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Number Cited by Other Article(s)
451
Rider SD, Morgan MS, Arlian LG. Draft genome of the scabies mite. Parasit Vectors 2015;8:585. [PMID: 26555130 PMCID: PMC4641413 DOI: 10.1186/s13071-015-1198-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/05/2015] [Indexed: 12/11/2022]  Open
452
Henson MW, Santo Domingo JW, Kourtev PS, Jensen RV, Dunn JA, Learman DR. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PeerJ 2015;3:e1395. [PMID: 26587353 PMCID: PMC4647564 DOI: 10.7717/peerj.1395] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/19/2015] [Indexed: 01/04/2023]  Open
453
Greshake B, Zehr S, Dal Grande F, Meiser A, Schmitt I, Ebersberger I. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol Ecol Resour 2015;16:511-23. [PMID: 26345272 DOI: 10.1111/1755-0998.12463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/28/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
454
Wang D, Xu J, Yu J. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation. Biol Direct 2015;10:53. [PMID: 26376976 PMCID: PMC4573299 DOI: 10.1186/s13062-015-0083-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/11/2015] [Indexed: 11/28/2022]  Open
455
Benoit G, Lemaitre C, Lavenier D, Drezen E, Dayris T, Uricaru R, Rizk G. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics 2015;16:288. [PMID: 26370285 PMCID: PMC4570262 DOI: 10.1186/s12859-015-0709-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/17/2015] [Indexed: 01/09/2023]  Open
456
Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol 2015;15:509. [PMID: 25398208 PMCID: PMC4248469 DOI: 10.1186/s13059-014-0509-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/02/2023]  Open
457
Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, Schupp JM, Keim P, Morrow JB, Salit ML, Zook JM. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Front Genet 2015. [PMID: 26217378 PMCID: PMC4493402 DOI: 10.3389/fgene.2015.00235] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
458
Pelin A, Selman M, Aris-Brosou S, Farinelli L, Corradi N. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environ Microbiol 2015;17:4443-58. [PMID: 25914091 DOI: 10.1111/1462-2920.12883] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 12/23/2022]
459
De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PLoS One 2015;10:e0128331. [PMID: 26047102 PMCID: PMC4457790 DOI: 10.1371/journal.pone.0128331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/26/2015] [Indexed: 11/19/2022]  Open
460
Mans BJ, de Klerk D, Pienaar R, de Castro MH, Latif AA. Next-generation sequencing as means to retrieve tick systematic markers, with the focus on Nuttalliella namaqua (Ixodoidea: Nuttalliellidae). Ticks Tick Borne Dis 2015;6:450-62. [DOI: 10.1016/j.ttbdis.2015.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
461
Draft Genome Sequence of Lachancea lanzarotensis CBS 12615T, an Ascomycetous Yeast Isolated from Grapes. GENOME ANNOUNCEMENTS 2015;3:3/2/e00292-15. [PMID: 25883293 PMCID: PMC4400436 DOI: 10.1128/genomea.00292-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
462
Szövényi P, Frangedakis E, Ricca M, Quandt D, Wicke S, Langdale JA. Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts. BMC PLANT BIOLOGY 2015;15:98. [PMID: 25886741 PMCID: PMC4393856 DOI: 10.1186/s12870-015-0481-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/24/2015] [Indexed: 05/18/2023]
463
Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res 2015;43:e46. [PMID: 25586223 PMCID: PMC4402509 DOI: 10.1093/nar/gkv002] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/04/2015] [Indexed: 11/12/2022]  Open
464
Campana MG, Robles García NM, Tuross N. America's red gold: multiple lineages of cultivated cochineal in Mexico. Ecol Evol 2015;5:607-17. [PMID: 25691985 PMCID: PMC4328766 DOI: 10.1002/ece3.1398] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 12/15/2014] [Accepted: 12/18/2014] [Indexed: 01/31/2023]  Open
465
Bloom Filter Trie – A Data Structure for Pan-Genome Storage. LECTURE NOTES IN COMPUTER SCIENCE 2015. [DOI: 10.1007/978-3-662-48221-6_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
466
Shariat B, Movahedi NS, Chitsaz H, Boucher C. HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly. BMC Genomics 2014;15 Suppl 10:S9. [PMID: 25558875 PMCID: PMC4304221 DOI: 10.1186/1471-2164-15-s10-s9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
467
The complex task of choosing a de novo assembly: Lessons from fungal genomes. Comput Biol Chem 2014;53 Pt A:97-107. [DOI: 10.1016/j.compbiolchem.2014.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 12/21/2022]
468
Draft Genome Sequence of Taylorella equigenitalis Strain MCE529, Isolated from a Belgian Warmblood Horse. GENOME ANNOUNCEMENTS 2014;2:2/6/e01214-14. [PMID: 25428969 PMCID: PMC4246161 DOI: 10.1128/genomea.01214-14] [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]
469
Melsted P, Halldórsson BV. KmerStream: streaming algorithms for k-mer abundance estimation. ACTA ACUST UNITED AC 2014;30:3541-7. [PMID: 25355787 DOI: 10.1093/bioinformatics/btu713] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
470
Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One 2014;9:e107014. [PMID: 25198770 PMCID: PMC4157817 DOI: 10.1371/journal.pone.0107014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/07/2014] [Indexed: 12/28/2022]  Open
471
Zhang Q, Pell J, Canino-Koning R, Howe AC, Brown CT. These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure. PLoS One 2014;9:e101271. [PMID: 25062443 PMCID: PMC4111482 DOI: 10.1371/journal.pone.0101271] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 06/04/2014] [Indexed: 11/19/2022]  Open
472
Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD. Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. ACTA ACUST UNITED AC 2014;30:2709-16. [PMID: 24930142 PMCID: PMC4173024 DOI: 10.1093/bioinformatics/btu391] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
473
Garmendia J, Viadas C, Calatayud L, Mell JC, Martí-Lliteras P, Euba B, Llobet E, Gil C, Bengoechea JA, Redfield RJ, Liñares J. Characterization of nontypable Haemophilus influenzae isolates recovered from adult patients with underlying chronic lung disease reveals genotypic and phenotypic traits associated with persistent infection. PLoS One 2014;9:e97020. [PMID: 24824990 PMCID: PMC4019658 DOI: 10.1371/journal.pone.0097020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/14/2014] [Indexed: 01/09/2023]  Open
474
Trivedi UH, Cézard T, Bridgett S, Montazam A, Nichols J, Blaxter M, Gharbi K. Quality control of next-generation sequencing data without a reference. Front Genet 2014;5:111. [PMID: 24834071 PMCID: PMC4018527 DOI: 10.3389/fgene.2014.00111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/14/2014] [Indexed: 01/07/2023]  Open
475
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 2014;15:126. [PMID: 24884846 PMCID: PMC4030574 DOI: 10.1186/1471-2105-15-126] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/24/2014] [Indexed: 11/12/2022]  Open
476
Heo Y, Wu XL, Chen D, Ma J, Hwu WM. BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. ACTA ACUST UNITED AC 2014;30:1354-62. [PMID: 24451628 DOI: 10.1093/bioinformatics/btu030] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
477
Simpson JT. Exploring genome characteristics and sequence quality without a reference. ACTA ACUST UNITED AC 2014;30:1228-35. [PMID: 24443382 PMCID: PMC3998141 DOI: 10.1093/bioinformatics/btu023] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
478
MOLECULAR MECHANISM OF THE CAROTENOID BIOSYNTHESIS ACTIVATION IN THE PRODUCER Streptomyces globisporus 1912. BIOTECHNOLOGIA ACTA 2014. [DOI: 10.15407/biotech7.06.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
479
Anvar SY, Khachatryan L, Vermaat M, van Galen M, Pulyakhina I, Ariyurek Y, Kraaijeveld K, den Dunnen JT, de Knijff P, ’t Hoen PAC, Laros JFJ. Determining the quality and complexity of next-generation sequencing data without a reference genome. Genome Biol 2014;15:555. [PMID: 25514851 PMCID: PMC4298064 DOI: 10.1186/s13059-014-0555-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/27/2014] [Indexed: 01/22/2023]  Open
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