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For: Li H. BFC: correcting Illumina sequencing errors. Bioinformatics 2015;31:2885-7. [PMID: 25953801 DOI: 10.1093/bioinformatics/btv290] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/02/2015] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
51
Outhred AC, Gurjav U, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages. Front Public Health 2020;8:455. [PMID: 32974265 PMCID: PMC7481465 DOI: 10.3389/fpubh.2020.00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/22/2020] [Indexed: 11/13/2022]  Open
52
Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem. mSystems 2020;5:5/4/e00504-20. [PMID: 32753510 PMCID: PMC7406229 DOI: 10.1128/msystems.00504-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
53
Jarett JK, Džunková M, Schulz F, Roux S, Paez-Espino D, Eloe-Fadrosh E, Jungbluth SP, Ivanova N, Spear JR, Carr SA, Trivedi CB, Corsetti FA, Johnson HA, Becraft E, Kyrpides N, Stepanauskas R, Woyke T. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME JOURNAL 2020;14:2527-2541. [PMID: 32661357 PMCID: PMC7490370 DOI: 10.1038/s41396-020-0705-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
54
Yan J, Li J, Bai W, Yu L, Nie D, Xiang Z, Wu S. The complete chloroplast genome of Prunus conradinae (Rosaceae), a wild flowering cherry from China. Mitochondrial DNA B Resour 2020;5:2153-2154. [PMID: 33457763 PMCID: PMC7782140 DOI: 10.1080/23802359.2020.1768934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]  Open
55
Mason AS, Lund AR, Hocking PM, Fulton JE, Burt DW. Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data. Mob DNA 2020;11:22. [PMID: 32617122 PMCID: PMC7325683 DOI: 10.1186/s13100-020-00216-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]  Open
56
Reji L, Francis CA. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME JOURNAL 2020;14:2105-2115. [PMID: 32405026 DOI: 10.1038/s41396-020-0675-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022]
57
Hurley D, Hoffmann M, Muruvanda T, Allard MW, Brown EW, Martins M, Fanning S. Atypical Salmonella enterica Serovars in Murine and Human Macrophage Infection Models. Infect Immun 2020;88:e00353-19. [PMID: 32014897 PMCID: PMC7093118 DOI: 10.1128/iai.00353-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 01/28/2020] [Indexed: 11/20/2022]  Open
58
Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. Benchmarking of computational error-correction methods for next-generation sequencing data. Genome Biol 2020;21:71. [PMID: 32183840 PMCID: PMC7079412 DOI: 10.1186/s13059-020-01988-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 03/06/2020] [Indexed: 12/16/2022]  Open
59
Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities. Microbiol Resour Announc 2020;9:9/10/e01599-19. [PMID: 32139564 PMCID: PMC7171226 DOI: 10.1128/mra.01599-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
60
Skarzyńska A, Pawełkowicz M, Pląder W. Genome-wide discovery of DNA variants in cucumber somaclonal lines. Gene 2020;736:144412. [PMID: 32007586 DOI: 10.1016/j.gene.2020.144412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/30/2023]
61
Lubośny M, Śmietanka B, Przyłucka A, Burzyński A. Highly divergent mitogenomes ofGeukensia demissa(Bivalvia, Mytilidae) with extreme AT content. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
62
Liao X, Li M, Luo J, Zou Y, Wu FX, Pan Y, Luo F, Wang J. Improving de novo Assembly Based on Read Classification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:177-188. [PMID: 30059317 DOI: 10.1109/tcbb.2018.2861380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
63
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019;20:284. [PMID: 31849336 DOI: 10.1101/631648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 05/29/2023]  Open
64
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019;20:284. [PMID: 31849336 PMCID: PMC6918601 DOI: 10.1186/s13059-019-1899-5] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022]  Open
65
Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nat Microbiol 2019;5:265-271. [PMID: 31819214 DOI: 10.1038/s41564-019-0628-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
66
Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 2019;6:285. [PMID: 31772173 PMCID: PMC6879543 DOI: 10.1038/s41597-019-0287-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/31/2019] [Indexed: 11/17/2022]  Open
67
A high-quality cucumber genome assembly enhances computational comparative genomics. Mol Genet Genomics 2019;295:177-193. [PMID: 31620884 DOI: 10.1007/s00438-019-01614-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023]
68
The Parauncinula polyspora Draft Genome Provides Insights into Patterns of Gene Erosion and Genome Expansion in Powdery Mildew Fungi. mBio 2019;10:mBio.01692-19. [PMID: 31551331 PMCID: PMC6759760 DOI: 10.1128/mbio.01692-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
69
Meccariello A, Salvemini M, Primo P, Hall B, Koskinioti P, Dalíková M, Gravina A, Gucciardino MA, Forlenza F, Gregoriou ME, Ippolito D, Monti SM, Petrella V, Perrotta MM, Schmeing S, Ruggiero A, Scolari F, Giordano E, Tsoumani KT, Marec F, Windbichler N, Arunkumar KP, Bourtzis K, Mathiopoulos KD, Ragoussis J, Vitagliano L, Tu Z, Papathanos PA, Robinson MD, Saccone G. Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. Science 2019;365:1457-1460. [PMID: 31467189 DOI: 10.1126/science.aax1318] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
70
Chen X, Dong Z, Liu G, He J, Zhao R, Wang W, Peng Y, Li X. Phylogenetic analysis provides insights into the evolution of Asian fireflies and adult bioluminescence. Mol Phylogenet Evol 2019;140:106600. [PMID: 31445200 DOI: 10.1016/j.ympev.2019.106600] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/09/2019] [Accepted: 08/20/2019] [Indexed: 02/04/2023]
71
Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019;21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
72
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Sci Data 2019;6:129. [PMID: 31332186 PMCID: PMC6646334 DOI: 10.1038/s41597-019-0132-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/19/2019] [Indexed: 11/09/2022]  Open
73
Bartaula R, Melo ATO, Kingan S, Jin Y, Hale I. Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid. BMC PLANT BIOLOGY 2019;19:319. [PMID: 31311507 PMCID: PMC6636152 DOI: 10.1186/s12870-019-1893-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/19/2019] [Indexed: 05/17/2023]
74
Ellison C, Bachtrog D. Recurrent gene co-amplification on Drosophila X and Y chromosomes. PLoS Genet 2019;15:e1008251. [PMID: 31329593 PMCID: PMC6690552 DOI: 10.1371/journal.pgen.1008251] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 08/12/2019] [Accepted: 06/18/2019] [Indexed: 12/19/2022]  Open
75
Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019;94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022]  Open
76
Heydari M, Miclotte G, Van de Peer Y, Fostier J. Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinformatics 2019;20:298. [PMID: 31159722 PMCID: PMC6545690 DOI: 10.1186/s12859-019-2906-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022]  Open
77
Casey JM, Meyer CP, Morat F, Brandl SJ, Planes S, Parravicini V. Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13206] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
78
Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ 2019;7:e6902. [PMID: 31119088 PMCID: PMC6511391 DOI: 10.7717/peerj.6902] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/03/2019] [Indexed: 12/13/2022]  Open
79
Liu Y, Zhang LY, Li J. Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers. Bioinformatics 2019;35:4560-4567. [DOI: 10.1093/bioinformatics/btz273] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/31/2019] [Accepted: 04/11/2019] [Indexed: 11/13/2022]  Open
80
Tian S, Yan H, Klee EW, Kalmbach M, Slager SL. Comparative analysis of de novo assemblers for variation discovery in personal genomes. Brief Bioinform 2019;19:893-904. [PMID: 28407084 PMCID: PMC6169673 DOI: 10.1093/bib/bbx037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/08/2017] [Indexed: 12/30/2022]  Open
81
Limasset A, Flot JF, Peterlongo P. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 2019;36:1374-1381. [DOI: 10.1093/bioinformatics/btz102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/07/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022]  Open
82
Ellison C, Bachtrog D. Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila. PLoS Biol 2019;17:e3000094. [PMID: 30742611 PMCID: PMC6417741 DOI: 10.1371/journal.pbio.3000094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 01/18/2019] [Indexed: 11/18/2022]  Open
83
Tambe A, Pachter L. Barcode identification for single cell genomics. BMC Bioinformatics 2019;20:32. [PMID: 30654736 PMCID: PMC6337828 DOI: 10.1186/s12859-019-2612-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/07/2019] [Indexed: 02/07/2023]  Open
84
Rane RV, Pearce SL, Li F, Coppin C, Schiffer M, Shirriffs J, Sgrò CM, Griffin PC, Zhang G, Lee SF, Hoffmann AA, Oakeshott JG. Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species. BMC Genomics 2019;20:52. [PMID: 30651071 PMCID: PMC6335815 DOI: 10.1186/s12864-018-5413-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/26/2018] [Indexed: 12/14/2022]  Open
85
Zhao L, Xie J, Bai L, Chen W, Wang M, Zhang Z, Wang Y, Zhao Z, Li J. Mining statistically-solid k-mers for accurate NGS error correction. BMC Genomics 2018;19:912. [PMID: 30598110 PMCID: PMC6311904 DOI: 10.1186/s12864-018-5272-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
86
Bernards MA, Schorno S, McKenzie E, Winegard TM, Oke I, Plachetzki D, Fudge DS. Unraveling inter-species differences in hagfish slime skein deployment. J Exp Biol 2018;221:221/24/jeb176925. [DOI: 10.1242/jeb.176925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/08/2018] [Indexed: 01/11/2023]
87
Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T. Hidden diversity of soil giant viruses. Nat Commun 2018;9:4881. [PMID: 30451857 PMCID: PMC6243002 DOI: 10.1038/s41467-018-07335-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/30/2018] [Indexed: 01/23/2023]  Open
88
Mukherjee K, Washimkar D, Muggli MD, Salmela L, Boucher C. Error correcting optical mapping data. Gigascience 2018;7:5005021. [PMID: 29846578 PMCID: PMC6007263 DOI: 10.1093/gigascience/giy061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/16/2018] [Indexed: 12/31/2022]  Open
89
Grau JH, Hackl T, Koepfli KP, Hofreiter M. Improving draft genome contiguity with reference-derived in silico mate-pair libraries. Gigascience 2018;7:4980916. [PMID: 29688527 PMCID: PMC5967465 DOI: 10.1093/gigascience/giy029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 03/20/2018] [Indexed: 11/29/2022]  Open
90
Yeo S, Coombe L, Warren RL, Chu J, Birol I. ARCS: scaffolding genome drafts with linked reads. Bioinformatics 2018;34:725-731. [PMID: 29069293 PMCID: PMC6030987 DOI: 10.1093/bioinformatics/btx675] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]  Open
91
Turner I, Garimella KV, Iqbal Z, McVean G. Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 2018;34:2556-2565. [PMID: 29554215 PMCID: PMC6061703 DOI: 10.1093/bioinformatics/bty157] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/25/2017] [Accepted: 03/14/2018] [Indexed: 12/27/2022]  Open
92
Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. A graph-based approach to diploid genome assembly. Bioinformatics 2018;34:i105-i114. [PMID: 29949989 PMCID: PMC6022571 DOI: 10.1093/bioinformatics/bty279] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
93
Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority. Sci Rep 2018;8:8090. [PMID: 29795402 PMCID: PMC5967342 DOI: 10.1038/s41598-018-26332-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/09/2018] [Indexed: 11/08/2022]  Open
94
Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res 2018. [PMID: 29535149 PMCID: PMC5880247 DOI: 10.1101/gr.221028.117] [Citation(s) in RCA: 274] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
95
Guo X, Hu Q, Hao G, Wang X, Zhang D, Ma T, Liu J. The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. DNA Res 2018;25:4831046. [PMID: 29394339 PMCID: PMC6014361 DOI: 10.1093/dnares/dsy003] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/24/2018] [Indexed: 11/12/2022]  Open
96
Andújar C, Arribas P, Gray C, Bruce C, Woodward G, Yu DW, Vogler AP. Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill. Mol Ecol 2017;27:146-166. [DOI: 10.1111/mec.14410] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022]
97
Wala J, Beroukhim R. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics 2017;33:751-753. [PMID: 28011768 DOI: 10.1093/bioinformatics/btw741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 11/14/2022]  Open
98
Schuelke TA, Wu G, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes MD. Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia. Genome Biol Evol 2017;9:3312-3327. [PMID: 29186370 PMCID: PMC5737690 DOI: 10.1093/gbe/evx242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2017] [Indexed: 12/29/2022]  Open
99
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 2017;8:2264. [PMID: 29234309 PMCID: PMC5712423 DOI: 10.3389/fmicb.2017.02264] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023]  Open
100
Anes J, Hurley D, Martins M, Fanning S. Exploring the Genome and Phenotype of Multi-Drug Resistant Klebsiella pneumoniae of Clinical Origin. Front Microbiol 2017;8:1913. [PMID: 29109700 PMCID: PMC5660112 DOI: 10.3389/fmicb.2017.01913] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022]  Open
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