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Items: 22

1.

Benchmarking Metagenomics Tools for Taxonomic Classification.

Ye SH, Siddle KJ, Park DJ, Sabeti PC.

Cell. 2019 Aug 8;178(4):779-794. doi: 10.1016/j.cell.2019.07.010. Review.

PMID:
31398336
2.

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.

Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A; Viral Hemorrhagic Fever Consortium, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB.

Nat Biotechnol. 2019 Feb;37(2):160-168. doi: 10.1038/s41587-018-0006-x. Epub 2019 Feb 4.

3.

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.

Siddle KJ, Eromon P, Barnes KG, Mehta S, Oguzie JU, Odia I, Schaffner SF, Winnicki SM, Shah RR, Qu J, Wohl S, Brehio P, Iruolagbe C, Aiyepada J, Uyigue E, Akhilomen P, Okonofua G, Ye S, Kayode T, Ajogbasile F, Uwanibe J, Gaye A, Momoh M, Chak B, Kotliar D, Carter A, Gladden-Young A, Freije CA, Omoregie O, Osiemi B, Muoebonam EB, Airende M, Enigbe R, Ebo B, Nosamiefan I, Oluniyi P, Nekoui M, Ogbaini-Emovon E, Garry RF, Andersen KG, Park DJ, Yozwiak NL, Akpede G, Ihekweazu C, Tomori O, Okogbenin S, Folarin OA, Okokhere PO, MacInnis BL, Sabeti PC, Happi CT.

N Engl J Med. 2018 Nov 1;379(18):1745-1753. doi: 10.1056/NEJMoa1804498. Epub 2018 Oct 17.

4.

Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever.

Boisen ML, Hartnett JN, Shaffer JG, Goba A, Momoh M, Sandi JD, Fullah M, Nelson DKS, Bush DJ, Rowland MM, Heinrich ML, Koval AP, Cross RW, Barnes KG, Lachenauer AE, Lin AE, Nekoui M, Kotliar D, Winnicki SM, Siddle KJ, Gbakie M, Fonnie M, Koroma VJ, Kanneh L, Kulakosky PC, Hastie KM, Wilson RB, Andersen KG, Folarin OO, Happi CT, Sabeti PC, Geisbert TW, Saphire EO, Khan SH, Grant DS, Schieffelin JS, Branco LM, Garry RF.

Sci Rep. 2018 Apr 12;8(1):5939. doi: 10.1038/s41598-018-24246-w.

5.

Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood.

Choi K, Ryu H, Siddle KJ, Piantadosi A, Freimark L, Park DJ, Sabeti P, Han J.

Anal Chem. 2018 Apr 3;90(7):4657-4662. doi: 10.1021/acs.analchem.7b05200. Epub 2018 Mar 21.

6.

miR-222 isoforms are differentially regulated by type-I interferon.

Nejad C, Pillman KA, Siddle KJ, Pépin G, Änkö ML, McCoy CE, Beilharz TH, Quintana-Murci L, Goodall GJ, Bracken CP, Gantier MP.

RNA. 2018 Mar;24(3):332-341. doi: 10.1261/rna.064550.117. Epub 2017 Dec 20.

7.

Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery.

Barnes KG, Kindrachuk J, Lin AE, Wohl S, Qu J, Tostenson SD, Dorman WR, Busby M, Siddle KJ, Luo CY, Matranga CB, Davey RT, Sabeti PC, Chertow DS.

Clin Infect Dis. 2017 Oct 15;65(8):1400-1403. doi: 10.1093/cid/cix518.

8.

Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection.

Pai AA, Baharian G, Pagé Sabourin A, Brinkworth JF, Nédélec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson ZP, Lanford RE, Burge CB, Barreiro LB.

PLoS Genet. 2016 Sep 30;12(9):e1006338. doi: 10.1371/journal.pgen.1006338. eCollection 2016 Sep.

9.

The epigenomic landscape of African rainforest hunter-gatherers and farmers.

Fagny M, Patin E, MacIsaac JL, Rotival M, Flutre T, Jones MJ, Siddle KJ, Quach H, Harmant C, McEwen LM, Froment A, Heyer E, Gessain A, Betsem E, Mouguiama-Daouda P, Hombert JM, Perry GH, Barreiro LB, Kobor MS, Quintana-Murci L.

Nat Commun. 2015 Nov 30;6:10047. doi: 10.1038/ncomms10047.

10.

bacterial infection drives the expression dynamics of microRNAs and their isomiRs.

Siddle KJ, Tailleux L, Deschamps M, Loh YH, Deluen C, Gicquel B, Antoniewski C, Barreiro LB, Farinelli L, Quintana-Murci L.

PLoS Genet. 2015 Mar 20;11(3):e1005064. doi: 10.1371/journal.pgen.1005064. eCollection 2015 Mar. Erratum in: PLoS Genet. 2015 Jun;11(6):e1005321.

11.

The Red Queen's long race: human adaptation to pathogen pressure.

Siddle KJ, Quintana-Murci L.

Curr Opin Genet Dev. 2014 Dec;29:31-8. doi: 10.1016/j.gde.2014.07.004. Epub 2014 Aug 24. Review.

PMID:
25170983
12.

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists.

Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A, Régnault B, Lemée L, Gravel S, Hombert JM, Van der Veen L, Dominy NJ, Perry GH, Barreiro LB, Verdu P, Heyer E, Quintana-Murci L.

Nat Commun. 2014;5:3163. doi: 10.1038/ncomms4163.

PMID:
24495941
13.

A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection.

Siddle KJ, Deschamps M, Tailleux L, Nédélec Y, Pothlichet J, Lugo-Villarino G, Libri V, Gicquel B, Neyrolles O, Laval G, Patin E, Barreiro LB, Quintana-Murci L.

Genome Res. 2014 May;24(5):850-9. doi: 10.1101/gr.161471.113. Epub 2014 Jan 30.

14.

Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome.

Siddle KJ, Goodship JA, Keavney B, Santibanez-Koref MF.

Bioinformatics. 2011 Apr 1;27(7):895-8. doi: 10.1093/bioinformatics/btr067. Epub 2011 Feb 11.

PMID:
21317137
15.

Corrosion of lead shielding in a radiology department.

Schick DK, Casey RN, Sim LH, Siddle KJ.

Australas Radiol. 1999 Feb;43(1):47-51.

PMID:
10901870
16.

After-hours radiology.

Wong DC, Siddle KJ.

Australas Radiol. 1994 Nov;38(4):326-30.

PMID:
7993264
19.

Evaluation of pre-operative chest x-ray.

Jeavons SJ, Siddle KJ, Mitchell C, O'Hare PM.

Australas Radiol. 1987 Aug;31(3):256-9. No abstract available.

PMID:
2963612
20.

Diaphyseal Paget's disease: an unusual finding in the tibia.

Schubert F, Siddle KJ, Harper JS.

Clin Radiol. 1984 Jan;35(1):71-4.

PMID:
6690185
21.

Transluminal angioplasty of a transplant renal artery stenosis.

Hayes PT, Siddle KJ, Harper J, Petrie JB.

Australas Radiol. 1982 Jul;26(2):171-3. No abstract available.

PMID:
6217809
22.

The ureter in renal transplantation: results of a simple technique of uretero-vesical anastomosis.

Clunie GJ, Siddle KJ, Hartley LC, Hardie IR.

Aust N Z J Surg. 1974 Feb;44(1):12-6. No abstract available.

PMID:
4605354

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