentially expressed gene lists. Comput Methods Programs Biomed. 2009 Feb;93(2):124-39. doi: 10.1016/j.cmpb.2008.07.013. Epub 2008 Oct 7. PubMed PMID: 18842321.
Deng X, Campagne F. Introduction to the development and validation of predictive biomarker models from high-throughput data sets. Methods Mol Biol. 2010;620:435-70. doi: 10.1007/978-1-60761-580-4_15. PubMed PMID: 20652515.
Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Löwenberg B, Delwel R, Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010 Jan 19;17(1):13-27. doi: 10.1016/j.ccr.2009.11.020. Epub 2010 Jan 7. PubMed PMID: 20060365; PubMed Central PMCID: PMC3008568.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30. PubMed PMID: 20676074; PubMed Central PMCID: PMC3315840.
Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics. 2011 Jun 29;12:267. doi: 10.1186/1471-2105-12-267. PubMed PMID: 21714929; PubMed Central PMCID: PMC3148209.
Chen Z, Liu Z, Li W, Qu K, Deng X, Varma MG, Fichera A, Pigazzi A, Garcia-Aguilar J. Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer. Genes Chromosomes Cancer. 2011 Sep;50(9):689-99. doi: 10.1002/gcc.20891. Epub 2011 May 16. PubMed PMID: 21584903; PubMed Central PMCID: PMC3134546.
Lin HH, Li X, Chen JL, Sun X, Cooper FN, Chen YR, Zhang W, Chung Y, Li A, Cheng CT, Yang L, Deng X, Liu X, Yen Y, Johnson DL, Shih HM, Yang A, Ann DK. Identification of an AAA ATPase VPS4B-dependent pathway that modulates epidermal growth factor receptor abundance and signaling during hypoxia. Mol Cell Biol. 2012 Mar;32(6):1124-38. doi: 10.1128/MCB.06053-11. Epub 2012 Jan 17. PubMed PMID: 22252323; PubMed Central PMCID: PMC3295017.
Chen Z, Liu Z, Deng X, Warden C, Li W, Garcia-Aguilar J. Chromosomal copy number alterations are associated with persistent lymph node metastasis after chemoradiation in locally advanced rectal cancer. Dis Colon Rectum. 2012 Jun;55(6):677-85. doi: 10.1097/DCR.0b013e31824f873f. PubMed PMID: 22595848; PubMed Central PMCID: PMC3356567.
Li L, Diab S, McGraw S, Barr B, Traslavina R, Higgins R, Talbot T, Blanchard P, Rimoldi G, Fahsbender E, Page B, Phan TG, Wang C, Deng X, Pesavento P, Delwart E. Divergent astrovirus associated with neurologic disease in cattle. Emerg Infect Dis. 2013;19(9):1385-92. doi: 10.3201/eid1909.130682. PubMed PMID: 23965613; PubMed Central PMCID: PMC3810933.
Li L, Pesavento PA, Leutenegger CM, Estrada M, Coffey LL, Naccache SN, Samayoa E, Chiu C, Qiu J, Wang C, Deng X, Delwart E. A novel bocavirus in canine liver. Virol J. 2013 Feb 13;10:54. doi: 10.1186/1743-422X-10-54. PubMed PMID: 23402347; PubMed Central PMCID: PMC3577433.
Jackman RP, Deng X, Bolgiano D, Lebedeva M, Heitman JW, Busch MP, Slichter SJ, Norris PJ. Low-level HLA antibodies do not predict platelet transfusion failure in TRAP study participants. Blood. 2013 Apr 18;121(16):3261-6; quiz 3299. doi: 10.1182/blood-2012-12-472779. Epub 2013 Feb 7. PubMed PMID: 23393051; PubMed Central PMCID: PMC3630837.
Feng J, Zhang Z, Wu X, Mao A, Chang F, Deng X, Gao H, Ouyang C, Dery KJ, Le K, Longmate J, Marek C, St Amand RP, Krontiris TG, Shively JE. Discovery of potential new gene variants and inflammatory cytokine associations with fibromyalgia syndrome by whole exome sequencing. PLoS One. 2013;8(6):e65033. doi: 10.1371/journal.pone.0065033. Print 2013. PubMed PMID: 23762283; PubMed Central PMCID: PMC3677902.
Phan TG, Vo NP, Boros Á, Pankovics P, Reuter G, Li OT, Wang C, Deng X, Poon LL, Delwart E. The viruses of wild pigeon droppings. PLoS One. 2013;8(9):e72787. doi: 10.1371/journal.pone.0072787. eCollection 2013. PubMed PMID: 24023772; PubMed Central PMCID: PMC3762862.
Li L, Deng X, Linsuwanon P, Bangsberg D, Bwana MB, Hunt P, Martin JN, Deeks SG, Delwart E. AIDS alters the commensal plasma virome. J Virol. 2013 Oct;87(19):10912-5. doi: 10.1128/JVI.01839-13. Epub 2013 Jul 31. PubMed PMID: 23903845; PubMed Central PMCID: PMC3807392.
Abdel-Mohsen M, Raposo RA, Deng X, Li M, Liegler T, Sinclair E, Salama MS, Ghanem Hel-D, Hoh R, Wong JK, David M, Nixon DF, Deeks SG, Pillai SK. Expression profile of host restriction factors in HIV-1 elite controllers. Retrovirology. 2013 Oct 16;10:106. doi: 10.1186/1742-4690-10-106. PubMed PMID: 24131498; PubMed Central PMCID: PMC3827935.
Brown CE, Warden CD, Starr R, Deng X, Badie B, Yuan YC, Forman SJ, Barish ME. Glioma IL13Rα2 is associated with mesenchymal signature gene expression and poor patient prognosis. PLoS One. 2013;8(10):e77769. doi: 10.1371/journal.pone.0077769. eCollection 2013. PubMed PMID: 24204956; PubMed Central PMCID: PMC3800130.
Gia Phan T, Phung Vo N, Sdiri-Loulizi K, Aouni M, Pothier P, Ambert-Balay K, Deng X, Delwart E. Divergent gyroviruses in the feces of Tunisian children. Virology. 2013 Nov;446(1-2):346-8. doi: 10.1016/j.virol.2013.08.020. Epub 2013 Sep 8. PubMed PMID: 24074598; PubMed Central PMCID: PMC3804065.
Deng X, Sabino EC, Cunha-Neto E, Ribeiro AL, Ianni B, Mady C, Busch MP, Seielstad M. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. PLoS One. 2013;8(11):e79629. doi: 10.1371/journal.pone.0079629. eCollection 2013. PubMed PMID: 24324551; PubMed Central PMCID: PMC3854669.
Abdel-Mohsen M, Deng X, Liegler T, Guatelli JC, Salama MS, Ghanem Hel-D, Rauch A, Ledergerber B, Deeks SG, Günthard HF, Wong JK, Pillai SK. Effects of alpha interferon treatment on intrinsic anti-HIV-1 immunity in vivo. J Virol. 2014 Jan;88(1):763-7. doi: 10.1128/JVI.02687-13. Epub 2013 Oct 23. PubMed PMID: 24155399; PubMed Central PMCID: PMC3911728.
Coffey LL, Page BL, Greninger AL, Herring BL, Russell RC, Doggett SL, Haniotis J, Wang C, Deng X, Delwart EL. Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes. Virology. 2014 Jan 5;448:146-58. doi: 10.1016/j.virol.2013.09.026. Epub 2013 Oct 25. PubMed PMID: 24314645; PubMed Central PMCID: PMC3870893.
Danesh A, Inglis HC, Jackman RP, Wu S, Deng X, Muench MO, Heitman JW, Norris PJ. Exosomes from red blood cell units bind to monocytes and induce proinflammatory cytokines, boosting T-cell responses in vitro. Blood. 2014 Jan 30;123(5):687-96. doi: 10.1182/blood-2013-10-530469. Epub 2013 Dec 12. PubMed PMID: 24335232; PubMed Central PMCID: PMC3907755.
Jackman RP, Deng X, Bolgiano D, Utter GH, Schechterly C, Lebedeva M, Operskalski E, Luban NL, Alter H, Busch MP, Slichter SJ, Norris PJ. Leukoreduction and ultraviolet treatment reduce both the magnitude and the duration of the HLA antibody response. Transfusion. 2014 Mar;54(3):672-80. doi: 10.1111/trf.12317. Epub 2013 Jun 30. PubMed PMID: 23808544; PubMed Central PMCID: PMC3825847.
Keating SM, Heitman JD, Wu S, Deng X, Stramer SL, Kuhns MC, Mullen C, Norris PJ, Busch MP. Cytokine and chemokine responses in the acute phase of hepatitis B virus replication in naive and previously vaccinated blood and plasma donors. J Infect Dis. 2014 Mar;209(6):845-54. doi: 10.1093/infdis/jit563. Epub 2013 Oct 24. PubMed PMID: 24158960; PubMed Central PMCID: PMC4817642.
Phan TG, Luchsinger V, Avendaño LF, Deng X, Delwart E. Cyclovirus in nasopharyngeal aspirates of Chilean children with respiratory infections. J Gen Virol. 2014 Apr;95(Pt 4):922-927. doi: 10.1099/vir.0.061143-0. Epub 2014 Jan 13. PubMed PMID: 24421114; PubMed Central PMCID: PMC3973479.
Ng TF, Vega E, Kondov NO, Markey C, Deng X, Gregoricus N, Vinjé J, Delwart E. Divergent picobirnaviruses in human feces. Genome Announc. 2014 May 15;2(3). doi: 10.1128/genomeA.00415-14. PubMed PMID: 24831146; PubMed Central PMCID: PMC4022810.
Phan TG, Nordgren J, Ouermi D, Simpore J, Nitiema LW, Deng X, Delwart E. New astrovirus in human feces from Burkina Faso. J Clin Virol. 2014 Jun;60(2):161-4. doi: 10.1016/j.jcv.2014.03.024. Epub 2014 Apr 13. PubMed PMID: 24775733; PubMed Central PMCID: PMC4047031.
Ng TF, Mesquita JR, Nascimento MS, Kondov NO, Wong W, Reuter G, Knowles NJ, Vega E, Esona MD, Deng X, Vinjé J, Delwart E. Feline fecal virome reveals novel and prevalent enteric viruses. Vet Microbiol. 2014 Jun 25;171(1-2):102-11. doi: 10.1016/j.vetmic.2014.04.005. Epub 2014 Apr 13. PubMed PMID: 24793097; PubMed Central PMCID: PMC4080910.
Jacobs ES, Persad D, Ran L, Danesh A, Heitman JW, Deng X, Cameron MJ, Kelvin DJ, Norris PJ. A CD4+ T cell antagonist epitope down-regulates activating signaling proteins, up-regulates inhibitory signaling proteins and abrogates HIV-specific T cell function. Retrovirology. 2014 Jul 5;11:57. doi: 10.1186/1742-4690-11-57. PubMed PMID: 24996903; PubMed Central PMCID: PMC4227135.
Long D, Fix OK, Deng X, Seielstad M, Lauring AS. Whole genome sequencing to identify host genetic risk factors for severe outcomes of hepatitis a virus infection. J Med Virol. 2014 Oct;86(10):1661-8. doi: 10.1002/jmv.24007. Epub 2014 Jun 30. PubMed PMID: 24978929; PubMed Central PMCID: PMC4374731.
Raposo RA, Abdel-Mohsen M, Deng X, Hecht FM, Pilcher CD, Pillai SK, Nixon DF. Dynamic regulation of host restriction factor expression over the course of HIV-1 infection in vivo. J Virol. 2014 Oct;88(19):11624-9. doi: 10.1128/JVI.01771-14. Epub 2014 Jul 16. PubMed PMID: 25031350; PubMed Central PMCID: PMC4178813.
Abdel-Mohsen M, Deng X, Danesh A, Liegler T, Jacobs ES, Rauch A, Ledergerber B, Norris PJ, Günthard HF, Wong JK, Pillai SK. Role of microRNA modulation in the interferon-α/ribavirin suppression of HIV-1 in vivo. PLoS One. 2014;9(10):e109220. doi: 10.1371/journal.pone.0109220. eCollection 2014. PubMed PMID: 25275557; PubMed Central PMCID: PMC4183579.
Phan TG, Sdiri-Loulizi K, Aouni M, Ambert-Balay K, Pothier P, Deng X, Delwart E. New parvovirus in child with unexplained diarrhea, Tunisia. Emerg Infect Dis. 2014 Nov;20(11):1911-3. doi: 10.3201/eid2011.140428. PubMed PMID: 25340816; PubMed Central PMCID: PMC4214302.
Zhang W, Li L, Deng X, Kapusinszky B, Delwart E. What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken. Virology. 2014 Nov;468-470:303-310. doi: 10.1016/j.virol.2014.08.025. Epub 2014 Sep 16. PubMed PMID: 25217712; PubMed Central PMCID: PMC4252299.
Zhang W, Li L, Deng X, Kapusinszky B, Pesavento PA, Delwart E. Faecal virome of cats in an animal shelter. J Gen Virol. 2014 Nov;95(Pt 11):2553-2564. doi: 10.1099/vir.0.069674-0. Epub 2014 Jul 30. PubMed PMID: 25078300; PubMed Central PMCID: PMC4202271.
Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E. Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16842-7. doi: 10.1073/pnas.1410429111. Epub 2014 Oct 27. PubMed PMID: 25349412; PubMed Central PMCID: PMC4250163.
Sachsenröder J, Braun A, Machnowska P, Ng TFF, Deng X, Guenther S, Bernstein S, Ulrich RG, Delwart E, Johne R. Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus. J Gen Virol. 2014 Dec;95(Pt 12):2734-2747. doi: 10.1099/vir.0.070029-0. Epub 2014 Aug 13. PubMed PMID: 25121550; PubMed Central PMCID: PMC4811644.
Phan TG, Gulland F, Simeone C, Deng X, Delwart E. Sesavirus: prototype of a new parvovirus genus in feces of a sea lion. Virus Genes. 2015 Feb;50(1):134-6. doi: 10.1007/s11262-014-1123-3. Epub 2014 Oct 2. PubMed PMID: 25272961; PubMed Central PMCID: PMC4478086.
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