• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5081207)   Today's Articles (1159)
For: Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. ACTA ACUST UNITED AC 2014;30:3506-14. [PMID: 25165095 PMCID: PMC4253826 DOI: 10.1093/bioinformatics/btu538] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
401
Ma JE, Jiang HY, Li LM, Zhang XJ, Li HM, Li GY, Mo DY, Chen JP. SMRT sequencing of the full-length transcriptome of the Sunda pangolin (Manis javanica). Gene 2019;692:208-216. [PMID: 30664913 DOI: 10.1016/j.gene.2019.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/26/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
402
A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads. Genes (Basel) 2019;10:genes10010044. [PMID: 30646604 PMCID: PMC6356754 DOI: 10.3390/genes10010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/19/2022]  Open
403
Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Computational aspects underlying genome to phenome analysis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019;97:182-198. [PMID: 30500991 PMCID: PMC6849790 DOI: 10.1111/tpj.14179] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
404
Cheng YW, Chen YM, Zhao QQ, Zhao X, Wu YR, Chen DZ, Liao LD, Chen Y, Yang Q, Xu LY, Li EM, Xu JZ. Long Read Single-Molecule Real-Time Sequencing Elucidates Transcriptome-Wide Heterogeneity and Complexity in Esophageal Squamous Cells. Front Genet 2019;10:915. [PMID: 31636653 PMCID: PMC6787290 DOI: 10.3389/fgene.2019.00915] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/29/2019] [Indexed: 02/05/2023]  Open
405
Efficiency of PacBio long read correction by 2nd generation Illumina sequencing. Genomics 2019;111:43-49. [DOI: 10.1016/j.ygeno.2017.12.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/11/2017] [Accepted: 12/17/2017] [Indexed: 12/17/2022]
406
Luo S, Tang M, Frandsen PB, Stewart RJ, Zhou X. The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). Gigascience 2018;7:5202446. [PMID: 30476205 PMCID: PMC6302954 DOI: 10.1093/gigascience/giy143] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/15/2018] [Indexed: 12/18/2022]  Open
407
Wee Y, Bhyan SB, Liu Y, Lu J, Li X, Zhao M. The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing. Brief Funct Genomics 2018;18:1-12. [DOI: 10.1093/bfgp/ely037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/03/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023]  Open
408
Zeng D, Chen X, Peng J, Yang C, Peng M, Zhu W, Xie D, He P, Wei P, Lin Y, Zhao Y, Chen X. Single-molecule long-read sequencing facilitates shrimp transcriptome research. Sci Rep 2018;8:16920. [PMID: 30446694 PMCID: PMC6240054 DOI: 10.1038/s41598-018-35066-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 10/31/2018] [Indexed: 12/26/2022]  Open
409
Zhang B, Liu J, Wang X, Wei Z. Full-length RNA sequencing reveals unique transcriptome composition in bermudagrass. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018;132:95-103. [PMID: 30176433 DOI: 10.1016/j.plaphy.2018.08.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
410
Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res 2018;28:1709-1719. [PMID: 30352806 PMCID: PMC6211647 DOI: 10.1101/gr.235119.118] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022]
411
Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform 2018;19:23-40. [PMID: 27742661 DOI: 10.1093/bib/bbw096] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 12/15/2022]  Open
412
Tilak MK, Botero-Castro F, Galtier N, Nabholz B. Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA. Genome Biol Evol 2018;10:616-622. [PMID: 29385572 PMCID: PMC5808798 DOI: 10.1093/gbe/evy022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 02/06/2023]  Open
413
Lakhundi S, Zhang K. Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology. Clin Microbiol Rev 2018;31:e00020-18. [PMID: 30209034 PMCID: PMC6148192 DOI: 10.1128/cmr.00020-18] [Citation(s) in RCA: 903] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
414
Shi Y, Liu Y, Zhang S, Zou R, Tang J, Mu W, Peng Y, Dong S. Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica 'JinhuaiJ2'. PLoS One 2018;13:e0202485. [PMID: 30114217 PMCID: PMC6095553 DOI: 10.1371/journal.pone.0202485] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/04/2018] [Indexed: 11/18/2022]  Open
415
Complete Genome Sequences of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Strains CMRSA3 and CMRSA6. Microbiol Resour Announc 2018;7:MRA00892-18. [PMID: 30533890 PMCID: PMC6256457 DOI: 10.1128/mra.00892-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 11/20/2022]  Open
416
Panthee S, Hamamoto H, Ishijima SA, Paudel A, Sekimizu K. Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768. Genome Biol Evol 2018;10:2017-2022. [PMID: 30059981 PMCID: PMC6097704 DOI: 10.1093/gbe/evy166] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 11/25/2022]  Open
417
Choudhury O, Chakrabarty A, Emrich SJ. HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning. Sci Rep 2018;8:9936. [PMID: 29967328 PMCID: PMC6028576 DOI: 10.1038/s41598-018-28364-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/31/2018] [Indexed: 11/22/2022]  Open
418
Sohn JI, Nam K, Hong H, Kim JM, Lim D, Lee KT, Do YJ, Cho CY, Kim N, Chai HH, Nam JW. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 2018;7:5052204. [PMID: 30010758 PMCID: PMC6065499 DOI: 10.1093/gigascience/giy086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/19/2018] [Accepted: 07/04/2018] [Indexed: 12/30/2022]  Open
419
Yin D, Ji C, Ma X, Li H, Zhang W, Li S, Liu F, Zhao K, Li F, Li K, Ning L, He J, Wang Y, Zhao F, Xie Y, Zheng H, Zhang X, Zhang Y, Zhang J. Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly. Gigascience 2018;7:5040258. [PMID: 29931126 PMCID: PMC6009596 DOI: 10.1093/gigascience/giy066] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/13/2018] [Accepted: 05/24/2018] [Indexed: 12/16/2022]  Open
420
Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng 2018;115:2087-2100. [PMID: 29704459 PMCID: PMC6045439 DOI: 10.1002/bit.26722] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/13/2018] [Accepted: 04/25/2018] [Indexed: 12/20/2022]
421
A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination. G3-GENES GENOMES GENETICS 2018;8:1675-1686. [PMID: 29602812 PMCID: PMC5940159 DOI: 10.1534/g3.118.200154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
422
Di Genova A, Ruz GA, Sagot MF, Maass A. Fast-SG: an alignment-free algorithm for hybrid assembly. Gigascience 2018;7:4993155. [PMID: 29741627 PMCID: PMC6007556 DOI: 10.1093/gigascience/giy048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/01/2018] [Accepted: 04/19/2018] [Indexed: 12/01/2022]  Open
423
Pavlovich SS, Lovett SP, Koroleva G, Guito JC, Arnold CE, Nagle ER, Kulcsar K, Lee A, Thibaud-Nissen F, Hume AJ, Mühlberger E, Uebelhoer LS, Towner JS, Rabadan R, Sanchez-Lockhart M, Kepler TB, Palacios G. The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity. Cell 2018;173:1098-1110.e18. [PMID: 29706541 PMCID: PMC7112298 DOI: 10.1016/j.cell.2018.03.070] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022]
424
Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T. Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella. G3 (BETHESDA, MD.) 2018;8:1327-1333. [PMID: 29476024 PMCID: PMC5873921 DOI: 10.1534/g3.117.300467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022]
425
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res 2018;28:396-411. [PMID: 29440222 PMCID: PMC5848618 DOI: 10.1101/gr.222976.117] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 01/08/2018] [Indexed: 01/15/2023]
426
Wang JR, Holt J, McMillan L, Jones CD. FMLRC: Hybrid long read error correction using an FM-index. BMC Bioinformatics 2018;19:50. [PMID: 29426289 PMCID: PMC5807796 DOI: 10.1186/s12859-018-2051-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/01/2018] [Indexed: 11/16/2022]  Open
427
Dominguez Del Angel V, Hjerde E, Sterck L, Capella-Gutierrez S, Notredame C, Vinnere Pettersson O, Amselem J, Bouri L, Bocs S, Klopp C, Gibrat JF, Vlasova A, Leskosek BL, Soler L, Binzer-Panchal M, Lantz H. Ten steps to get started in Genome Assembly and Annotation. F1000Res 2018;7. [PMID: 29568489 PMCID: PMC5850084 DOI: 10.12688/f1000research.13598.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/16/2022]  Open
428
Lin R, Qin F, Shen B, Shi Q, Liu C, Zhang X, Jiao Y, Lu J, Gao Y, Suarez-Fernandez M, Lopez-Moya F, Lopez-Llorca LV, Wang G, Mao Z, Ling J, Yang Y, Cheng X, Xie B. Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms. Sci Rep 2018;8:1123. [PMID: 29348510 PMCID: PMC5773674 DOI: 10.1038/s41598-018-19169-5] [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: 08/25/2017] [Accepted: 12/22/2017] [Indexed: 11/24/2022]  Open
429
An D, Cao HX, Li C, Humbeck K, Wang W. Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. Genes (Basel) 2018;9:genes9010043. [PMID: 29346292 PMCID: PMC5793194 DOI: 10.3390/genes9010043] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/30/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022]  Open
430
Filichkin SA, Hamilton M, Dharmawardhana PD, Singh SK, Sullivan C, Ben-Hur A, Reddy ASN, Jaiswal P. Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching. FRONTIERS IN PLANT SCIENCE 2018;9:5. [PMID: 29483921 PMCID: PMC5816337 DOI: 10.3389/fpls.2018.00005] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 05/19/2023]
431
Zaccaron AZ, Bluhm BH. The genome sequence of Bipolaris cookei reveals mechanisms of pathogenesis underlying target leaf spot of sorghum. Sci Rep 2017;7:17217. [PMID: 29222463 PMCID: PMC5722872 DOI: 10.1038/s41598-017-17476-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 11/23/2022]  Open
432
Liu Y, Lan C, Blumenstein M, Li J. Bi-level error correction for PacBio long reads. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;17:899-905. [PMID: 29990239 DOI: 10.1109/tcbb.2017.2780832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
433
Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017;6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
434
Li Y, Wei W, Feng J, Luo H, Pi M, Liu Z, Kang C. Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. DNA Res 2017;25:61-70. [PMID: 29036429 PMCID: PMC5824900 DOI: 10.1093/dnares/dsx038] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/29/2017] [Indexed: 01/30/2023]  Open
435
Argout X, Martin G, Droc G, Fouet O, Labadie K, Rivals E, Aury JM, Lanaud C. The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. BMC Genomics 2017;18:730. [PMID: 28915793 PMCID: PMC5603072 DOI: 10.1186/s12864-017-4120-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/06/2017] [Indexed: 11/21/2022]  Open
436
Zaccaron AZ, Woloshuk CP, Bluhm BH. Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis. Fungal Biol 2017;121:966-983. [PMID: 29029703 DOI: 10.1016/j.funbio.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
437
A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. Sci Rep 2017;7:7648. [PMID: 28794490 PMCID: PMC5550469 DOI: 10.1038/s41598-017-08138-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/07/2017] [Indexed: 01/08/2023]  Open
438
Haghshenas E, Hach F, Sahinalp SC, Chauve C. CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinformatics 2017;32:i545-i551. [PMID: 27587673 DOI: 10.1093/bioinformatics/btw463] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
439
Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun 2017;8:59. [PMID: 28680106 PMCID: PMC5498581 DOI: 10.1038/s41467-017-00050-4] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 05/02/2017] [Indexed: 12/30/2022]  Open
440
Kremer FS, McBride AJA, Pinto LDS. Approaches for in silico finishing of microbial genome sequences. Genet Mol Biol 2017;40:553-576. [PMID: 28898352 PMCID: PMC5596377 DOI: 10.1590/1678-4685-gmb-2016-0230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 03/13/2017] [Indexed: 12/15/2022]  Open
441
Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13:e1005595. [PMID: 28594827 PMCID: PMC5481147 DOI: 10.1371/journal.pcbi.1005595] [Citation(s) in RCA: 5235] [Impact Index Per Article: 654.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 06/22/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]  Open
442
Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB. Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome. Mol Ecol Resour 2017;17:1243-1256. [PMID: 28316149 DOI: 10.1111/1755-0998.12670] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 01/11/2023]
443
Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017. [PMID: 28594827 DOI: 10.1371/journal.pcbi.1005595b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]  Open
444
Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 2017;18:395. [PMID: 28532419 PMCID: PMC5440902 DOI: 10.1186/s12864-017-3757-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022]  Open
445
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res 2017. [PMID: 28130360 DOI: 10.1101/gr.2134c5.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
446
Bao E, Lan L. HALC: High throughput algorithm for long read error correction. BMC Bioinformatics 2017;18:204. [PMID: 28381259 PMCID: PMC5382505 DOI: 10.1186/s12859-017-1610-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/24/2017] [Indexed: 11/24/2022]  Open
447
Li Y, Dai C, Hu C, Liu Z, Kang C. Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017;90:164-176. [PMID: 27997733 DOI: 10.1111/tpj.13462] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 05/21/2023]
448
Genome-wide analysis of complex wheat gliadins, the dominant carriers of celiac disease epitopes. Sci Rep 2017;7:44609. [PMID: 28300172 PMCID: PMC5353739 DOI: 10.1038/srep44609] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/09/2017] [Indexed: 01/08/2023]  Open
449
Salmela L, Walve R, Rivals E, Ukkonen E. Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinformatics 2017;33:799-806. [PMID: 27273673 PMCID: PMC5351550 DOI: 10.1093/bioinformatics/btw321] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/03/2016] [Accepted: 05/16/2016] [Indexed: 12/04/2022]  Open
450
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017;27:722-736. [PMID: 28298431 PMCID: PMC5411767 DOI: 10.1101/gr.215087.116] [Citation(s) in RCA: 4775] [Impact Index Per Article: 596.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
PrevPage 9 of 10 12678910Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA