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Items: 1 to 20 of 32

1.

Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology.

Shaik S, Kumar N, Lankapalli AK, Tiwari SK, Baddam R, Ahmed N.

PLoS One. 2016 Jun 1;11(6):e0155459. doi: 10.1371/journal.pone.0155459. eCollection 2016.

2.

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.

Gupta A, Kumar S, Prasoodanan VP, Harish K, Sharma AK, Sharma VK.

Front Microbiol. 2016 Apr 12;7:469. doi: 10.3389/fmicb.2016.00469. eCollection 2016.

3.

Metagenomics: Retrospect and Prospects in High Throughput Age.

Kumar S, Krishnani KK, Bhushan B, Brahmane MP.

Biotechnol Res Int. 2015;2015:121735. doi: 10.1155/2015/121735. Epub 2015 Nov 17. Review.

4.

Exact approaches for scaffolding.

Weller M, Chateau A, Giroudeau R.

BMC Bioinformatics. 2015;16 Suppl 14:S2. doi: 10.1186/1471-2105-16-S14-S2. Epub 2015 Oct 2.

5.

Ancestral gene synteny reconstruction improves extant species scaffolding.

Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Bérard S.

BMC Genomics. 2015;16 Suppl 10:S11. doi: 10.1186/1471-2164-16-S10-S11. Epub 2015 Oct 2.

6.

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data.

Farrant GK, Hoebeke M, Partensky F, Andres G, Corre E, Garczarek L.

BMC Bioinformatics. 2015 Sep 3;16:281. doi: 10.1186/s12859-015-0705-y.

7.

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

Lai B, Wang F, Wang X, Duan L, Zhu H.

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.

8.

Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment.

Johnson SS, Chevrette MG, Ehlmann BL, Benison KC.

PLoS One. 2015 Apr 29;10(4):e0122869. doi: 10.1371/journal.pone.0122869. eCollection 2015.

9.

Integrative workflows for metagenomic analysis.

Ladoukakis E, Kolisis FN, Chatziioannou AA.

Front Cell Dev Biol. 2014 Nov 19;2:70. doi: 10.3389/fcell.2014.00070. eCollection 2014. Review.

10.

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.

Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19.

11.

ILP-based maximum likelihood genome scaffolding.

Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.

12.

A de novo genome assembly algorithm for repeats and nonrepeats.

Lian S, Li Q, Dai Z, Xiang Q, Dai X.

Biomed Res Int. 2014;2014:736473. doi: 10.1155/2014/736473. Epub 2014 May 25. Erratum in: Biomed Res Int. 2014;2014:218569.

13.

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.

Roux S, Tournayre J, Mahul A, Debroas D, Enault F.

BMC Bioinformatics. 2014 Mar 19;15:76. doi: 10.1186/1471-2105-15-76.

14.

RepARK--de novo creation of repeat libraries from whole-genome NGS reads.

Koch P, Platzer M, Downie BR.

Nucleic Acids Res. 2014 May;42(9):e80. doi: 10.1093/nar/gku210. Epub 2014 Mar 14.

15.

A comprehensive evaluation of assembly scaffolding tools.

Hunt M, Newbold C, Berriman M, Otto TD.

Genome Biol. 2014 Mar 3;15(3):R42. doi: 10.1186/gb-2014-15-3-r42.

16.

Next-generation sequence assembly: four stages of data processing and computational challenges.

El-Metwally S, Hamza T, Zakaria M, Helmy M.

PLoS Comput Biol. 2013;9(12):e1003345. doi: 10.1371/journal.pcbi.1003345. Epub 2013 Dec 12. Review.

17.

An extended genovo metagenomic assembler by incorporating paired-end information.

Afiahayati, Sato K, Sakakibara Y.

PeerJ. 2013 Oct 31;1:e196. doi: 10.7717/peerj.196. eCollection 2013.

18.

Analytical tools and databases for metagenomics in the next-generation sequencing era.

Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H.

Genomics Inform. 2013 Sep;11(3):102-13. doi: 10.5808/GI.2013.11.3.102. Epub 2013 Sep 30. Review.

19.

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.

Nijkamp JF, Pop M, Reinders MJ, de Ridder D.

Bioinformatics. 2013 Nov 15;29(22):2826-34. doi: 10.1093/bioinformatics/btt502. Epub 2013 Sep 20.

20.

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.

Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Khurana JP, Gilbert JA, Lal R.

ISME J. 2014 Feb;8(2):398-408. doi: 10.1038/ismej.2013.153. Epub 2013 Sep 12.

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