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Publication breakdown of dataset

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162 records returned (1 - 25 displayed). Click the hyperlinks for detailed information.

PubMed idYearCitationTitle Isolates in database
302104812018Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB (2018) Front Microbiol 9: 2012 Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides.
251016442014Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J (2014) PLoS Genet 10: e1004547 Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.
258262082015Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP (2015) PLoS Genet 11: e1005095 Selective and genetic constraints on pneumococcal serotype switching.
282078132017Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J (2017) PLoS Genet 13: e1006508 Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.
245094792014Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD (2014) Nat Genet 46: 305-9 Dense genomic sampling identifies highways of pneumococcal recombination.
252534552014Numminen E, Chewapreecha C, Sirén J, Turner C, Turner P, Bentley SD, Corander J (2014) Proc Biol Sci 281: 20141324 Two-phase importance sampling for inference about transmission trees.
276338312016Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J (2016) Nat Commun 7: 12797 Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.
255048472015Haubold B, Klötzl F, Pfaffelhuber P (2015) Bioinformatics 31: 1169-75 andi: fast and accurate estimation of evolutionary distances between closely related genomes.
306058962019Gao CY, Cecconi F, Vulpiani A, Zhou HJ, Aurell E (2019) Phys Biol 16: 026002 DCA for genome-wide epistasis analysis: the statistical genetics perspective.
276725162016Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK (2016) PeerJ 4: e2477 Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline.
281005962017Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP (2017) J Clin Microbiol 55: 1104-1115 Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.
302579062018Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Sigurdsson S, Bentley SD, Haraldsson Á, Brueggemann AB, Kristinsson KG (2018) J Clin Microbiol 56: Effect of Vaccination on Pneumococci Isolated from the Nasopharynx of Healthy Children and the Middle Ear of Children with Otitis Media in Iceland.
280078872017Lin M, Kussell E (2017) Genetics 205: 891-917 Correlated Mutations and Homologous Recombination Within Bacterial Populations.
296174402018Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M (2018) PLoS Pathog 14: e1006966 The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.
290266522017Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN, Clarke SC (2017) Microb Genom 3: e000119 Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK.
297742452018Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD, Harris SR (2018) Wellcome Open Res 3: 33 Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.
265283972015Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP (2015) Sci Data 2: 150058 Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.
259561322015Li Y, Croucher NJ, Thompson CM, Trzciński K, Hanage WP, Lipsitch M (2015) BMC Genomics 16: 369 Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.
281996982017Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P (2017) Mol Biol Evol 34: 1167-1182 Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.
254070232014Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP (2014) Nat Commun 5: 5471 Diversification of bacterial genome content through distinct mechanisms over different timescales.
236444932013Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M (2013) Nat Genet 45: 656-63 Population genomics of post-vaccine changes in pneumococcal epidemiology.
257769202015Gladstone RA, Jefferies JM, Tocheva AS, Beard KR, Garley D, Chong WW, Bentley SD, Faust SN, Clarke SC (2015) Vaccine 33: 2015-21 Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction.
282182612017Brueggemann AB, Harrold CL, Rezaei Javan R, van Tonder AJ, McDonnell AJ, Edwards BA (2017) Sci Rep 7: 42976 Pneumococcal prophages are diverse, but not without structure or history.
264928622015Cremers AJ, Mobegi FM, de Jonge MI, van Hijum SA, Meis JF, Hermans PW, Ferwerda G, Bentley SD, Zomer AL (2015) Sci Rep 5: 14952 The post-vaccine microevolution of invasive Streptococcus pneumoniae.
262150502015Bogaardt C, van Tonder AJ, Brueggemann AB (2015) BMC Genomics 16: 554 Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin.