| Year |
Citation |
Score |
| 2023 |
Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. Microbiome. 11: 158. PMID 37491320 DOI: 10.1186/s40168-023-01591-1 |
0.716 |
|
| 2023 |
Krishnan S, DeMaere MZ, Beck D, Ostrowski M, Seymour JR, Darling AE. Rhometa: Population recombination rate estimation from metagenomic read datasets. Plos Genetics. 19: e1010683. PMID 36972309 DOI: 10.1371/journal.pgen.1010683 |
0.31 |
|
| 2022 |
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, ... ... Darling AE, et al. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 19: 429-440. PMID 35396482 DOI: 10.1038/s41592-022-01431-4 |
0.377 |
|
| 2022 |
Gaio D, Anantanawat K, To J, Liu M, Monahan L, Darling AE. Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction. Microbial Genomics. 8. PMID 35014949 DOI: 10.1099/mgen.0.000744 |
0.327 |
|
| 2021 |
DeMaere MZ, Darling AE. qc3C: Reference-free quality control for Hi-C sequencing data. Plos Computational Biology. 17: e1008839. PMID 34634030 DOI: 10.1371/journal.pcbi.1008839 |
0.341 |
|
| 2021 |
Gaio D, DeMaere MZ, Anantanawat K, Chapman TA, Djordjevic SP, Darling AE. Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes. Microbial Genomics. 7. PMID 34370660 DOI: 10.1099/mgen.0.000501 |
0.378 |
|
| 2021 |
Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE. STRONG: metagenomics strain resolution on assembly graphs. Genome Biology. 22: 214. PMID 34311761 DOI: 10.1186/s13059-021-02419-7 |
0.306 |
|
| 2021 |
Vicedomini R, Quince C, Darling AE, Chikhi R. Strainberry: automated strain separation in low-complexity metagenomes using long reads. Nature Communications. 12: 4485. PMID 34301928 DOI: 10.1038/s41467-021-24515-9 |
0.366 |
|
| 2020 |
Hastak P, Fourment M, Darling AE, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Chowdhury PR. ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex. Emerging Microbes & Infections. 1-35. PMID 32686595 DOI: 10.1080/22221751.2020.1797541 |
0.424 |
|
| 2020 |
Zingali T, Reid CJ, Chapman TA, Gaio D, Liu M, Darling AE, Djordjevic SP. Whole Genome Sequencing Analysis of Porcine Faecal Commensal Carrying Class 1 Integrons from Sows and Their Offspring. Microorganisms. 8. PMID 32512857 DOI: 10.3390/microorganisms8060843 |
0.316 |
|
| 2020 |
Yasir M, Turner AK, Bastkowski S, Baker D, Page AJ, Telatin A, Phan MD, Monahan L, Savva GM, Darling A, Webber MA, Charles IG. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance. Genome Research. PMID 32051187 DOI: 10.1101/Gr.254391.119 |
0.436 |
|
| 2019 |
Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller D, Voolstra CR, Adamska M. Molecular techniques and their limitations shape our view of the holobiont. Zoology (Jena, Germany). 137: 125695. PMID 31759226 DOI: 10.1016/J.Zool.2019.125695 |
0.333 |
|
| 2019 |
Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O'Flynn C. Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. Plos One. 14: e0214354. PMID 31181071 DOI: 10.1371/Journal.Pone.0214354 |
0.692 |
|
| 2019 |
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. PMID 31034053 DOI: 10.1093/Sysbio/Syz020 |
0.309 |
|
| 2019 |
Chowdhury PR, Fourment M, DeMaere MZ, Monahan L, Merlino J, Gottlieb T, Darling AE, Djordjevic SP. Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids. Plasmid. PMID 30885788 DOI: 10.1016/J.Plasmid.2019.03.002 |
0.324 |
|
| 2019 |
Bogema DR, McKinnon J, Liu M, Hitchick N, Miller N, Venturini C, Iredell J, Darling AE, Roy Chowdury P, Djordjevic SP. Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups. Microbial Genomics. PMID 30810518 DOI: 10.1099/mgen.0.000255 |
0.438 |
|
| 2019 |
DeMaere MZ, Darling AE. bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes. Genome Biology. 20: 46. PMID 30808380 DOI: 10.1186/S13059-019-1643-1 |
0.518 |
|
| 2019 |
Monahan LG, DeMaere MZ, Cummins ML, Djordjevic SP, Roy Chowdhury P, Darling AE. High contiguity genome sequence of a multidrug-resistant hospital isolate of . Gut Pathogens. 11: 3. PMID 30805030 DOI: 10.1186/S13099-019-0288-7 |
0.488 |
|
| 2019 |
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. CAMISIM: simulating metagenomes and microbial communities. Microbiome. 7: 17. PMID 30736849 DOI: 10.1186/S40168-019-0633-6 |
0.368 |
|
| 2018 |
Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, et al. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. Plos Biology. 16: e2006352. PMID 30086128 DOI: 10.1371/Journal.Pbio.2006352 |
0.725 |
|
| 2018 |
Deutscher AT, Burke CM, Darling AE, Riegler M, Reynolds OL, Chapman TA. Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae. Microbiome. 6: 85. PMID 29729663 DOI: 10.1186/S40168-018-0463-Y |
0.368 |
|
| 2018 |
Bogema DR, Micallef ML, Liu M, Padula MP, Djordjevic SP, Darling AE, Jenkins C. Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes. Bmc Genomics. 19: 298. PMID 29703152 DOI: 10.1186/S12864-018-4701-2 |
0.478 |
|
| 2017 |
Reid CJ, Wyrsch ER, Roy Chowdhury P, Zingali T, Liu M, Darling AE, Chapman TA, Djordjevic SP. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microbial Genomics. 3. PMID 29306352 DOI: 10.1099/mgen.0.000143 |
0.344 |
|
| 2017 |
Dinh V, Darling AE, Matsen Iv FA. Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo. Systematic Biology. PMID 29244177 DOI: 10.1093/Sysbio/Syx087 |
0.42 |
|
| 2017 |
Fourment M, Claywell BC, Dinh V, McCoy C, Matsen Iv FA, Darling AE. Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals. Systematic Biology. PMID 29186587 DOI: 10.1093/Sysbio/Syx090 |
0.365 |
|
| 2017 |
DeMaere MZ, Darling AE. Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies. Gigascience. PMID 29149264 DOI: 10.1093/Gigascience/Gix103 |
0.465 |
|
| 2017 |
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, ... ... Darling AE, et al. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature Methods. PMID 28967888 DOI: 10.1038/Nmeth.4458 |
0.45 |
|
| 2017 |
Liu MY, Worden P, Monahan LG, DeMaere MZ, Burke CM, Djordjevic SP, Charles IG, Darling AE. Evaluation of ddRADseq for reduced representation metagenome sequencing. Peerj. 5: e3837. PMID 28948110 DOI: 10.7717/Peerj.3837 |
0.411 |
|
| 2017 |
Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM. DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biology. 18: 181. PMID 28934976 DOI: 10.1186/S13059-017-1309-9 |
0.496 |
|
| 2017 |
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. The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence. Open Biology. 7. PMID 28878043 DOI: 10.1098/Rsob.170029 |
0.339 |
|
| 2016 |
DeMaere MZ, Darling AE. Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C). Peerj. 4: e2676. PMID 27843713 DOI: 10.7717/Peerj.2676 |
0.437 |
|
| 2016 |
Burke CM, Darling AE. A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq. Peerj. 4: e2492. PMID 27688981 DOI: 10.7717/Peerj.2492 |
0.426 |
|
| 2016 |
Roy Chowdhury P, DeMaere M, Chapman T, Worden P, Charles IG, Darling AE, Djordjevic SP. Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease. Bmc Microbiology. 16: 41. PMID 26971047 DOI: 10.1186/S12866-016-0653-3 |
0.364 |
|
| 2015 |
Liu M, Darling A. Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges. F1000research. 4: 1377. PMID 27006753 DOI: 10.12688/F1000Research.7281.1 |
0.349 |
|
| 2015 |
Joss TV, Burke CM, Hudson BJ, Darling AE, Forer M, Alber DG, Charles IG, Stow NW. Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients. Frontiers in Microbiology. 6: 1532. PMID 26834708 DOI: 10.3389/Fmicb.2015.01532 |
0.368 |
|
| 2015 |
O'Flynn C, Deusch O, Darling A, Eisen JA, Wallis C, Davis I, Harris S. Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis. Genome Biology and Evolution. PMID 26568374 DOI: 10.1093/Gbe/Evv220 |
0.608 |
|
| 2015 |
Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Swabs to genomes: a comprehensive workflow. Peerj. 3: e960. PMID 26020012 DOI: 10.7717/Peerj.960 |
0.773 |
|
| 2015 |
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. Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome. Genome Announcements. 3. PMID 25858832 DOI: 10.1128/Genomea.00187-15 |
0.606 |
|
| 2015 |
Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics (Oxford, England). 31: 587-9. PMID 25338718 DOI: 10.1093/Bioinformatics/Btu661 |
0.507 |
|
| 2015 |
Darling A. Understanding microbes through the lens of comparative genomics... a biased perspective F1000research. 4. DOI: 10.7490/F1000Research.1110381.1 |
0.529 |
|
| 2014 |
Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. Plos Genetics. 10: e1004784. PMID 25393412 DOI: 10.1371/Journal.Pgen.1004784 |
0.761 |
|
| 2014 |
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, ... ... Darling AE, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114 |
0.46 |
|
| 2014 |
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. The common oceanographer: crowdsourcing the collection of oceanographic data. Plos Biology. 12: e1001947. PMID 25203659 DOI: 10.1371/Journal.Pbio.1001947 |
0.71 |
|
| 2014 |
Darling AE, McKinnon J, Worden P, Santos J, Charles IG, Roy Chowdhury P, Djordjevic SP. A draft genome of Escherichia coli sequence type 127 strain 2009-46. Gut Pathogens. 6: 32. PMID 25197321 DOI: 10.1186/1757-4749-6-32 |
0.425 |
|
| 2014 |
Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. Peerj. 2: e415. PMID 24918035 DOI: 10.7717/Peerj.415 |
0.72 |
|
| 2014 |
Darling AE, Worden P, Chapman TA, Roy Chowdhury P, Charles IG, Djordjevic SP. The genome of Clostridium difficile 5.3. Gut Pathogens. 6: 4. PMID 24565059 DOI: 10.1186/1757-4749-6-4 |
0.36 |
|
| 2014 |
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. Peerj. 2: e243. PMID 24482762 DOI: 10.7717/Peerj.243 |
0.775 |
|
| 2013 |
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499: 431-7. PMID 23851394 DOI: 10.1038/Nature12352 |
0.677 |
|
| 2013 |
Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). Genome Announcements. 1. PMID 23792744 DOI: 10.1128/Genomea.00325-13 |
0.766 |
|
| 2013 |
Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements. 1. PMID 23682147 DOI: 10.1128/Genomea.00244-13 |
0.778 |
|
| 2013 |
Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements. 1. PMID 23661480 DOI: 10.1128/Genomea.00197-13 |
0.775 |
|
| 2013 |
Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements. 1. PMID 23661474 DOI: 10.1128/Genomea.00172-13 |
0.746 |
|
| 2013 |
Lang JM, Darling AE, Eisen JA. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. Plos One. 8: e62510. PMID 23638103 DOI: 10.1371/Journal.Pone.0062510 |
0.745 |
|
| 2013 |
Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announcements. 1: e0012013. PMID 23516225 DOI: 10.1128/Genomea.00120-13 |
0.761 |
|
| 2013 |
Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announcements. 1: e0008613. PMID 23516213 DOI: 10.1128/Genomea.00086-13 |
0.738 |
|
| 2013 |
Islam A, Labbate M, Djordjevic SP, Alam M, Darling A, Melvold J, Holmes AJ, Johura FT, Cravioto A, Charles IG, Stokes HW. Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic. Open Biology. 3: 120181. PMID 23407641 DOI: 10.1098/Rsob.120181 |
0.317 |
|
| 2013 |
Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, et al. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. Bmc Genomics. 14: 95. PMID 23402223 DOI: 10.1186/1471-2164-14-95 |
0.648 |
|
| 2013 |
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology. 14: R2. PMID 23320958 DOI: 10.1186/Gb-2013-14-1-R2 |
0.455 |
|
| 2013 |
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, et al. Progressive genome-wide introgression in agricultural Campylobacter coli. Molecular Ecology. 22: 1051-64. PMID 23279096 DOI: 10.1111/Mec.12162 |
0.431 |
|
| 2012 |
Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. Plos One. 7: e42304. PMID 23028432 DOI: 10.1371/Journal.Pone.0042304 |
0.621 |
|
| 2012 |
Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. Plos One. 7: e41389. PMID 22848480 DOI: 10.1371/Journal.Pone.0041389 |
0.814 |
|
| 2012 |
Didelot X, Méric G, Falush D, Darling AE. Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. Bmc Genomics. 13: 256. PMID 22712577 DOI: 10.1186/1471-2164-13-256 |
0.498 |
|
| 2012 |
Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, Krause DJ, Whitaker RJ. Patterns of gene flow define species of thermophilic Archaea. Plos Biology. 10: e1001265. PMID 22363207 DOI: 10.1371/Journal.Pbio.1001265 |
0.449 |
|
| 2012 |
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/Sysbio/Syr100 |
0.339 |
|
| 2012 |
Kehr B, Reinert K, Darling A. Hidden breakpoints in genome alignments F1000research. 3. DOI: 10.7490/F1000Research.1092189.1 |
0.553 |
|
| 2011 |
Attie O, Darling AE, Yancopoulos S. The rise and fall of breakpoint reuse depending on genome resolution. Bmc Bioinformatics. 12: S1. PMID 22151330 DOI: 10.1186/1471-2105-12-S9-S1 |
0.551 |
|
| 2011 |
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111 |
0.486 |
|
| 2011 |
Darling AE, Tritt A, Eisen JA, Facciotti MT. Mauve assembly metrics. Bioinformatics (Oxford, England). 27: 2756-7. PMID 21810901 DOI: 10.1093/Bioinformatics/Btr451 |
0.622 |
|
| 2010 |
Didelot X, Lawson D, Darling A, Falush D. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics. 186: 1435-49. PMID 20923983 DOI: 10.1534/Genetics.110.120121 |
0.572 |
|
| 2010 |
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 466: 720-6. PMID 20686567 DOI: 10.1038/Nature09201 |
0.537 |
|
| 2010 |
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. Plos One. 5: e11147. PMID 20593022 DOI: 10.1371/Journal.Pone.0011147 |
0.72 |
|
| 2010 |
Morgan JL, Darling AE, Eisen JA. Metagenomic sequencing of an in vitro-simulated microbial community. Plos One. 5: e10209. PMID 20419134 DOI: 10.1371/Journal.Pone.0010209 |
0.544 |
|
| 2009 |
Chan CX, Beiko RG, Darling AE, Ragan MA. Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution. 1: 429-38. PMID 20333212 DOI: 10.1093/Gbe/Evp044 |
0.388 |
|
| 2009 |
Miklós I, Darling AE. Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia. Genome Biology and Evolution. 1: 153-64. PMID 20333186 DOI: 10.1093/Gbe/Evp015 |
0.357 |
|
| 2009 |
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (Oxford, England). 25: 2071-3. PMID 19515959 DOI: 10.1093/Bioinformatics/Btp356 |
0.747 |
|
| 2009 |
Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP. A novel heuristic for local multiple alignment of interspersed DNA repeats. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 180-9. PMID 19407343 DOI: 10.1109/Tcbb.2009.9 |
0.474 |
|
| 2009 |
Esteban-Marcos A, Darling AE, Ragan MA. Seevolution: visualizing chromosome evolution. Bioinformatics (Oxford, England). 25: 960-1. PMID 19233896 DOI: 10.1093/Bioinformatics/Btp096 |
0.49 |
|
| 2009 |
Chan CX, Darling AE, Beiko RG, Ragan MA. Are protein domains modules of lateral genetic transfer? Plos One. 4: e4524. PMID 19229333 DOI: 10.1371/Journal.Pone.0004524 |
0.374 |
|
| 2009 |
Kropinski AM, Borodovsky M, Carver TJ, Cerdeño-Tárraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS. In silico identification of genes in bacteriophage DNA. Methods in Molecular Biology (Clifton, N.J.). 502: 57-89. PMID 19082552 DOI: 10.1007/978-1-60327-565-1_6 |
0.52 |
|
| 2009 |
Didelot X, Darling A, Falush D. Inferring genomic flux in bacteria. Genome Research. 19: 306-17. PMID 19015321 DOI: 10.1101/Gr.082263.108 |
0.543 |
|
| 2008 |
Darling AE, Miklós I, Ragan MA. Dynamics of genome rearrangement in bacterial populations. Plos Genetics. 4: e1000128. PMID 18650965 DOI: 10.1371/Journal.Pgen.1000128 |
0.547 |
|
| 2008 |
Friedberg R, Darling AE, Yancopoulos S. Genome rearrangement by the double cut and join operation. Methods in Molecular Biology (Clifton, N.J.). 452: 385-416. PMID 18566774 DOI: 10.1007/978-1-60327-159-2_18 |
0.332 |
|
| 2008 |
Glasner JD, Plunkett G, Anderson BD, Baumler DJ, Biehl BS, Burland V, Cabot EL, Darling AE, Mau B, Neeno-Eckwall EC, Pot D, Qiu Y, Rissman AI, Worzella S, Zaremba S, et al. Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Research. 36: D519-23. PMID 17999997 DOI: 10.1093/Nar/Gkm973 |
0.691 |
|
| 2007 |
Darling AE, Treangen TJ, Messeguer X, Perna NT. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods in Molecular Biology (Clifton, N.J.). 396: 135-52. PMID 18025691 DOI: 10.1007/978-1-59745-515-2_10 |
0.743 |
|
| 2006 |
Mau B, Glasner JD, Darling AE, Perna NT. Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biology. 7: R44. PMID 16737554 DOI: 10.1186/Gb-2006-7-5-R44 |
0.763 |
|
| 2006 |
Glasner JD, Rusch M, Liss P, Plunkett G, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gilson MC, Perna NT. ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Research. 34: D41-5. PMID 16381899 DOI: 10.1093/Nar/Gkj164 |
0.765 |
|
| 2004 |
Darling AE, Mau B, Blattner FR, Perna NT. GRIL: genome rearrangement and inversion locator. Bioinformatics (Oxford, England). 20: 122-4. PMID 14693819 DOI: 10.1093/Bioinformatics/Btg378 |
0.736 |
|
| 2003 |
Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infection and Immunity. 71: 2775-86. PMID 12704152 DOI: 10.1128/Iai.71.5.2775-2786.2003 |
0.764 |
|
| 2003 |
Glasner JD, Liss P, Plunkett G, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Research. 31: 147-51. PMID 12519969 DOI: 10.1093/Nar/Gkg125 |
0.769 |
|
| 2003 |
Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, et al. Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T Infection and Immunity. 71: 4223-4223. DOI: 10.1128/Iai.71.7.4223.2003 |
0.749 |
|
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