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For: Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420-8. [PMID: 22495754 DOI: 10.1093/bioinformatics/bts174] [Citation(s) in RCA: 2083] [Impact Index Per Article: 160.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1951
Luef B, Frischkorn KR, Wrighton KC, Holman HYN, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 2015;6:6372. [DOI: 10.1038/ncomms7372] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/23/2015] [Indexed: 02/04/2023]  Open
1952
Lee YP, Gan HM, Tan MH, Lys I, Page R, Dias Wanigasekera B, Austin CM. The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3333-4. [DOI: 10.3109/19401736.2015.1018209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
1953
Gan HY, Gan HM, Lee YP, Austin CM. The complete mitogenome of the Australian freshwater shrimp Paratya australiensis Kemp, 1917 (Crustacea: Decapoda: Atyidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3157-8. [PMID: 25693707 DOI: 10.3109/19401736.2015.1007312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1954
Gan HY, Gan HM, Lee YP, Austin CM. The complete mitogenome of the rock pool prawn Palaemon serenus (Heller, 1862) (Crustacea: Decapoda: Palaemonidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3155-6. [PMID: 25693708 DOI: 10.3109/19401736.2015.1007311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
1955
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 2015;25:690-701. [PMID: 25702576 DOI: 10.1016/j.cub.2015.01.014] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/30/2014] [Accepted: 01/06/2015] [Indexed: 01/23/2023]
1956
Zhong C, Yang Y, Yooseph S. GRASP: guided reference-based assembly of short peptides. Nucleic Acids Res 2015;43:e18. [PMID: 25414351 PMCID: PMC4330339 DOI: 10.1093/nar/gku1210] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/01/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]  Open
1957
Ellison CE, Bachtrog D. Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements. eLife 2015;4. [PMID: 25688566 PMCID: PMC4384637 DOI: 10.7554/elife.05899] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/16/2015] [Indexed: 12/02/2022]  Open
1958
Den Unkultivierbaren auf der Spur. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s12268-015-0526-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
1959
Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. mBio 2015;6:mBio.02083-14. [PMID: 25670777 PMCID: PMC4337565 DOI: 10.1128/mbio.02083-14] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
1960
Gan HM, Gan HY, Lee YP, Grandjean F, Austin CM. The complete mitogenome of the invasive spiny-cheek crayfish Orconectes limosus (Rafinesque, 1817) (Crustacea: Decapoda: Cambaridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3181-3. [DOI: 10.3109/19401736.2015.1007326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1961
Gan HM, Tan MH, Gan HY, Lee YP, Austin CM. The complete mitogenome of the Norway lobster Nephrops norvegicus (Linnaeus, 1758) (Crustacea: Decapoda: Nephropidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3179-80. [PMID: 25648918 DOI: 10.3109/19401736.2015.1007325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
1962
Gan HM, Gan HY, Tan MH, Penny SS, Willan RC, Austin CM. The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3220-1. [PMID: 25648928 DOI: 10.3109/19401736.2015.1007355] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1963
Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME JOURNAL 2015;9:1846-56. [PMID: 25647349 DOI: 10.1038/ismej.2015.2] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 12/17/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
1964
Wawrzyniak I, Courtine D, Osman M, Hubans-Pierlot C, Cian A, Nourrisson C, Chabe M, Poirier P, Bart A, Polonais V, Delgado-Viscogliosi P, El Alaoui H, Belkorchia A, van Gool T, Tan KSW, Ferreira S, Viscogliosi E, Delbac F. Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1. GENOMICS DATA 2015;4:22-3. [PMID: 26484170 PMCID: PMC4535960 DOI: 10.1016/j.gdata.2015.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 11/27/2022]
1965
De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015;2015:875784. [PMID: 25709557 PMCID: PMC4330952 DOI: 10.1155/2015/875784] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/02/2014] [Accepted: 09/16/2014] [Indexed: 11/29/2022]
1966
Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell 2015;158:1187-1198. [PMID: 25171416 DOI: 10.1016/j.cell.2014.07.034] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/18/2014] [Accepted: 07/03/2014] [Indexed: 10/24/2022]
1967
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DPB, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 2015;160:447-60. [PMID: 25619688 DOI: 10.1016/j.cell.2015.01.002] [Citation(s) in RCA: 899] [Impact Index Per Article: 89.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 10/13/2014] [Accepted: 12/24/2014] [Indexed: 12/13/2022]
1968
Jørgensen TS, Kiil AS, Hansen MA, Sørensen SJ, Hansen LH. Current strategies for mobilome research. Front Microbiol 2015;5:750. [PMID: 25657641 PMCID: PMC4302988 DOI: 10.3389/fmicb.2014.00750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/10/2014] [Indexed: 11/30/2022]  Open
1969
Park JY, An YR, Kanda N, An CM, An HS, Kang JH, Kim EM, An DH, Jung H, Joung M, Park MH, Yoon SH, Lee BY, Lee T, Kim KW, Park WC, Shin DH, Lee YS, Kim J, Kwak W, Kim HJ, Kwon YJ, Moon S, Kim Y, Burt DW, Cho S, Kim H. Cetaceans evolution: insights from the genome sequences of common minke whales. BMC Genomics 2015;16:13. [PMID: 25609461 PMCID: PMC4311506 DOI: 10.1186/s12864-015-1213-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 01/02/2015] [Indexed: 12/11/2022]  Open
1970
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. ACTA ACUST UNITED AC 2015;31:1674-6. [PMID: 25609793 DOI: 10.1093/bioinformatics/btv033] [Citation(s) in RCA: 4627] [Impact Index Per Article: 462.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/14/2015] [Indexed: 01/25/2023]
1971
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
1972
Sim M, Kim J. Metagenome assembly through clustering of next-generation sequencing data using protein sequences. J Microbiol Methods 2015;109:180-7. [PMID: 25572018 DOI: 10.1016/j.mimet.2015.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/03/2015] [Accepted: 01/03/2015] [Indexed: 11/16/2022]
1973
Hamilton TL, Jones DS, Schaperdoth I, Macalady JL. Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. Front Microbiol 2015;5:756. [PMID: 25620962 PMCID: PMC4288042 DOI: 10.3389/fmicb.2014.00756] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022]  Open
1974
Clingenpeel S, Clum A, Schwientek P, Rinke C, Woyke T. Reconstructing each cell's genome within complex microbial communities-dream or reality? Front Microbiol 2015;5:771. [PMID: 25620966 PMCID: PMC4287102 DOI: 10.3389/fmicb.2014.00771] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/17/2014] [Indexed: 11/24/2022]  Open
1975
Baker BJ, Lazar CS, Teske AP, Dick GJ. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. MICROBIOME 2015;3:14. [PMID: 25922666 PMCID: PMC4411801 DOI: 10.1186/s40168-015-0077-6] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 05/20/2023]
1976
Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, Haas AR, Abbas A, Frye L, Christie JD, Bushman FD, Collman RG. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant 2015;15:200-9. [PMID: 25403800 PMCID: PMC4276431 DOI: 10.1111/ajt.13031] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/01/2014] [Accepted: 08/28/2014] [Indexed: 01/25/2023]
1977
Hodkinson BP, Grice EA. Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research. Adv Wound Care (New Rochelle) 2015;4:50-58. [PMID: 25566414 DOI: 10.1089/wound.2014.0542] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/23/2014] [Indexed: 12/26/2022]  Open
1978
Walter MC, Öhrman C, Myrtennäs K, Sjödin A, Byström M, Larsson P, Macellaro A, Forsman M, Frangoulidis D. Genome sequence of Coxiella burnetii strain Namibia. Stand Genomic Sci 2014;9:22. [PMID: 25593636 PMCID: PMC4286197 DOI: 10.1186/1944-3277-9-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]  Open
1979
Tan MH, Gan HM, Lee YP, Austin CM. The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura). Mitochondrial DNA A DNA Mapp Seq Anal 2014;27:3983-3984. [DOI: 10.3109/19401736.2014.989515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
1980
Tan MH, Gan HM, Lee YP, Austin CM. The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea). Mitochondrial DNA A DNA Mapp Seq Anal 2014;27:3981-3982. [DOI: 10.3109/19401736.2014.989514] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1981
Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment. GENOME ANNOUNCEMENTS 2014;2:2/6/e01337-14. [PMID: 25540349 PMCID: PMC4276827 DOI: 10.1128/genomea.01337-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
1982
Leung HCM, Yiu SM, Chin FYL. IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. J Comput Biol 2014;22:367-76. [PMID: 25535824 DOI: 10.1089/cmb.2014.0139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
1983
Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME JOURNAL 2014;9:1619-34. [PMID: 25535935 DOI: 10.1038/ismej.2014.249] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 11/09/2022]
1984
Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 2014;3:e03318. [PMID: 25517076 PMCID: PMC4381813 DOI: 10.7554/elife.03318] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 11/05/2014] [Indexed: 12/18/2022]  Open
1985
Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014;15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023]  Open
1986
Kwak W, Song KD, Oh JD, Heo KN, Lee JH, Lee WK, Yoon SH, Kim H, Cho S, Lee HK. Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing. PLoS One 2014;9:e114763. [PMID: 25501044 PMCID: PMC4263466 DOI: 10.1371/journal.pone.0114763] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022]  Open
1987
Abbas MM, Malluhi QM, Balakrishnan P. Assessment of de novo assemblers for draft genomes: a case study with fungal genomes. BMC Genomics 2014;15 Suppl 9:S10. [PMID: 25521762 PMCID: PMC4290589 DOI: 10.1186/1471-2164-15-s9-s10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
1988
Facile, high quality sequencing of bacterial genomes from small amounts of DNA. Int J Genomics 2014;2014:434575. [PMID: 25478564 PMCID: PMC4247979 DOI: 10.1155/2014/434575] [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] [Received: 05/29/2014] [Accepted: 10/02/2014] [Indexed: 11/26/2022]  Open
1989
Zhu X, Leung HCM, Chin FYL, Yiu SM, Quan G, Liu B, Wang Y. PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach. PLoS One 2014;9:e114253. [PMID: 25461763 PMCID: PMC4252104 DOI: 10.1371/journal.pone.0114253] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022]  Open
1990
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]
1991
Afiahayati, Sato K, Sakakibara Y. MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res 2014;22:69-77. [PMID: 25431440 PMCID: PMC4379979 DOI: 10.1093/dnares/dsu041] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
1992
Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat Commun 2014;5:5497. [PMID: 25425419 DOI: 10.1038/ncomms6497] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/07/2014] [Indexed: 02/03/2023]  Open
1993
Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat Commun 2014;5:5603. [PMID: 25424998 PMCID: PMC4263124 DOI: 10.1038/ncomms6603] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/20/2014] [Indexed: 11/08/2022]  Open
1994
Human papillomavirus type 197 is commonly present in skin tumors. Int J Cancer 2014;136:2546-55. [DOI: 10.1002/ijc.29325] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 11/07/2022]
1995
Tan MH, Gan HM, Lee YP, Austin CM. The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014;27:2121-2. [PMID: 25423510 DOI: 10.3109/19401736.2014.982585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
1996
Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez‐Valera F. Key roles for freshwater A ctinobacteria revealed by deep metagenomic sequencing. Mol Ecol 2014;23:6073-90. [DOI: 10.1111/mec.12985] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 02/04/2023]
1997
Predicting the functional repertoire of an organism from unassembled RNA-seq data. BMC Genomics 2014;15:1003. [PMID: 25409897 PMCID: PMC4258056 DOI: 10.1186/1471-2164-15-1003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/30/2014] [Indexed: 11/10/2022]  Open
1998
Lo CC, Chain PSG. Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinformatics 2014;15:366. [PMID: 25408143 PMCID: PMC4246454 DOI: 10.1186/s12859-014-0366-2] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/29/2014] [Indexed: 11/15/2022]  Open
1999
McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA. NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. BMC Bioinformatics 2014;15:357. [PMID: 25407910 PMCID: PMC4245761 DOI: 10.1186/s12859-014-0357-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 10/22/2014] [Indexed: 11/10/2022]  Open
2000
Aguirre de Cárcer D, Angly FE, Alcamí A. Evaluation of viral genome assembly and diversity estimation in deep metagenomes. BMC Genomics 2014;15:989. [PMID: 25407630 PMCID: PMC4247695 DOI: 10.1186/1471-2164-15-989] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/30/2014] [Indexed: 01/21/2023]  Open
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