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Items: 1 to 50 of 63

1.

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment.

Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O'Flynn C.

PLoS One. 2019 Jun 10;14(6):e0214354. doi: 10.1371/journal.pone.0214354. eCollection 2019.

2.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Apr 23. pii: syz020. doi: 10.1093/sysbio/syz020. [Epub ahead of print]

PMID:
31034053
3.

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids.

Roy Chowdhury P, Fourment M, DeMaere MZ, Monahan L, Merlino J, Gottlieb T, Darling AE, Djordjevic SP.

Plasmid. 2019 Mar;102:56-61. doi: 10.1016/j.plasmid.2019.03.002. Epub 2019 Mar 15.

PMID:
30885788
4.

Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups.

Bogema DR, McKinnon J, Liu M, Hitchick N, Miller N, Venturini C, Iredell J, Darling AE, Roy Chowdury P, Djordjevic SP.

Microb Genom. 2019 Feb 27. doi: 10.1099/mgen.0.000255. [Epub ahead of print]

5.

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.

DeMaere MZ, Darling AE.

Genome Biol. 2019 Feb 26;20(1):46. doi: 10.1186/s13059-019-1643-1.

6.

High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei.

Monahan LG, DeMaere MZ, Cummins ML, Djordjevic SP, Roy Chowdhury P, Darling AE.

Gut Pathog. 2019 Feb 13;11:3. doi: 10.1186/s13099-019-0288-7. eCollection 2019.

7.

CAMISIM: simulating metagenomes and microbial communities.

Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, Sczyrba A, Bremges A, McHardy AC.

Microbiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.

8.

Local and relaxed clocks: the best of both worlds.

Fourment M, Darling AE.

PeerJ. 2018 Jul 3;6:e5140. doi: 10.7717/peerj.5140. eCollection 2018.

9.

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.

Deutscher AT, Burke CM, Darling AE, Riegler M, Reynolds OL, Chapman TA.

Microbiome. 2018 May 5;6(1):85. doi: 10.1186/s40168-018-0463-y.

10.

Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.

Bogema DR, Micallef ML, Liu M, Padula MP, Djordjevic SP, Darling AE, Jenkins C.

BMC Genomics. 2018 Apr 27;19(1):298. doi: 10.1186/s12864-018-4701-2.

11.

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.

Reid CJ, Wyrsch ER, Roy Chowdhury P, Zingali T, Liu M, Darling AE, Chapman TA, Djordjevic SP.

Microb Genom. 2017 Dec;3(12). doi: 10.1099/mgen.0.000143.

12.

Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo.

Dinh V, Darling AE, Matsen Iv FA.

Syst Biol. 2018 May 1;67(3):503-517. doi: 10.1093/sysbio/syx087.

13.

Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals.

Fourment M, Claywell BC, Dinh V, McCoy C, Matsen Iv FA, Darling AE.

Syst Biol. 2018 May 1;67(3):490-502. doi: 10.1093/sysbio/syx090.

14.

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

DeMaere MZ, Darling AE.

Gigascience. 2018 Feb 1;7(2). doi: 10.1093/gigascience/gix103.

15.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

16.

Evaluation of ddRADseq for reduced representation metagenome sequencing.

Liu MY, Worden P, Monahan LG, DeMaere MZ, Burke CM, Djordjevic SP, Charles IG, Darling AE.

PeerJ. 2017 Sep 19;5:e3837. doi: 10.7717/peerj.3837. eCollection 2017.

17.

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM.

Genome Biol. 2017 Sep 21;18(1):181. doi: 10.1186/s13059-017-1309-9.

18.

The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence.

Wang K, Chen YQ, Salido MM, Kohli GS, Kong JL, Liang HJ, Yao ZT, Xie YT, Wu HY, Cai SQ, Drautz-Moses DI, Darling AE, Schuster SC, Yang L, Ding Y.

Open Biol. 2017 Sep;7(9). pii: 170029. doi: 10.1098/rsob.170029.

19.

The impact of migratory flyways on the spread of avian influenza virus in North America.

Fourment M, Darling AE, Holmes EC.

BMC Evol Biol. 2017 May 25;17(1):118. doi: 10.1186/s12862-017-0965-4.

21.

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq.

Burke CM, Darling AE.

PeerJ. 2016 Sep 20;4:e2492. doi: 10.7717/peerj.2492. eCollection 2016.

22.

Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease.

Roy Chowdhury P, DeMaere M, Chapman T, Worden P, Charles IG, Darling AE, Djordjevic SP.

BMC Microbiol. 2016 Mar 12;16:41. doi: 10.1186/s12866-016-0653-3.

23.

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.

Joss TV, Burke CM, Hudson BJ, Darling AE, Forer M, Alber DG, Charles IG, Stow NW.

Front Microbiol. 2016 Jan 22;6:1532. doi: 10.3389/fmicb.2015.01532. eCollection 2015.

24.

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis.

O'Flynn C, Deusch O, Darling AE, Eisen JA, Wallis C, Davis IJ, Harris SJ.

Genome Biol Evol. 2015 Nov 13;7(12):3397-413. doi: 10.1093/gbe/evv220.

25.

Swabs to genomes: a comprehensive workflow.

Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA.

PeerJ. 2015 May 14;3:e960. doi: 10.7717/peerj.960. eCollection 2015.

26.

Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.

Wyrsch E, Roy Chowdhury P, Abraham S, Santos J, Darling AE, Charles IG, Chapman TA, Djordjevic SP.

BMC Genomics. 2015 Mar 10;16:165. doi: 10.1186/s12864-015-1382-y.

27.

Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome.

Coil DA, Alexiev A, Wallis C, O'Flynn C, Deusch O, Davis I, Horsfall A, Kirkwood N, Jospin G, Eisen JA, Harris S, Darling AE.

Genome Announc. 2015 Apr 9;3(2). pii: e00187-15. doi: 10.1128/genomeA.00187-15.

28.

Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.

Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT.

PLoS Genet. 2014 Nov 13;10(11):e1004784. doi: 10.1371/journal.pgen.1004784. eCollection 2014 Nov.

29.

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

Coil D, Jospin G, Darling AE.

Bioinformatics. 2015 Feb 15;31(4):587-9. doi: 10.1093/bioinformatics/btu661. Epub 2014 Oct 22.

PMID:
25338718
30.

Alignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B.

Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1.

31.

The common oceanographer: crowdsourcing the collection of oceanographic data.

Lauro FM, Senstius SJ, Cullen J, Neches R, Jensen RM, Brown MV, Darling AE, Givskov M, McDougald D, Hoeke R, Ostrowski M, Philip GK, Paulsen IT, Grzymski JJ.

PLoS Biol. 2014 Sep 9;12(9):e1001947. doi: 10.1371/journal.pbio.1001947. eCollection 2014 Sep. No abstract available.

32.

A draft genome of Escherichia coli sequence type 127 strain 2009-46.

Darling AE, McKinnon J, Worden P, Santos J, Charles IG, Chowdhury PR, Djordjevic SP.

Gut Pathog. 2014 Sep 1;6:32. doi: 10.1186/1757-4749-6-32. eCollection 2014.

33.

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.

Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE.

PeerJ. 2014 May 27;2:e415. doi: 10.7717/peerj.415. eCollection 2014.

34.

The genome of Clostridium difficile 5.3.

Darling AE, Worden P, Chapman TA, Roy Chowdhury P, Charles IG, Djordjevic SP.

Gut Pathog. 2014 Feb 24;6(1):4. doi: 10.1186/1757-4749-6-4.

35.

PhyloSift: phylogenetic analysis of genomes and metagenomes.

Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.

PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243. eCollection 2014.

36.

Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).

Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA.

Genome Announc. 2013 Jun 27;1(3). pii: e00325-13. doi: 10.1128/genomeA.00325-13.

37.

Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).

Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA.

Genome Announc. 2013 May 16;1(3). pii: e00244-13. doi: 10.1128/genomeA.00244-13.

38.

Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).

Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA.

Genome Announc. 2013 May 9;1(3). pii: e00197-13. doi: 10.1128/genomeA.00197-13.

39.

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA.

Genome Announc. 2013 May 9;1(3). pii: e00172-13. doi: 10.1128/genomeA.00172-13.

40.

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

Lang JM, Darling AE, Eisen JA.

PLoS One. 2013 Apr 25;8(4):e62510. doi: 10.1371/journal.pone.0062510. Print 2013.

41.

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).

Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA.

Genome Announc. 2013 Mar 21;1(2):e0012013. doi: 10.1128/genomeA.00120-13.

42.

Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4.

Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA.

Genome Announc. 2013 Mar 21;1(2):e0008613. doi: 10.1128/genomeA.00086-13.

43.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

44.

Progressive genome-wide introgression in agricultural Campylobacter coli.

Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MC, Falush D.

Mol Ecol. 2013 Feb;22(4):1051-64. doi: 10.1111/mec.12162. Epub 2012 Dec 20.

45.

An integrated pipeline for de novo assembly of microbial genomes.

Tritt A, Eisen JA, Facciotti MT, Darling AE.

PLoS One. 2012;7(9):e42304. doi: 10.1371/journal.pone.0042304. Epub 2012 Sep 13.

46.

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.

Didelot X, Méric G, Falush D, Darling AE.

BMC Genomics. 2012 Jun 19;13:256. doi: 10.1186/1471-2164-13-256.

47.

The rise and fall of breakpoint reuse depending on genome resolution.

Attie O, Darling AE, Yancopoulos S.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S1. doi: 10.1186/1471-2105-12-S9-S1.

48.

Mauve assembly metrics.

Darling AE, Tritt A, Eisen JA, Facciotti MT.

Bioinformatics. 2011 Oct 1;27(19):2756-7. doi: 10.1093/bioinformatics/btr451. Epub 2011 Aug 2.

49.

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

Darling AE, Mau B, Perna NT.

PLoS One. 2010 Jun 25;5(6):e11147. doi: 10.1371/journal.pone.0011147.

50.

Metagenomic sequencing of an in vitro-simulated microbial community.

Morgan JL, Darling AE, Eisen JA.

PLoS One. 2010 Apr 16;5(4):e10209. doi: 10.1371/journal.pone.0010209.

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