TY - JOUR AU - Hu, V. H. PY - 2010 DA - 2010// TI - Epidemiology and control of trachoma: systematic review JO - Tropical Med Int Health VL - 15 UR - https://doi.org/10.1111/j.1365-3156.2010.02521.x DO - 10.1111/j.1365-3156.2010.02521.x ID - Hu2010 ER - TY - BOOK PY - 2016 DA - 2016// TI - Sexually transmitted infections (STIs) ID - ref2 ER - TY - JOUR AU - Rodriguez, P. PY - 1991 DA - 1991// TI - Typing of Chlamydia trachomatis by restriction endonuclease analysis of the amplified major outer membrane protein gene JO - J Clin Microbiol VL - 29 ID - Rodriguez1991 ER - TY - JOUR AU - Harris, S. R. PY - 2012 DA - 2012// TI - Whole genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.2214 DO - 10.1038/ng.2214 ID - Harris2012 ER - TY - JOUR AU - Caldwell, H. D. PY - 2003 DA - 2003// TI - Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiates between genital and ocular isolates: implications in pathogenesis and infection tropism JO - J Clin Invest VL - 111 UR - https://doi.org/10.1172/JCI17993 DO - 10.1172/JCI17993 ID - Caldwell2003 ER - TY - JOUR AU - Jeffrey, B. M. PY - 2010 DA - 2010// TI - Genome sequencing of recent clinical Chlamydia trachomatis strains identifies loci associated with tissue tropism and regions of apparent recombination JO - Infect Immun VL - 78 UR - https://doi.org/10.1128/IAI.01324-09 DO - 10.1128/IAI.01324-09 ID - Jeffrey2010 ER - TY - JOUR AU - Nunes, A. AU - Borrego, M. J. AU - Gomes, J. P. PY - 2013 DA - 2013// TI - Genomic features beyond C. trachomatis phenotypes: what do we think we know? JO - Infect Genet Evol VL - 16 UR - https://doi.org/10.1016/j.meegid.2013.03.018 DO - 10.1016/j.meegid.2013.03.018 ID - Nunes2013 ER - TY - JOUR AU - Kari, L. PY - 2008 DA - 2008// TI - Pathogenic diversity among Chlamydia trachomatis ocular strains in non-human primates is affected by subtle genomic variations JO - J Infect Dis VL - 197 UR - https://doi.org/10.1086/525285 DO - 10.1086/525285 ID - Kari2008 ER - TY - JOUR AU - Butcher, R. M. R. PY - 2016 DA - 2016// TI - Low prevalence of conjunctival infection with Chlamydia trachomatis in a treatment-naive trachoma-endemic region of the Solomon Islands JO - PLoS Negl Trop Dis VL - 10 UR - https://doi.org/10.1371/journal.pntd.0005051 DO - 10.1371/journal.pntd.0005051 ID - Butcher2016 ER - TY - JOUR AU - Andersson, P. PY - 2016 DA - 2016// TI - Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms10688 DO - 10.1038/ncomms10688 ID - Andersson2016 ER - TY - JOUR AU - Feng, L. PY - 2017 DA - 2017// TI - Survey, culture and genome analysis of ocular Chlamydia trachomatis in Tibetan boarding primary schools in Qinghai Province, China JO - Front Cell Infect Microbiol VL - 6 UR - https://doi.org/10.3389/fcimb.2016.00207 DO - 10.3389/fcimb.2016.00207 ID - Feng2017 ER - TY - JOUR AU - Borges, V. PY - 2014 DA - 2014// TI - Complete genome sequence of Chlamydia trachomatis ocular serovar C strain TW-3 JO - Genome Announc VL - 2 UR - https://doi.org/10.1128/genomeA.01204-13 DO - 10.1128/genomeA.01204-13 ID - Borges2014 ER - TY - JOUR AU - Darville, T. AU - Hiltke, T. PY - 2010 DA - 2010// TI - Pathogenesis of genital tract disease due to Chlamydia trachomatis JO - J Infect Dis VL - 201 UR - https://doi.org/10.1086/652397 DO - 10.1086/652397 ID - Darville2010 ER - TY - JOUR AU - van Valkengoed, I. G. PY - 2004 DA - 2004// TI - Overestimation of complication rates in evaluations of Chlamydia trachomatis screening programmes—implications for cost-effectiveness analyses JO - Int J Epidemiol VL - 33 UR - https://doi.org/10.1093/ije/dyh029 DO - 10.1093/ije/dyh029 ID - van Valkengoed2004 ER - TY - JOUR AU - Bailey, R. L. PY - 1994 DA - 1994// TI - Molecular epidemiology of trachoma in a Gambian village JO - Br J Ophthalmol VL - 78 UR - https://doi.org/10.1136/bjo.78.11.813 DO - 10.1136/bjo.78.11.813 ID - Bailey1994 ER - TY - JOUR AU - Andreasen, A. A. PY - 2008 DA - 2008// TI - Chlamydia trachomatis ompA variants in trachoma: what do they tell us? JO - PLoS Negl Trop Dis VL - 2 UR - https://doi.org/10.1371/journal.pntd.0000306 DO - 10.1371/journal.pntd.0000306 ID - Andreasen2008 ER - TY - JOUR AU - Wang, Y. PY - 2011 DA - 2011// TI - Development of a transformation system for Chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector JO - PLoS Pathog VL - 7 UR - https://doi.org/10.1371/journal.ppat.1002258 DO - 10.1371/journal.ppat.1002258 ID - Wang2011 ER - TY - JOUR AU - Wang, Y. PY - 2013 DA - 2013// TI - Transformation of a plasmid-free genital tract isolate with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype JO - Pathogens Dis VL - 67 UR - https://doi.org/10.1111/2049-632X.12024 DO - 10.1111/2049-632X.12024 ID - Wang2013 ER - TY - JOUR AU - Longbottom, D. PY - 1998 DA - 1998// TI - Molecular cloning and characterization of genes coding for the highly immunogenic cluster of 90 kilodalton envelope proteins from the Chlamydia psittaci subtype that causes abortion in sheep JO - Infect Immun VL - 66 ID - Longbottom1998 ER - TY - JOUR AU - Gomes, J. P. PY - 2006 DA - 2006// TI - Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar Da recombination and correlation with tissue tropism JO - J Bacteriol VL - 188 UR - https://doi.org/10.1128/JB.188.1.275-286.2006 DO - 10.1128/JB.188.1.275-286.2006 ID - Gomes2006 ER - TY - JOUR AU - Rockey, D. D. AU - Heinzen, R. A. AU - Hackstadt, T. PY - 1995 DA - 1995// TI - Cloning and characterization of a Chlamydia psittaci gene coding for a protein localized in the inclusion membrane of infected cells JO - Mol Microbiol VL - 15 UR - https://doi.org/10.1111/j.1365-2958.1995.tb02371.x DO - 10.1111/j.1365-2958.1995.tb02371.x ID - Rockey1995 ER - TY - JOUR AU - Hefty, P. S. AU - Stephens, R. S. PY - 2007 DA - 2007// TI - Chlamydia trachomatis type III secretion system is encoded on ten operons preceded by a sigma 70-like promoter element JO - J Bacteriol VL - 189 UR - https://doi.org/10.1128/JB.01034-06 DO - 10.1128/JB.01034-06 ID - Hefty2007 ER - TY - JOUR AU - Carlson, J. H. PY - 2006 DA - 2006// TI - In vivo and in vitro studies of Chlamydia trachomatis TrpR:DNA interaction JO - Mol Microbiol VL - 59 UR - https://doi.org/10.1111/j.1365-2958.2006.05045.x DO - 10.1111/j.1365-2958.2006.05045.x ID - Carlson2006 ER - TY - JOUR AU - O’Connell, C. M. PY - 2011 DA - 2011// TI - Toll-like receptor 2 activation by Chlamydia trachomatis is plasmid dependent, and plasmid-responsive chromosomal loci are coordinately regulated in response to glucose limitation by C. trachomatis but not by C. muridarum JO - Infect Immun VL - 79 UR - https://doi.org/10.1128/IAI.01118-10 DO - 10.1128/IAI.01118-10 ID - O’Connell2011 ER - TY - JOUR AU - Hackstadt, T. AU - Scidmore-Carlson, M. A. AU - Shaw, E. I. AU - Fischer, E. R. PY - 1999 DA - 1999// TI - Chlamydia trachomatis IncA protein is required for homotypic vesicle fusion JO - Cell Microbiol VL - 1 UR - https://doi.org/10.1046/j.1462-5822.1999.00012.x DO - 10.1046/j.1462-5822.1999.00012.x ID - Hackstadt1999 ER - TY - JOUR AU - Nelson, D. E. PY - 2006 DA - 2006// TI - Inhibition of Chlamydiae by primary alcohols correlates with strain specific complement of plasticity zone phospholipase D genes JO - Infect Immun VL - 74 UR - https://doi.org/10.1128/IAI.74.1.73-80.2006 DO - 10.1128/IAI.74.1.73-80.2006 ID - Nelson2006 ER - TY - JOUR AU - Carlson, J. H. AU - Hughes, S. AU - Hogan, D. PY - 2004 DA - 2004// TI - Polymorphisms in the Chlamydia trachomatis cytotoxin locus associated with ocular and genital isolates JO - Infect Immun VL - 72 UR - https://doi.org/10.1128/IAI.72.12.7063-7072.2004 DO - 10.1128/IAI.72.12.7063-7072.2004 ID - Carlson2004 ER - TY - JOUR AU - Carlson, J. H. PY - 2008 DA - 2008// TI - The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factor JO - Infect Immun VL - 76 UR - https://doi.org/10.1128/IAI.00102-08 DO - 10.1128/IAI.00102-08 ID - Carlson2008 ER - TY - JOUR AU - Frazer, L. C. PY - 2012 DA - 2012// TI - Plasmid-cured Chlamydia caviae activates TLR2-dependent signaling and retains virulence in the guinea pig model of genital tract infection JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0030747 DO - 10.1371/journal.pone.0030747 ID - Frazer2012 ER - TY - JOUR AU - Song, L. PY - 2013 DA - 2013// TI - Chlamydia trachomatis plasmid-encoded pgp4 is a transcriptional regulator of virulence-associated genes JO - Infect Immun VL - 81 UR - https://doi.org/10.1128/IAI.01305-12 DO - 10.1128/IAI.01305-12 ID - Song2013 ER - TY - JOUR AU - Christiansen, M. T. PY - 2014 DA - 2014// TI - Whole genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples JO - BMC Infect Dis VL - 14 UR - https://doi.org/10.1186/s12879-014-0591-3 DO - 10.1186/s12879-014-0591-3 ID - Christiansen2014 ER - TY - JOUR AU - Borges, V. PY - 2013 DA - 2013// TI - Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics JO - Infect Genet Evol VL - 17 UR - https://doi.org/10.1016/j.meegid.2013.03.035 DO - 10.1016/j.meegid.2013.03.035 ID - Borges2013 ER - TY - JOUR AU - Borges, V. PY - 2015 DA - 2015// TI - Chlamydia trachomatis in vivo to in vitro transition reveals mechanisms of phase variation and downregulation of virulence factors JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0133420 DO - 10.1371/journal.pone.0133420 ID - Borges2015 ER - TY - JOUR AU - Bonner, C. PY - 2015 DA - 2015// TI - Chlamydia trachomatis virulence factor CT135 is stable in vivo but highly polymorphic in vitro JO - Pathog Dis VL - 73 UR - https://doi.org/10.1093/femspd/ftv043 DO - 10.1093/femspd/ftv043 ID - Bonner2015 ER - TY - JOUR AU - Burton, M. J. PY - 2003 DA - 2003// TI - Which members of a community need antibiotics to control trachoma? Conjunctival Chlamydia trachomatis load in Gambian villages JO - Invest Ophthalmol Vis Sci VL - 44 UR - https://doi.org/10.1167/iovs.03-0107 DO - 10.1167/iovs.03-0107 ID - Burton2003 ER - TY - JOUR AU - Conway, D. J. PY - 1997 DA - 1997// TI - Scarring trachoma is associated with polymorphisms in TNF-alpha gene promoter and with increased TNF-alpha levels in tear fluid JO - Infect Immun VL - 65 ID - Conway1997 ER - TY - JOUR AU - West, S. K. PY - 2001 DA - 2001// TI - Progression of active trachoma to scarring in a cohort of Tanzanian children JO - Ophthalmic Epidemiol VL - 8 UR - https://doi.org/10.1076/opep.8.2.137.4158 DO - 10.1076/opep.8.2.137.4158 ID - West2001 ER - TY - JOUR AU - Burton, M. J. PY - 2015 DA - 2015// TI - Pathogenesis of progressive scarring trachoma in Ethiopia and Tanzania: two cohort studies JO - PLoS Negl Trop Dis VL - 9 UR - https://doi.org/10.1371/journal.pntd.0003763 DO - 10.1371/journal.pntd.0003763 ID - Burton2015 ER - TY - BOOK AU - Dawson, C. R. AU - Jones, B. R. AU - Tarizzo, M. L. PY - 1981 DA - 1981// TI - Guide to trachoma control in programs for the prevention of blindness PB - World Health Organization CY - Geneva ID - Dawson1981 ER - TY - JOUR AU - Reid, J. S. PY - 2016 DA - 2016// TI - A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape JO - Nat Comms VL - 7 UR - https://doi.org/10.1038/ncomms13357 DO - 10.1038/ncomms13357 ID - Reid2016 ER - TY - JOUR AU - Yang, J. PY - 2012 DA - 2012// TI - Conditional and joint multiple SNP analysis of GWAS summary statistics identifies additional variance influencing complex traits JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.1057 DO - 10.1038/ng.1057 ID - Yang2012 ER - TY - JOUR AU - Aschard, H. PY - 2014 DA - 2014// TI - Maximising the power of principal component analysis of correlated phenotypes in genome wide association studies JO - Am J Hum Genet VL - 94 UR - https://doi.org/10.1016/j.ajhg.2014.03.016 DO - 10.1016/j.ajhg.2014.03.016 ID - Aschard2014 ER - TY - JOUR AU - Last, A. R. PY - 2014 DA - 2014// TI - Risk factors for active trachoma and ocular Chlamydia trachomatis infection in treatment-naïve trachoma-hyperendemic communities of the Bijagós Archipelago, Guinea Bissau JO - PLoS Negl Trop Dis VL - 8 UR - https://doi.org/10.1371/journal.pntd.0002900 DO - 10.1371/journal.pntd.0002900 ID - Last2014 ER - TY - JOUR AU - Last, A. PY - 2014 DA - 2014// TI - Plasmid copy number and disease severity in naturally occurring ocular Chlamydia trachomatis infection JO - J Clin Microbiol VL - 52 UR - https://doi.org/10.1128/JCM.02618-13 DO - 10.1128/JCM.02618-13 ID - Last2014 ER - TY - JOUR AU - Roberts, C. PY - 2013 DA - 2013// TI - Development and evaluation of a next generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections JO - J Clin Microbiol VL - 51 UR - https://doi.org/10.1128/JCM.00622-13 DO - 10.1128/JCM.00622-13 ID - Roberts2013 ER - TY - JOUR AU - Burton, M. J. PY - 2006 DA - 2006// TI - Conjunctival chlamydial 16S ribosomal RNA expression in trachoma: is chlamydial metabolic activity required for disease to develop? JO - Clin Infect Dis VL - 42 UR - https://doi.org/10.1086/499814 DO - 10.1086/499814 ID - Burton2006 ER - TY - JOUR AU - Faal, N. PY - 2006 DA - 2006// TI - Conjunctival FOXP3 expression in trachoma: do regulatory T cells have a role in human ocular Chlamydia trachomatis infection? JO - PLoS Med VL - 3 UR - https://doi.org/10.1371/journal.pmed.0030266 DO - 10.1371/journal.pmed.0030266 ID - Faal2006 ER - TY - JOUR AU - Derrick, T. PY - 2016 DA - 2016// TI - Inverse relationship between micro RNA-155 and -184 expression with increasing conjunctival inflammation during ocular Chlamydia trachomatis infection JO - BMC Infect Dis VL - 16 UR - https://doi.org/10.1186/s12879-016-1367-8 DO - 10.1186/s12879-016-1367-8 ID - Derrick2016 ER - TY - STD TI - Last A, et al. Spatial clustering of high load ocular Chlamydia trachomatis infection in trachoma: a cross-sectional population-based study. Pathog Dis. 2017;75(5) https://doi.org/10.1093/femspd/ftx050. ID - ref49 ER - TY - JOUR AU - Suo, C. PY - 2013 DA - 2013// TI - Analysis of multiple phenotypes in genome wide genetic mapping studies JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-151 DO - 10.1186/1471-2105-14-151 ID - Suo2013 ER - TY - JOUR AU - Skipp, P. AU - Robinson, J. AU - O’Connor, C. D. AU - Clarke, I. N. PY - 2005 DA - 2005// TI - Shotgun proteomic analysis of Chlamydia trachomatis JO - Proteomics VL - 5 UR - https://doi.org/10.1002/pmic.200401044 DO - 10.1002/pmic.200401044 ID - Skipp2005 ER - TY - JOUR AU - Seth-Smith, H. M. B. PY - 2009 DA - 2009// TI - Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain JO - BMC Genomics VL - 10 UR - https://doi.org/10.1186/1471-2164-10-239 DO - 10.1186/1471-2164-10-239 ID - Seth-Smith2009 ER - TY - BOOK AU - Andrews, S. PY - 2010 DA - 2010// TI - FastQC: a quality control tool for high throughput sequence data ID - Andrews2010 ER - TY - JOUR AU - Langmead, B. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 ID - Langmead2009 ER - TY - JOUR AU - Li, H. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - McKenna, A. PY - 2010 DA - 2010// TI - The Genome Analysis Tool Kit: a MapReduce framework for analysing next generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - JOUR AU - Cheng, A. Y. AU - Teo, Y. Y. AU - Ong, R. T. PY - 2014 DA - 2014// TI - Assessing single nucleotide variant detection and genotype calling on whole genome sequenced individuals JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu067 DO - 10.1093/bioinformatics/btu067 ID - Cheng2014 ER - TY - JOUR AU - Gudbjartsson, D. F. PY - 2015 DA - 2015// TI - Large-scale whole genome sequencing of the Icelandic population JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3247 DO - 10.1038/ng.3247 ID - Gudbjartsson2015 ER - TY - JOUR AU - Pickering, H. PY - 2017 DA - 2017// TI - Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-09193-2 DO - 10.1038/s41598-017-09193-2 ID - Pickering2017 ER - TY - JOUR AU - Coll, F. PY - 2014 DA - 2014// TI - PolyTB: a genomic variation map for Mycobacterium tuberculosis JO - Tuberculosis (Edinb) VL - 94 UR - https://doi.org/10.1016/j.tube.2014.02.005 DO - 10.1016/j.tube.2014.02.005 ID - Coll2014 ER - TY - JOUR AU - Hadfield, J. PY - 2017 DA - 2017// TI - Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.212647.116 DO - 10.1101/gr.212647.116 ID - Hadfield2017 ER - TY - JOUR AU - Stamatakis, A. AU - Hoover, P. AU - Rougemont, J. PY - 2008 DA - 2008// TI - A rapid bootstrap algorithm for the RAxML Web servers JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802429642 DO - 10.1080/10635150802429642 ID - Stamatakis2008 ER - TY - JOUR AU - Bruen, T. C. AU - Philippe, H. AU - Bryant, D. PY - 2006 DA - 2006// TI - A simple and robust statistical test for detecting the presence of recombination JO - Genetics VL - 172 UR - https://doi.org/10.1534/genetics.105.048975 DO - 10.1534/genetics.105.048975 ID - Bruen2006 ER - TY - JOUR AU - Solomon, A. W. PY - 2003 DA - 2003// TI - Strategies for control of trachoma: observational study with quantitative PCR JO - Lancet VL - 362 UR - https://doi.org/10.1016/S0140-6736(03)13909-8 DO - 10.1016/S0140-6736(03)13909-8 ID - Solomon2003 ER - TY - JOUR AU - Gouy, M. AU - Guindon, S. AU - Gascuel, O. PY - 2010 DA - 2010// TI - SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp259 DO - 10.1093/molbev/msp259 ID - Gouy2010 ER - TY - JOUR AU - Heger, A. AU - Holm, L. PY - 2000 DA - 2000// TI - Rapid automatic detection and alignment of repeats in protein sequences JO - Proteins VL - 41 UR - https://doi.org/3.0.CO;2-Z DO - 3.0.CO;2-Z ID - Heger2000 ER - TY - JOUR AU - Sonnhammer, E. L. AU - Eddy, S. R. AU - Durbin, R. PY - 1997 DA - 1997// TI - Pfam: a comprehensive database of protein domain families based on seed alignments JO - Proteins VL - 28 UR - https://doi.org/3.0.CO;2-L DO - 3.0.CO;2-L ID - Sonnhammer1997 ER - TY - JOUR AU - Nei, M. AU - Masatoshi, N. AU - Wen-Hsiung, L. PY - 1979 DA - 1979// TI - Mathematical model for studying genetic variation in terms of restriction endonucleases JO - Proc Natl Acad Sci VL - 76 UR - https://doi.org/10.1073/pnas.76.10.5269 DO - 10.1073/pnas.76.10.5269 ID - Nei1979 ER - TY - JOUR AU - Che, R. PY - 2014 DA - 2014// TI - An adaptive permutation approach for genome-wide association study JO - BioData Mining VL - 7 UR - https://doi.org/10.1186/1756-0381-7-9 DO - 10.1186/1756-0381-7-9 ID - Che2014 ER - TY - JOUR AU - Dudoit, S. PY - 2003 DA - 2003// TI - Multiple hypothesis testing in microarray experiments JO - Stat Sci VL - 18 UR - https://doi.org/10.1214/ss/1056397487 DO - 10.1214/ss/1056397487 ID - Dudoit2003 ER - TY - JOUR AU - Sham, P. C. AU - Purcell, S. M. PY - 2014 DA - 2014// TI - Statistical power and significance testing in large scale genetic studies JO - Nat Rev Genet VL - 15 UR - https://doi.org/10.1038/nrg3706 DO - 10.1038/nrg3706 ID - Sham2014 ER - TY - JOUR AU - Fairfax, B. P. PY - 2012 DA - 2012// TI - Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.2205 DO - 10.1038/ng.2205 ID - Fairfax2012 ER - TY - JOUR AU - Belland, R. J. PY - 2003 DA - 2003// TI - Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.1331135100 DO - 10.1073/pnas.1331135100 ID - Belland2003 ER - TY - JOUR AU - Yu, C. S. AU - Lin, C. J. AU - Hwang, J. K. PY - 2004 DA - 2004// TI - Predicting subcellular localization of proteins for Gram-negative bacterial by support vector machines based on n-peptide compositions JO - Protein Sci VL - 13 UR - https://doi.org/10.1110/ps.03479604 DO - 10.1110/ps.03479604 ID - Yu2004 ER - TY - JOUR AU - Yu, N. Y. PY - 2010 DA - 2010// TI - PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq249 DO - 10.1093/bioinformatics/btq249 ID - Yu2010 ER - TY - JOUR AU - Goldberg, T. PY - 2014 DA - 2014// TI - LocTree3 prediction of localization JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku396 DO - 10.1093/nar/gku396 ID - Goldberg2014 ER - TY - JOUR AU - Thomas, A. PY - 2011 DA - 2011// TI - Effect of linkage disequilibrium on the identification of functional variants JO - Genet Epidemiol VL - 35 UR - https://doi.org/10.1002/gepi.20660 DO - 10.1002/gepi.20660 ID - Thomas2011 ER - TY - JOUR AU - Lutter, E. I. PY - 2010 DA - 2010// TI - Phylogenetic analysis of Chlamydia trachomatis TARP and correlation with clinical phenotype JO - Infect Immun VL - 78 UR - https://doi.org/10.1128/IAI.00515-10 DO - 10.1128/IAI.00515-10 ID - Lutter2010 ER - TY - JOUR AU - Pepperell, C. S. PY - 2013 DA - 2013// TI - The role of selection in shaping diversity of natural Mycobacterium tuberculosis populations JO - PLoS Pathog VL - 9 UR - https://doi.org/10.1371/annotation/cff22061-44d5-4301-b853-41702d160203 DO - 10.1371/annotation/cff22061-44d5-4301-b853-41702d160203 ID - Pepperell2013 ER - TY - JOUR AU - Fey, P. D. PY - 2012 DA - 2012// TI - Assessment of whole genome mapping in a well-defined outbreak of Salmonella enterica serotype Saintpaul JO - J Clin Microbiol VL - 50 UR - https://doi.org/10.1128/JCM.01320-12 DO - 10.1128/JCM.01320-12 ID - Fey2012 ER - TY - JOUR AU - Gilchrist, C. A. AU - Turner, S. D. AU - Riley, M. F. AU - Petri, W. A. AU - Hewlett, E. L. PY - 2015 DA - 2015// TI - Whole genome sequencing in outbreak analysis JO - Clin Microbiol Rev VL - 28 UR - https://doi.org/10.1128/CMR.00075-13 DO - 10.1128/CMR.00075-13 ID - Gilchrist2015 ER - TY - JOUR AU - Gomes, J. P. PY - 2007 DA - 2007// TI - Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5674706 DO - 10.1101/gr.5674706 ID - Gomes2007 ER - TY - JOUR AU - Sheppard, S. K. PY - 2013 DA - 2013// TI - Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1305559110 DO - 10.1073/pnas.1305559110 ID - Sheppard2013 ER - TY - JOUR AU - Laabei, M. PY - 2014 DA - 2014// TI - Predicting the virulence of MRSA from its genome sequence JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.165415.113 DO - 10.1101/gr.165415.113 ID - Laabei2014 ER - TY - JOUR AU - Alam, M. T. PY - 2014 DA - 2014// TI - Dissecting vancomycin intermediate resistance in Staphylococcus aureus using genome-wide association JO - Genome Biol Evol VL - 6 UR - https://doi.org/10.1093/gbe/evu092 DO - 10.1093/gbe/evu092 ID - Alam2014 ER - TY - JOUR AU - Chewapreecha, C. PY - 2014 DA - 2014// TI - Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004547 DO - 10.1371/journal.pgen.1004547 ID - Chewapreecha2014 ER - TY - JOUR AU - Maury, M. PY - 2016 DA - 2016// TI - Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity JO - Nat Genet VL - 48 UR - https://doi.org/10.1038/ng.3501 DO - 10.1038/ng.3501 ID - Maury2016 ER - TY - JOUR AU - Earle, S. G. PY - 2016 DA - 2016// TI - Identifying lineage effects when controlling for population structure improves power in bacterial association studies JO - Nature Microbiol VL - 1 UR - https://doi.org/10.1038/nmicrobiol.2016.41 DO - 10.1038/nmicrobiol.2016.41 ID - Earle2016 ER - TY - JOUR AU - Borges, V. AU - Gomes, J. P. PY - 2015 DA - 2015// TI - Deep comparative genomics among Chlamydia trachomatis lymphogranuloma venereum isolates highlights genes potentially involved in pathoadaptation JO - Infect Genet Evol VL - 32 UR - https://doi.org/10.1016/j.meegid.2015.02.026 DO - 10.1016/j.meegid.2015.02.026 ID - Borges2015 ER - TY - JOUR AU - Ferreira, R. PY - 2014 DA - 2014// TI - In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains JO - G3 VL - 5 UR - https://doi.org/10.1534/g3.114.015354 DO - 10.1534/g3.114.015354 ID - Ferreira2014 ER - TY - JOUR AU - Carlson, J. H. AU - Porcella, S. F. AU - McClarty, G. PY - 2005 DA - 2005// TI - Comparative genomic analysis of Chlamydia trachomatis oculotropic and geniotropic strains JO - Infect Immun VL - 73 UR - https://doi.org/10.1128/IAI.73.10.6407-6418.2005 DO - 10.1128/IAI.73.10.6407-6418.2005 ID - Carlson2005 ER - TY - JOUR AU - Brunelle, B. W. AU - Nicholson, T. L. AU - Stephens, R. S. PY - 2004 DA - 2004// TI - Micro-array based genomic surveying of gene polymorphisms in Chlamydia trachomatis JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-6-r42 DO - 10.1186/gb-2004-5-6-r42 ID - Brunelle2004 ER - TY - JOUR AU - Borges, V. AU - Nunes, A. AU - Ferreira, R. AU - Borrego, M. J. AU - Gomes, J. P. PY - 2012 DA - 2012// TI - Directional evolution of Chlamydia trachomatis towards niche-specific adaptation JO - J Bacteriol VL - 194 UR - https://doi.org/10.1128/JB.01291-12 DO - 10.1128/JB.01291-12 ID - Borges2012 ER - TY - JOUR AU - Clifton, D. R. PY - 2004 DA - 2004// TI - A Chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with the recruitment of actin JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0402829101 DO - 10.1073/pnas.0402829101 ID - Clifton2004 ER - TY - JOUR AU - Kari, L. PY - 2014 DA - 2014// TI - Chlamydia trachomatis polymorphic membrane protein D is a virulence factor involved in early host-cell interactions JO - Infect Immun VL - 82 UR - https://doi.org/10.1128/IAI.01686-14 DO - 10.1128/IAI.01686-14 ID - Kari2014 ER - TY - JOUR AU - Miyairi, I. PY - 2006 DA - 2006// TI - Different growth rates of Chlamydia trachomatis biovars reflect pathotype JO - J Infect Dis VL - 194 UR - https://doi.org/10.1086/505432 DO - 10.1086/505432 ID - Miyairi2006 ER - TY - JOUR AU - Da Cunha, M. PY - 2014 DA - 2014// TI - Identification of type THREE secretion substrates of Chlamydia trachomatis using Yersinia enterocolitica as a heterologous system JO - BMC Microbiol VL - 17 UR - https://doi.org/10.1186/1471-2180-14-40 DO - 10.1186/1471-2180-14-40 ID - Da Cunha2014 ER - TY - JOUR AU - Becker, E. AU - Hegemann, J. H. PY - 2014 DA - 2014// TI - All subtypes of the Pmp adhesion family are implicated in chlamydial virulence and show species-specific function JO - Microbiology VL - 3 ID - Becker2014 ER - TY - JOUR AU - Gangaiah, D. PY - 2013 DA - 2013// TI - Carbon storage regulator A contributes to the virulence of Haemophilus ducreyi in humans by multiple mechanisms JO - Infect Immun VL - 81 UR - https://doi.org/10.1128/IAI.01239-12 DO - 10.1128/IAI.01239-12 ID - Gangaiah2013 ER - TY - JOUR AU - Hogg, J. S. PY - 2007 DA - 2007// TI - Characterisation and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical non-typeable strains JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-6-r103 DO - 10.1186/gb-2007-8-6-r103 ID - Hogg2007 ER - TY - JOUR AU - Samuelson, J. C. PY - 2000 DA - 2000// TI - YidC mediates membrane protein insertion in bacteria JO - Nature VL - 406 UR - https://doi.org/10.1038/35020586 DO - 10.1038/35020586 ID - Samuelson2000 ER - TY - JOUR AU - Palmer, S. R. PY - 2012 DA - 2012// TI - YidC1 and YidC2 are functionally distinct proteins involved in protein secretion, biofilm formation and cariogenicity of Streptococcus mutans JO - Microbiology VL - 158 UR - https://doi.org/10.1099/mic.0.059139-0 DO - 10.1099/mic.0.059139-0 ID - Palmer2012 ER - TY - JOUR AU - Michel, G. PY - 2002 DA - 2002// TI - The structure of the RlmB 23S rRNA methyltransferase reveals a new methylation fold with a unique knot JO - Structure VL - 10 UR - https://doi.org/10.1016/S0969-2126(02)00852-3 DO - 10.1016/S0969-2126(02)00852-3 ID - Michel2002 ER - TY - JOUR AU - Lovgren, J. M. AU - Wikstrom, P. M. PY - 2001 DA - 2001// TI - The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli JO - J Bacteriol VL - 183 UR - https://doi.org/10.1128/JB.183.23.6957-6960.2001 DO - 10.1128/JB.183.23.6957-6960.2001 ID - Lovgren2001 ER - TY - JOUR AU - Power, R. A. AU - Parkhill, J. AU - de Oliveira, T. PY - 2017 DA - 2017// TI - Microbial genome-wide association studies: lessons from human GWAS JO - Nat Rev Genet VL - 18 UR - https://doi.org/10.1038/nrg.2016.132 DO - 10.1038/nrg.2016.132 ID - Power2017 ER - TY - JOUR AU - Le Negrate, G. PY - 2008 DA - 2008// TI - ChaDub1 of Chlamydia trachomatis suppresses NF-KappaB activation and inhibits 1-KappaB-alpha ubiquitination and degradation JO - Cell Microbiol VL - 10 UR - https://doi.org/10.1111/j.1462-5822.2008.01178.x DO - 10.1111/j.1462-5822.2008.01178.x ID - Le Negrate2008 ER - TY - JOUR AU - Misaghi, S. PY - 2006 DA - 2006// TI - Chlamydia trachomatis-derived deubiquinating enzymes in mammalian cells during infection JO - Mol Microbiol VL - 61 UR - https://doi.org/10.1111/j.1365-2958.2006.05199.x DO - 10.1111/j.1365-2958.2006.05199.x ID - Misaghi2006 ER - TY - JOUR AU - Li, Z. PY - 2012 DA - 2012// TI - Induction of protective immunity against Chlamydia muridarum intravaginal infection with a chlamydial glycogen phosphorylase JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0032997 DO - 10.1371/journal.pone.0032997 ID - Li2012 ER - TY - JOUR AU - Lu, C. PY - 2013 DA - 2013// TI - Chlamydia trachomatis GlgA is secreted into host cell cytoplasm JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0068764 DO - 10.1371/journal.pone.0068764 ID - Lu2013 ER - TY - JOUR AU - Swanson, K. A. PY - 2009 DA - 2009// TI - Chlamydia trachomatis polymorphic membrane protein D is an oligomeric autotransporter with a higher-order structure JO - Infect Immun VL - 77 UR - https://doi.org/10.1128/IAI.01173-08 DO - 10.1128/IAI.01173-08 ID - Swanson2009 ER - TY - JOUR AU - Werhl, W. PY - 2004 DA - 2004// TI - From the inside out — processing of the chlamydial autotransporter Pmp D and its role in bacterial adhesion and activation of human host cells JO - Mol Micribiol VL - 51 UR - https://doi.org/10.1046/j.1365-2958.2003.03838.x DO - 10.1046/j.1365-2958.2003.03838.x ID - Werhl2004 ER - TY - JOUR AU - Nunes, A. AU - Gomes, J. P. AU - Karunakaran, K. P. AU - Brunham, R. C. PY - 2015 DA - 2015// TI - Bioinformatic analysis of Chlamydia trachomatis PmpE, PmpF, PmpG and PmpH as potential vaccine antigens JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0131695 DO - 10.1371/journal.pone.0131695 ID - Nunes2015 ER - TY - STD TI - Tan C, Spitznagel JK, Shou HZ, et al. The polymorphic membrane protein gene family of the chlamydiaciae. In: Bavoil PM, Wyrick PB, editors. Chlamydia: genomics and pathogenesis. Norfolk: Horizon Bioscience; 2006. p. 195–218. ID - ref113 ER - TY - JOUR AU - Liu, X. PY - 2010 DA - 2010// TI - Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomics JO - J Bacteriol VL - 192 UR - https://doi.org/10.1128/JB.01628-09 DO - 10.1128/JB.01628-09 ID - Liu2010 ER -