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Items: 11

1.

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.

Van Puyvelde S, Pickard D, Vandelannoote K, Heinz E, Barbé B, de Block T, Clare S, Coomber EL, Harcourt K, Sridhar S, Lees EA, Wheeler NE, Klemm EJ, Kuijpers L, Mbuyi Kalonji L, Phoba MF, Falay D, Ngbonda D, Lunguya O, Jacobs J, Dougan G, Deborggraeve S.

Nat Commun. 2019 Sep 19;10(1):4280. doi: 10.1038/s41467-019-11844-z.

2.

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.

Lees 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.

Nat Commun. 2019 May 15;10(1):2176. doi: 10.1038/s41467-019-09976-3.

3.

Convergent regulatory evolution and loss of flight in paleognathous birds.

Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV.

Science. 2019 Apr 5;364(6435):74-78. doi: 10.1126/science.aat7244.

PMID:
30948549
4.

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.

Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP, Biggs PJ.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000251. Epub 2019 Feb 19.

5.

Tracing outbreaks with machine learning.

Wheeler NE.

Nat Rev Microbiol. 2019 May;17(5):269. doi: 10.1038/s41579-019-0153-1. Review. No abstract available.

PMID:
30742026
6.

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Wheeler NE, Gardner PP, Barquist L.

PLoS Genet. 2018 May 8;14(5):e1007333. doi: 10.1371/journal.pgen.1007333. eCollection 2018 May.

7.

Breaking the code of antibiotic resistance.

Lo SW, Kumar N, Wheeler NE.

Nat Rev Microbiol. 2018 May;16(5):262. doi: 10.1038/nrmicro.2018.33. Epub 2018 Mar 26. No abstract available.

PMID:
29576619
8.

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts.

Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP, MacKichan JK.

mSystems. 2017 Nov 14;2(6). pii: e00127-17. doi: 10.1128/mSystems.00127-17. eCollection 2017 Nov-Dec.

9.

Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.

Coray DS, Wheeler NE, Heinemann JA, Gardner PP.

RNA Biol. 2017 Mar 4;14(3):275-280. doi: 10.1080/15476286.2016.1272747. Epub 2017 Jan 9. Review.

10.

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Wheeler NE, Barquist L, Kingsley RA, Gardner PP.

Bioinformatics. 2016 Dec 1;32(23):3566-3574. doi: 10.1093/bioinformatics/btw518. Epub 2016 Aug 8.

11.

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003907. doi: 10.1371/journal.pcbi.1003907. eCollection 2014 Oct.

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