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(2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in <italic>Saccharomyces cerevisiae<\/italic>. Nucleic Acids Res.","DOI":"10.1093\/nar\/gks804"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e141","DOI":"10.1093\/nar\/gkn705","article-title":"Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms","volume":"36","author":"PA t Hoen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3820","DOI":"10.1093\/nar\/gkq1223","article-title":"RNA-Seq analysis of splicing in <italic>Plasmodium falciparum<\/italic> uncovers new splice junctions, alternative splicing and splicing of antisense transcripts","volume":"39","author":"K Sorber","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref27","unstructured":"Neidhardt FC, Umbarger HE (1996) Chemical composition of <italic>Escherichia coli<\/italic>. In: Neidhardt FC, editor. <italic>Escherichia coli<\/italic> And <italic>Salmonella<\/italic>: Cellular And Molecular Biology. 2nd ed. Washington D.C.: ASM Press. 13\u201317."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1000459","DOI":"10.1371\/journal.pgen.1000459","article-title":"The genetic signatures of noncoding RNAs","volume":"5","author":"JS Mattick","year":"2009","journal-title":"PLoS Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1111\/j.1462-5822.2009.01364.x","article-title":"New insights into <italic>Chlamydia<\/italic> intracellular survival mechanisms","volume":"11","author":"JL Cocchiaro","year":"2009","journal-title":"Cell Microbiol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"S114","DOI":"10.1086\/652397","article-title":"Pathogenesis of genital tract disease due to <italic>Chlamydia trachomatis<\/italic>","volume":"201","author":"T Darville","year":"2010","journal-title":"J Infect Dis"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"S88","DOI":"10.1086\/652394","article-title":"<italic>Chlamydia trachomatis<\/italic> persistence <italic>in vitro<\/italic>: an overview","volume":"201","author":"PB Wyrick","year":"2010","journal-title":"J Infect Dis"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1073\/pnas.0806768106","article-title":"Transformation and isolation of allelic exchange mutants of <italic>Chlamydia psittaci<\/italic> using recombinant DNA introduced by electroporation","volume":"106","author":"R Binet","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1139\/m94-093","article-title":"Expression of recombinant DNA introduced into <italic>Chlamydia trachomatis<\/italic> by electroporation","volume":"40","author":"JE Tam","year":"1994","journal-title":"Can J Microbiol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e1002258","DOI":"10.1371\/journal.ppat.1002258","article-title":"Development of a transformation system for <italic>Chlamydia trachomatis<\/italic>: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector","volume":"7","author":"Y Wang","year":"2011","journal-title":"PLoS Pathogens"},{"key":"ref35","unstructured":"Myers GSA, Crabtree J, Huot Creasy H (2012) Deep and wide: comparative genomics of <italic>Chlamydia<\/italic>. In: Tan M, Bavoil PM, editors. Intracellular Pathogens I: Chlamydiales. Washington D.C.: ASM Press. 27\u201350."},{"key":"ref36","doi-asserted-by":"crossref","first-page":"8478","DOI":"10.1073\/pnas.1331135100","article-title":"Genomic transcriptional profiling of the developmental cycle of <italic>Chlamydia trachomatis<\/italic>","volume":"100","author":"RJ Belland","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e83","DOI":"10.1371\/journal.ppat.0030083","article-title":"Gene expression profiles of <italic>Chlamydophila pneumoniae<\/italic> during the developmental cycle and iron depletion-mediated persistence","volume":"3","author":"AP Maurer","year":"2007","journal-title":"PLoS Pathog"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1128\/JB.185.10.3179-3189.2003","article-title":"Global stage-specific gene regulation during the developmental cycle of <italic>Chlamydia trachomatis<\/italic>","volume":"185","author":"TL 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Albrecht","year":"2011","journal-title":"Genome Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1128\/IAI.69.3.1420-1427.2001","article-title":"cDNA array analysis of altered gene expression in human endothelial cells in response to <italic>Chlamydia pneumoniae<\/italic> infection","volume":"69","author":"BK Coombes","year":"2001","journal-title":"Infect Immun"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1128\/IAI.00888-10","article-title":"Conjunctival transcriptome in scarring trachoma","volume":"79","author":"MJ Burton","year":"2011","journal-title":"Infect Immun"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1111\/cmi.12071","article-title":"Transcription factor complex AP-1 mediates inflammation initiated by <italic>Chlamydia pneumoniae<\/italic> infection","volume":"15","author":"A Wang","year":"2013","journal-title":"Cell Microbiol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1128\/JB.01462-09","article-title":"A systemic network for <italic>Chlamydia pneumoniae<\/italic> entry into human cells","volume":"192","author":"A Wang","year":"2010","journal-title":"J Bacteriol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1046\/j.1462-5822.2003.00319.x","article-title":"More than just innate immunity: comparative analysis of <italic>Chlamydophila pneumoniae<\/italic> and <italic>Chlamydia trachomatis<\/italic> effects on host-cell gene regulation","volume":"5","author":"S Hess","year":"2003","journal-title":"Cell Microbiol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2392","DOI":"10.1002\/1529-0131(200110)44:10<2392::AID-ART404>3.0.CO;2-I","article-title":"The reprogrammed host: <italic>Chlamydia trachomatis<\/italic>-induced up-regulation of glycoprotein 130 cytokines, transcription factors, and antiapoptotic genes","volume":"44","author":"S Hess","year":"2001","journal-title":"Arthritis Rheum"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1111\/j.1749-6632.2003.tb07447.x","article-title":"Comparative DNA microarray analysis of host cell transcriptional responses to infection by <italic>Coxiella burnetii<\/italic> or <italic>Chlamydia trachomatis<\/italic>","volume":"990","author":"Q Ren","year":"2003","journal-title":"Ann N Y Acad Sci"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"R54","DOI":"10.1186\/ar2209","article-title":"Expression of inflammatory host genes in <italic>Chlamydia trachomatis<\/italic>-infected human monocytes","volume":"9","author":"S Schrader","year":"2007","journal-title":"Arthritis Res Ther"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1086\/379047","article-title":"Infection of U937 monocytic cells with <italic>Chlamydia pneumoniae<\/italic> induces extensive changes in host cell gene expression","volume":"188","author":"D Virok","year":"2003","journal-title":"J Infect Dis"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1086\/367962","article-title":"<italic>Chlamydia trachomatis<\/italic> infection alters host cell transcription in diverse cellular pathways","volume":"187","author":"M Xia","year":"2003","journal-title":"J Infect Dis"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"R23","DOI":"10.1186\/gb-2012-13-3-r23","article-title":"Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes","volume":"13","author":"G Giannoukos","year":"2012","journal-title":"Genome Biol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrmicro2852","article-title":"Dual RNA-seq of pathogen and host","volume":"10","author":"AJ Westermann","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1128\/jb.165.2.379-385.1986","article-title":"Synthesis of disulfide-bonded outer membrane proteins during the developmental cycle of <italic>Chlamydia psittaci<\/italic> and <italic>Chlamydia trachomatis<\/italic>","volume":"165","author":"TP Hatch","year":"1986","journal-title":"J Bacteriol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1128\/MMBR.55.1.143-190.1991","article-title":"Interaction of chlamydiae and host cells <italic>in vitro<\/italic>","volume":"55","author":"JW Moulder","year":"1991","journal-title":"Microbiol Rev"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1128\/IAI.56.12.3021-3025.1988","article-title":"Protein synthesis early in the developmental cycle of <italic>Chlamydia psittaci<\/italic>","volume":"56","author":"MR Plaunt","year":"1988","journal-title":"Infect Immun"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1111\/j.1365-2958.2012.08077.x","article-title":"The early gene product EUO is a transcriptional repressor that selectively regulates promoters of <italic>Chlamydia<\/italic> late genes","volume":"84","author":"CJ Rosario","year":"2012","journal-title":"Mol Microbiol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1128\/jb.175.10.2936-2942.1993","article-title":"Identification of an early-stage gene of <italic>Chlamydia psittaci<\/italic> 6BC","volume":"175","author":"DG Wichlan","year":"1993","journal-title":"J Bacteriol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1046\/j.1365-2958.1999.01523.x","article-title":"Identification and characterization of a <italic>Chlamydia trachomatis<\/italic> early operon encoding four novel inclusion membrane proteins","volume":"33","author":"MA Scidmore-Carlson","year":"1999","journal-title":"Mol Microbiol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1128\/JB.181.4.1196-1202.1999","article-title":"Two nucleotide transport proteins in <italic>Chlamydia trachomatis<\/italic>, one for net nucleoside triphosphate uptake and the other for transport of energy","volume":"181","author":"J Tjaden","year":"1999","journal-title":"J Bacteriol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"7819","DOI":"10.1128\/AEM.01919-07","article-title":"Riboflavin biosynthesis is associated with assimilatory ferric reduction and iron acquisition by <italic>Campylobacter jejuni<\/italic>","volume":"73","author":"RA Crossley","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1128\/JB.180.6.1473-1479.1998","article-title":"<italic>Helicobacter pylori<\/italic> ribBA-mediated riboflavin production is involved in iron acquisition","volume":"180","author":"DJ Worst","year":"1998","journal-title":"J Bacteriol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1099\/mic.0.030247-0","article-title":"<italic>Chlamydia trachomatis<\/italic> YtgA is an iron-binding periplasmic protein induced by iron restriction","volume":"155","author":"JD Miller","year":"2009","journal-title":"Microbiology"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"10546","DOI":"10.1073\/pnas.1201398109","article-title":"Cleavage of a putative metal permease in <italic>Chlamydia trachomatis<\/italic> yields an iron-dependent transcriptional repressor","volume":"109","author":"CC Thompson","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"4045","DOI":"10.1128\/jb.175.13.4045-4051.1993","article-title":"Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in <italic>Escherichia coli<\/italic>","volume":"175","author":"G Richter","year":"1993","journal-title":"J Bacteriol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"4050","DOI":"10.1128\/jb.174.12.4050-4056.1992","article-title":"Biosynthesis of riboflavin: cloning, sequencing, and expression of the gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of <italic>Escherichia coli<\/italic>","volume":"174","author":"G Richter","year":"1992","journal-title":"J Bacteriol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/S1201-9712(00)90066-3","article-title":"Generation of reactive oxygen species and formation and membrane lipid peroxides in cells infected with <italic>Chlamydia trachomatis<\/italic>","volume":"4","author":"AA Azenabor","year":"2000","journal-title":"Int J Infect Dis"},{"key":"ref71","unstructured":"Darville T, O&apos;Connell CM (2012) <italic>Chlamydia<\/italic> immunopathogenesis. In: Bavoil PM, Tan M, editors. Intracellular Pathogens I: Chlamydiales. Washington DC: ASM Press. 241\u2013264."},{"key":"ref72","unstructured":"Nagarajan UM (2012) Immune Recognition and Host Cell Response during <italic>Chlamydia<\/italic> infection. In: Bavoil PM, Tan M, editors. Intracellular Pathogens I: Chlamydiales. Washington DC: ASM Press. 217\u2013239."},{"key":"ref73","doi-asserted-by":"crossref","first-page":"3291","DOI":"10.1128\/IAI.00200-11","article-title":"<italic>In vivo<\/italic> ultrastructural analysis of the intimate relationship between polymorphonuclear leukocytes and the chlamydial developmental cycle","volume":"79","author":"RG Rank","year":"2011","journal-title":"Infect Immun"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/S0966-842X(02)00011-2","article-title":"The cellular paradigm of chlamydial pathogenesis","volume":"11","author":"RS Stephens","year":"2003","journal-title":"Trends Microbiol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1172\/JCI119136","article-title":"Secretion of proinflammatory cytokines by epithelial cells in response to <italic>Chlamydia<\/italic> infection suggests a central role for epithelial cells in chlamydial pathogenesis","volume":"99","author":"SJ Rasmussen","year":"1997","journal-title":"J Clin Invest"},{"key":"ref76","doi-asserted-by":"crossref","unstructured":"Lu P, Takai K, Weaver VM, Werb Z (2011) Extracellular matrix degradation and remodeling in development and disease. Cold Spring Harb Perspect Biol 3.","DOI":"10.1101\/cshperspect.a005058"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1016\/j.mam.2008.05.002","article-title":"Progress in matrix metalloproteinase research","volume":"29","author":"G Murphy","year":"2008","journal-title":"Mol Aspects Med"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"21491","DOI":"10.1074\/jbc.274.31.21491","article-title":"Matrix metalloproteinases","volume":"274","author":"H Nagase","year":"1999","journal-title":"J Biol Chem"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1161\/01.RES.0000070112.80711.3D","article-title":"Matrix metalloproteinases and tissue inhibitors of metalloproteinases: structure, function, and biochemistry","volume":"92","author":"R Visse","year":"2003","journal-title":"Circ Res"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.mam.2011.10.015","article-title":"Human matrix metalloproteinases: an ubiquitarian class of enzymes involved in several pathological processes","volume":"33","author":"D Sbardella","year":"2012","journal-title":"Mol Aspects Med"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"6962","DOI":"10.1128\/IAI.73.10.6962-6973.2005","article-title":"Expression of matrix metalloproteinases subsequent to urogenital <italic>Chlamydia muridarum<\/italic> infection of mice","volume":"73","author":"KH Ramsey","year":"2005","journal-title":"Infect Immun"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1177\/039463201202500207","article-title":"Induction of VEGF and MMP-9 expression by toll-like receptor 2\/4 in human endothelial cells infected with <italic>Chlamydia pneumoniae<\/italic>","volume":"25","author":"R Paolillo","year":"2012","journal-title":"Int J Immunopathol Pharmacol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1067\/mob.2002.126850","article-title":"<italic>Chlamydia trachomatis<\/italic> enhances the expression of matrix metalloproteinases in an <italic>in vitro<\/italic> model of the human fallopian tube infection","volume":"187","author":"KA Ault","year":"2002","journal-title":"Am J Obstet Gynecol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.joca.2004.07.008","article-title":"Testican-1, an inhibitor of pro-MMP-2 activation, is expressed in cartilage","volume":"12","author":"HJ Hausser","year":"2004","journal-title":"Osteoarthritis Cartilage"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1111\/j.1600-0625.2008.00782.x","article-title":"Epilysin (MMP-28)-structure, expression and potential functions","volume":"17","author":"SA Illman","year":"2008","journal-title":"Exp Dermatol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1479-7364-4-1-43","article-title":"Evolutionary divergence and functions of the ADAM and ADAMTS gene families","volume":"4","author":"CN Brocker","year":"2009","journal-title":"Hum Genomics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1016\/j.ceb.2003.08.001","article-title":"ADAMs: modulators of cell-cell and cell-matrix interactions","volume":"15","author":"JM White","year":"2003","journal-title":"Curr Opin Cell Biol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/978-1-4614-0899-4_2","article-title":"The role of Adams in Notch signaling","volume":"727","author":"AJ Groot","year":"2012","journal-title":"Adv Exp Med Biol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"a004978","DOI":"10.1101\/cshperspect.a004978","article-title":"The collagen family","volume":"3","author":"S Ricard-Blum","year":"2011","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"ref90","doi-asserted-by":"crossref","unstructured":"Campbell ID, Humphries MJ (2011) Integrin structure, activation, and interactions. Cold Spring Harb Perspect Biol 3.","DOI":"10.1101\/cshperspect.a004994"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/eye.1998.179","article-title":"Collagen content and types in trachomatous conjunctivitis","volume":"4)","author":"AM Abu el-Asrar","year":"1998","journal-title":"Eye (Lond) 12 (Pt"},{"key":"ref92","doi-asserted-by":"crossref","unstructured":"Yurchenco PD (2011) Basement membranes: cell scaffoldings and signaling platforms. Cold Spring Harb Perspect Biol 3.","DOI":"10.1101\/cshperspect.a004911"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1007\/s00018-009-8632-6","article-title":"Fibulins: multiple roles in matrix structures and tissue functions","volume":"66","author":"S de Vega","year":"2009","journal-title":"Cell Mol Life Sci"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1093\/bmb\/ldm034","article-title":"Trachoma: an overview","volume":"84","author":"MJ Burton","year":"2007","journal-title":"Br Med Bull"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1007\/s00018-011-0783-6","article-title":"Advances in tenascin-C biology","volume":"68","author":"KS Midwood","year":"2011","journal-title":"Cell Mol Life Sci"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/s12079-009-0075-1","article-title":"The role of tenascin-C in tissue injury and tumorigenesis","volume":"3","author":"KS Midwood","year":"2009","journal-title":"J Cell Commun Signal"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/sj.eye.6701884","article-title":"Expression of growth factors in the conjunctiva from patients with active trachoma","volume":"20","author":"AM Abu El-Asrar","year":"2006","journal-title":"Eye (Lond)"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/nm.1987","article-title":"Tenascin-C is an endogenous activator of Toll-like receptor 4 that is essential for maintaining inflammation in arthritic joint disease","volume":"15","author":"K Midwood","year":"2009","journal-title":"Nat Med"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1002\/path.2277","article-title":"Cellular and molecular mechanisms of fibrosis","volume":"214","author":"TA Wynn","year":"2008","journal-title":"J Pathol"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"G950","DOI":"10.1152\/ajpgi.00132.2011","article-title":"The extracellular matrix: an active or passive player in fibrosis?","volume":"301","author":"TN Wight","year":"2011","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"e2020","DOI":"10.1371\/journal.pntd.0002020","article-title":"Trachoma: protective and pathogenic ocular immune responses to <italic>Chlamydia trachomatis<\/italic>","volume":"7","author":"VH Hu","year":"2013","journal-title":"PLoS Negl Trop Dis"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"e2117","DOI":"10.1371\/journal.pntd.0002117","article-title":"Conjunctival MicroRNA expression in inflammatory trachomatous scarring","volume":"7","author":"T Derrick","year":"2013","journal-title":"PLoS Negl Trop Dis"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/ncomms1734","article-title":"Activation of canonical Wnt signalling is required for TGF-beta-mediated fibrosis","volume":"3","author":"A Akhmetshina","year":"2012","journal-title":"Nat Commun"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.exer.2007.11.016","article-title":"Focus on molecules: gremlin","volume":"87","author":"RJ Wordinger","year":"2008","journal-title":"Exp Eye Res"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1080\/08977190412331279890","article-title":"Bone morphogenetic proteins","volume":"22","author":"D Chen","year":"2004","journal-title":"Growth Factors"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1165\/rcmb.2010-0070OC","article-title":"Transient overexpression of Gremlin results in epithelial activation and reversible fibrosis in rat lungs","volume":"44","author":"L Farkas","year":"2011","journal-title":"Am J Respir Cell Mol Biol"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1165\/rcmb.2009-0101TR","article-title":"Role of gremlin in the lung: development and disease","volume":"42","author":"CM Costello","year":"2010","journal-title":"Am J Respir Cell Mol Biol"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1128\/IAI.01566-08","article-title":"<italic>Chlamydia trachomatis<\/italic>-infected patients display variable antibody profiles against the nine-member polymorphic membrane protein family","volume":"77","author":"C Tan","year":"2009","journal-title":"Infect Immun"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2010","journal-title":"Genome Biol"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: accounting for selection bias","volume":"11","author":"MD Young","year":"2010","journal-title":"Genome Biol"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"R Edgar","year":"2002","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS 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