Browsing byAuthorDarling, AE

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Issue DateTitleAuthor(s)
2020-01-01Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groupsBogema, DR; McKinnon, J; Liu, M; Hitchick, N; Miller, N; Venturini, C; Iredell, J; Darling, AE; Chowdury, PR; Djordjevic, SP
2019-11-01BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical PhylogeneticsAyres, DL; Cummings, MP; Baele, G; Darling, AE; Lewis, PO; Swofford, DL; Huelsenbeck, JP; Lemey, P; Rambaut, A; Suchard, MA
2019-06-01Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignmentCoilID, DA; Jospin, G; Darling, AE; Wallis, C; Davis, IJ; Harris, S; Eisen, JA; Holcombe, LJ; O'Flynn, C
2019-03-01Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmidsRoy Chowdhury, P; Fourment, M; DeMaere, MZ; Monahan, L; Merlino, J; Gottlieb, T; Darling, AE; Djordjevic, SP
2019-02-26Bin3C: Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomesDemaere, MZ; Darling, AE
2019-02-13High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaecheiMonahan, LG; Demaere, MZ; Cummins, ML; Djordjevic, SP; Roy Chowdhury, P; Darling, AE
2019-02-08CAMISIM: Simulating metagenomes and microbial communitiesFritz, 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
2019-01-01Evaluating probabilistic programming and fast variational Bayesian inference in phylogeneticsFourment, M; Darling, AE
2018-07-20Visualization of Biomedical DataO'Donoghue, SI; Baldi, BF; Clark, SJ; Darling, AE; Hogan, JM; Kaur, S; Maier-Hein, L; McCarthy, DJ; Moore, WJ; Stenau, E; Swedlow, JR; Vuong, J; Procter, JB
2018-07-03Local and relaxed clocks, the best of both worldsFourment, M; Darling, AE
2018-05-05Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvaeDeutscher, AT; Burke, CM; Darling, AE; Riegler, M; Reynolds, OL; Chapman, TA
2018-05-01Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposalsFourment, M; Claywell, BC; Dinh, V; McCoy, C; Matsen, FA; Darling, AE
2018-05-01Online Bayesian phylogenetic inference: Theoretical foundations via sequential Monte CarloDinh, V; Darling, AE; Matsen, FA
2018-04-27Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypesBogema, DR; Micallef, ML; Liu, M; Padula, MP; Djordjevic, SP; Darling, AE; Jenkins, C
2018-04-13CAMISIM: Simulating metagenomes and microbial communitiesDarling, AE; Fritz, A; Hofmann, P; Majda, S; Dahms, E; Droge, J; Fiedler, J; Lesker, TR; Belmann, P; DeMaere, MZ; Sczyrba, A; Bremges, A; McHardy, AC
2018-01-01Local and relaxed clocks: The best of both worldsFourment, M; Darling, AE
2018-01-01Sim3C: Simulation of Hi-C and Meta3C proximity ligation sequencing technologiesDeMaere, MZ; Darling, AE
2017-12-01Porcine commensal escherichia coli: A reservoir for class 1 integrons associated with IS26Reid, CJ; Wyrsch, ER; Chowdhury, PR; Zingali, T; Liu, M; Darling, AE; Chapman, TA; Djordjevic, SP
2017-12Porcine 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
2017-10-31Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics softwareSczyrba, 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; Balvočiutė, 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