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Number Cited by Other Article(s)
401
Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies. G3 (BETHESDA, MD.) 2016;6:3655-3662. [PMID: 27638685 PMCID: PMC5100864 DOI: 10.1534/g3.116.034249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/08/2016] [Indexed: 11/18/2022]
402
Strassert JFH, Tikhonenkov DV, Pombert JF, Kolisko M, Tai V, Mylnikov AP, Keeling PJ. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome. Open Biol 2016;6:150239. [PMID: 26887409 PMCID: PMC4772810 DOI: 10.1098/rsob.150239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
403
Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden. GENOME ANNOUNCEMENTS 2016;4:4/5/e01196-16. [PMID: 27789643 PMCID: PMC5084867 DOI: 10.1128/genomea.01196-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
404
Draft Genome Sequence of Yarrowia lipolytica Strain A-101 Isolated from Polluted Soil in Poland. GENOME ANNOUNCEMENTS 2016;4:4/5/e01094-16. [PMID: 27795258 PMCID: PMC5054328 DOI: 10.1128/genomea.01094-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
405
Strepis N, Sánchez-Andrea I, van Gelder AH, van Kruistum H, Shapiro N, Kyrpides N, Göker M, Klenk HP, Schaap P, Stams AJM, Sousa DZ. Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. Int J Syst Evol Microbiol 2016;66:3957-3963. [DOI: 10.1099/ijsem.0.001294] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
406
Rare Spontaneous Loss of Multiresistance Gene Carrying IncI/ST12 Plasmid in Escherichia coli in Pig Microbiota. Antimicrob Agents Chemother 2016;60:6046-9. [PMID: 27480865 DOI: 10.1128/aac.00864-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022]  Open
407
Therkildsen NO, Palumbi SR. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Mol Ecol Resour 2016;17:194-208. [DOI: 10.1111/1755-0998.12593] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/27/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023]
408
Draft Genome Sequence of Endophytic Bacterium Enterobacter asburiae PDA134, Isolated from Date Palm (Phoenix dactylifera L.) Roots. GENOME ANNOUNCEMENTS 2016;4:4/4/e00848-16. [PMID: 27540071 PMCID: PMC4991716 DOI: 10.1128/genomea.00848-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
409
van der Weide RH, Simonis M, Hermsen R, Toonen P, Cuppen E, de Ligt J. The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats. PLoS One 2016;11:e0160036. [PMID: 27501045 PMCID: PMC4976967 DOI: 10.1371/journal.pone.0160036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 01/17/2023]  Open
410
Torre S, Tattini M, Brunetti C, Guidi L, Gori A, Marzano C, Landi M, Sebastiani F. De Novo Assembly and Comparative Transcriptome Analyses of Red and Green Morphs of Sweet Basil Grown in Full Sunlight. PLoS One 2016;11:e0160370. [PMID: 27483170 PMCID: PMC4970699 DOI: 10.1371/journal.pone.0160370] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022]  Open
411
Draft Genome Sequence of Ustilago trichophora RK089, a Promising Malic Acid Producer. GENOME ANNOUNCEMENTS 2016;4:4/4/e00749-16. [PMID: 27469969 PMCID: PMC4966473 DOI: 10.1128/genomea.00749-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
412
Akogwu I, Wang N, Zhang C, Gong P. A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis. Hum Genomics 2016;10 Suppl 2:20. [PMID: 27461106 PMCID: PMC4965716 DOI: 10.1186/s40246-016-0068-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
413
El-Metwally S, Zakaria M, Hamza T. LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads. Bioinformatics 2016;32:3215-3223. [PMID: 27412092 DOI: 10.1093/bioinformatics/btw470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022]  Open
414
Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat. G3-GENES GENOMES GENETICS 2016;6:1969-77. [PMID: 27172215 PMCID: PMC4938650 DOI: 10.1534/g3.116.029504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
415
Régnier M, Chassignet P. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes. Front Bioeng Biotechnol 2016;4:35. [PMID: 27376057 PMCID: PMC4896921 DOI: 10.3389/fbioe.2016.00035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/08/2016] [Indexed: 11/15/2022]  Open
416
Izuno A, Hatakeyama M, Nishiyama T, Tamaki I, Shimizu-Inatsugi R, Sasaki R, Shimizu KK, Isagi Y. Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. JOURNAL OF PLANT RESEARCH 2016;129:727-736. [PMID: 27052216 DOI: 10.1007/s10265-016-0822-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
417
Spence RJ, Noune C, Hauxwell C. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus. GENOME ANNOUNCEMENTS 2016;4:e00633-16. [PMID: 27365355 PMCID: PMC4929518 DOI: 10.1128/genomea.00633-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 11/23/2022]
418
Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria. GENOME ANNOUNCEMENTS 2016;4:4/3/e00550-16. [PMID: 27284158 PMCID: PMC4901242 DOI: 10.1128/genomea.00550-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
419
Wingfield BD, Ambler JM, Coetzee MP, de Beer ZW, Duong TA, Joubert F, Hammerbacher A, McTaggart AR, Naidoo K, Nguyen HD, Ponomareva E, Santana QS, Seifert KA, Steenkamp ET, Trollip C, van der Nest MA, Visagie CM, Wilken PM, Wingfield MJ, Yilmaz N. IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723. IMA Fungus 2016;7:217-27. [PMID: 27433447 PMCID: PMC4941685 DOI: 10.5598/imafungus.2016.07.01.11] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 10/25/2022]  Open
420
Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, Cavener DR. Giraffe genome sequence reveals clues to its unique morphology and physiology. Nat Commun 2016;7:11519. [PMID: 27187213 PMCID: PMC4873664 DOI: 10.1038/ncomms11519] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/01/2016] [Indexed: 11/12/2022]  Open
421
Schilthuizen M, Santos Pimenta LP, Lammers Y, Steenbergen PJ, Flohil M, Beveridge NGP, van Duijn PT, Meulblok MM, Sosef N, van de Ven R, Werring R, Beentjes KK, Meijer K, Vos RA, Vrieling K, Gravendeel B, Choi Y, Verpoorte R, Smit C, Beukeboom LW. Incorporation of an invasive plant into a native insect herbivore food web. PeerJ 2016;4:e1954. [PMID: 27190702 PMCID: PMC4867706 DOI: 10.7717/peerj.1954] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/30/2016] [Indexed: 11/23/2022]  Open
422
Zhong Z, Norvienyeku J, Chen M, Bao J, Lin L, Chen L, Lin Y, Wu X, Cai Z, Zhang Q, Lin X, Hong Y, Huang J, Xu L, Zhang H, Chen L, Tang W, Zheng H, Chen X, Wang Y, Lian B, Zhang L, Tang H, Lu G, Ebbole DJ, Wang B, Wang Z. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species. Sci Rep 2016;6:25591. [PMID: 27151494 PMCID: PMC4858695 DOI: 10.1038/srep25591] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/20/2016] [Indexed: 02/07/2023]  Open
423
Complete Genome Sequences of Seven Helicoverpa armigera SNPV-AC53-Derived Strains. GENOME ANNOUNCEMENTS 2016;4:4/3/e00260-16. [PMID: 27151787 PMCID: PMC4859169 DOI: 10.1128/genomea.00260-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
424
Lopes MR, Morais CG, Kominek J, Cadete RM, Soares MA, Uetanabaro APT, Fonseca C, Lachance MA, Hittinger CT, Rosa CA. Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov. FEMS Yeast Res 2016;16:fow044. [PMID: 27188884 DOI: 10.1093/femsyr/fow044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 02/03/2023]  Open
425
Durai DA, Schulz MH. Informed kmer selection for de novo transcriptome assembly. Bioinformatics 2016;32:1670-7. [PMID: 27153653 PMCID: PMC4892416 DOI: 10.1093/bioinformatics/btw217] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/17/2016] [Indexed: 11/23/2022]  Open
426
Draft Genome Sequence of Biocontrol Agent Pythium oligandrum Strain Po37, an Oomycota. GENOME ANNOUNCEMENTS 2016;4:4/2/e00215-16. [PMID: 27081125 PMCID: PMC4832153 DOI: 10.1128/genomea.00215-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
427
Holley G, Wittler R, Stoye J. Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms Mol Biol 2016;11:3. [PMID: 27087830 PMCID: PMC4832552 DOI: 10.1186/s13015-016-0066-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/31/2016] [Indexed: 12/21/2022]  Open
428
Nguyen HDT, McMullin DR, Ponomareva E, Riley R, Pomraning KR, Baker SE, Seifert KA. Ochratoxin A production by Penicillium thymicola. Fungal Biol 2016;120:1041-1049. [PMID: 27521635 DOI: 10.1016/j.funbio.2016.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 10/21/2022]
429
Cha S, Bird DM. Optimizing k-mer size using a variant grid search to enhance de novo genome assembly. Bioinformation 2016;12:36-40. [PMID: 28104957 PMCID: PMC5237644 DOI: 10.6026/97320630012036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 11/23/2022]  Open
430
Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016;1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
431
Abu Bakar S, Sampathrajan S, Loke KK, Goh HH, Mohd Noor N. DNA-seq analysis of Garcinia mangostana. GENOMICS DATA 2016;7:62-3. [PMID: 26981362 PMCID: PMC4778587 DOI: 10.1016/j.gdata.2015.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/22/2015] [Indexed: 11/05/2022]
432
Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money. J Microbiol Methods 2016;138:60-71. [PMID: 26995332 DOI: 10.1016/j.mimet.2016.02.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/26/2016] [Accepted: 02/24/2016] [Indexed: 12/16/2022]
433
Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R. LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. J Comput Biol 2016;23:137-49. [PMID: 26953874 DOI: 10.1089/cmb.2015.0172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
434
Fagerlund A, Langsrud S, Schirmer BCT, Møretrø T, Heir E. Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains. PLoS One 2016;11:e0151117. [PMID: 26953695 PMCID: PMC4783014 DOI: 10.1371/journal.pone.0151117] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/22/2016] [Indexed: 12/19/2022]  Open
435
Al-Okaily AA. HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads. BMC Genomics 2016;17:193. [PMID: 26945881 PMCID: PMC4779561 DOI: 10.1186/s12864-016-2515-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/23/2016] [Indexed: 11/15/2022]  Open
436
Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. BMC Bioinformatics 2016;17:115. [PMID: 26936254 PMCID: PMC4776351 DOI: 10.1186/s12859-016-0969-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022]  Open
437
Draft Genome Sequence of a Salmonella enterica subsp. enterica Serovar Gallinarum bv. Gallinarum Isolate Associated with Fowl Typhoid Outbreaks in Brazil. GENOME ANNOUNCEMENTS 2016;4:4/1/e00019-16. [PMID: 26950322 PMCID: PMC4767912 DOI: 10.1128/genomea.00019-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
438
Liu MS, Kuo TCY, Ko CY, Wu DC, Li KY, Lin WJ, Lin CP, Wang YW, Schafleitner R, Lo HF, Chen CY, Chen LFO. Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek). BMC PLANT BIOLOGY 2016;16:46. [PMID: 26887961 PMCID: PMC4756517 DOI: 10.1186/s12870-016-0736-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
439
Aluome C, Aubert G, Alves Carvalho S, Le Paslier MC, Burstin J, Brunel D. De novo construction of a "Gene-space" for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources. BMC Res Notes 2016;9:81. [PMID: 26864345 PMCID: PMC4750290 DOI: 10.1186/s13104-016-1903-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/02/2016] [Indexed: 11/29/2022]  Open
440
Tian RM, Sun J, Cai L, Zhang WP, Zhou GW, Qiu JW, Qian PY. The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur. Environ Microbiol 2016;18:2481-94. [PMID: 26637128 DOI: 10.1111/1462-2920.13161] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/27/2015] [Indexed: 11/30/2022]
441
Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform 2016;17:154-79. [PMID: 26026159 PMCID: PMC4719071 DOI: 10.1093/bib/bbv029] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Indexed: 12/23/2022]  Open
442
Schill KM, Wang Y, Butler RR, Pombert JF, Reddy NR, Skinner GE, Larkin JW. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing. Appl Environ Microbiol 2016;82:384-93. [PMID: 26519392 PMCID: PMC4702626 DOI: 10.1128/aem.02616-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/21/2015] [Indexed: 12/27/2022]  Open
443
Dos Santos RAC, Berretta AA, Barud HDS, Ribeiro SJL, González-García LN, Zucchi TD, Goldman GH, Riaño-Pachón DM. Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea. GENOME ANNOUNCEMENTS 2015;3:e01404-15. [PMID: 26634755 PMCID: PMC4669396 DOI: 10.1128/genomea.01404-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
444
Wingfield BD, Barnes I, Wilhelm de Beer Z, De Vos L, Duong TA, Kanzi AM, Naidoo K, Nguyen HD, Santana QC, Sayari M, Seifert KA, Steenkamp ET, Trollip C, van der Merwe NA, van der Nest MA, Markus Wilken P, Wingfield MJ. IMA Genome-F 5: Draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C. deuterocubensis, Davidsoniella virescens, Fusarium temperatum,Graphilbum fragrans, Penicillium nordicum, and Thielaviopsis musarum. IMA Fungus 2015;6:493-506. [PMID: 26734552 PMCID: PMC4681265 DOI: 10.5598/imafungus.2015.06.02.13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/23/2015] [Indexed: 12/05/2022]  Open
445
Van Hoeck A, Horemans N, Monsieurs P, Cao HX, Vandenhove H, Blust R. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. BIOTECHNOLOGY FOR BIOFUELS 2015;8:188. [PMID: 26609323 PMCID: PMC4659200 DOI: 10.1186/s13068-015-0381-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/10/2015] [Indexed: 05/21/2023]
446
Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J Clin Microbiol 2015;54:333-42. [PMID: 26607978 PMCID: PMC4733179 DOI: 10.1128/jcm.02344-15] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022]  Open
447
Prasad P, Varshney D, Adholeya A. Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum. BMC Genomics 2015;16:1004. [PMID: 26607873 PMCID: PMC4658809 DOI: 10.1186/s12864-015-2229-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023]  Open
448
Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K. Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica. PLoS One 2015;10:e0143525. [PMID: 26588467 PMCID: PMC4654569 DOI: 10.1371/journal.pone.0143525] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022]  Open
449
A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 2015;48:79-83. [PMID: 26569125 PMCID: PMC5218575 DOI: 10.1038/ng.3443] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
450
Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe. BMC Evol Biol 2015;15:246. [PMID: 26555390 PMCID: PMC4641410 DOI: 10.1186/s12862-015-0529-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/30/2015] [Indexed: 11/10/2022]  Open
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