Aaron E. Darling - Publications

Affiliations: 
University of California, Davis, Davis, CA 

53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.92
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  0.92
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  0.8
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  0.8
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  0.8
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  0.8
2015 Wyrsch E, Roy Chowdhury P, Abraham S, Santos J, Darling AE, Charles IG, Chapman TA, Djordjevic SP. Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs. Bmc Genomics. 16: 165. PMID 25888127 DOI: 10.1186/s12864-015-1382-y  0.8
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  0.92
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
2014 Pineda SS, Sollod BL, Wilson D, Darling A, Sunagar K, Undheim EA, Kely L, Antunes A, Fry BG, King GF. Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders. Bmc Genomics. 15: 177. PMID 24593665 DOI: 10.1186/1471-2164-15-177  0.8
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  0.8
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  0.8
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  0.8
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  0.92
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  0.92
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  0.92
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  0.92
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  0.8
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  0.92
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  0.92
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
2012 Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology. 61: 539-42. PMID 22357727 DOI: 10.1093/sysbio/sys029  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.52
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  0.8
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  0.52
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.52
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  0.52
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  0.8
2004 Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: Multiple alignment of conserved genomic sequence with rearrangements Genome Research. 14: 1394-1403. PMID 15231754 DOI: 10.1101/gr.2289704  0.8
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  0.8
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  0.8
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