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Publication breakdown of dataset

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

PubMed idYearCitationTitle Isolates in database
310039292019Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD (2019) EBioMedicine 43: 338-346 International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.
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.
310928172019Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D (2019) Nat Commun 10: 2176 Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.
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.
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.
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.
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.
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.
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.
255048472015Haubold B, Klötzl F, Pfaffelhuber P (2015) Bioinformatics 31: 1169-75 andi: fast and accurate estimation of evolutionary distances between closely related genomes.
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.
326513902020Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA (2020) Nat Commun 11: 3442 Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.
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.
320421292020Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP (2020) Nat Microbiol 5: 455-464 Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.
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.
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.
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.
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.