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Items: 1 to 20 of 106

1.

HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences.

Ghosh TS, Mohammed MH, Rajasingh H, Chadaram S, Mande SS.

BMC Bioinformatics. 2011;12 Suppl 13:S9. doi: 10.1186/1471-2105-12-S13-S9. Epub 2011 Nov 30.

2.

Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

Kuntal BK, Ghosh TS, Mande SS.

Genomics. 2013 Oct;102(4):409-18. doi: 10.1016/j.ygeno.2013.08.004. Epub 2013 Aug 24.

PMID:
23978768
3.

Metagenomic signatures of 86 microbial and viral metagenomes.

Willner D, Thurber RV, Rohwer F.

Environ Microbiol. 2009 Jul;11(7):1752-66. doi: 10.1111/j.1462-2920.2009.01901.x. Epub 2009 Mar 18.

PMID:
19302541
4.

Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets.

Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS.

J Biosci. 2011 Sep;36(4):709-17.

5.

i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets.

Mohammed MH, Ghosh TS, Chadaram S, Mande SS.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S12. doi: 10.1186/1471-2164-12-S3-S12. Epub 2011 Nov 30.

6.

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.

Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG.

BMC Bioinformatics. 2016 Jan 16;17:38. doi: 10.1186/s12859-015-0875-7.

7.

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets.

Haque MM, Bose T, Dutta A, Reddy CV, Mande SS.

Genomics. 2015 Aug;106(2):116-21. doi: 10.1016/j.ygeno.2015.04.005. Epub 2015 May 2.

PMID:
25944184
8.

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection.

Ding X, Cheng F, Cao C, Sun X.

BMC Bioinformatics. 2015 Oct 7;16:323. doi: 10.1186/s12859-015-0753-3.

9.

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S4. doi: 10.1186/1471-2164-12-S3-S4. Epub 2011 Nov 30.

10.

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.

Reddy RM, Mohammed MH, Mande SS.

Gene. 2012 Sep 1;505(2):259-65. doi: 10.1016/j.gene.2012.06.014. Epub 2012 Jun 15.

PMID:
22710135
11.

CoMet--a web server for comparative functional profiling of metagenomes.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W518-23. doi: 10.1093/nar/gkr388. Epub 2011 May 26.

12.

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.

Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO.

BMC Bioinformatics. 2004 Oct 26;5:163.

13.

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

Ghosh TS, Mehra V, Mande SS.

J Bioinform Comput Biol. 2015 Jun;13(3):1541004. doi: 10.1142/S0219720015410048. Epub 2015 Feb 8.

PMID:
25790784
14.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.

Wu YW, Simmons BA, Singer SW.

Bioinformatics. 2016 Feb 15;32(4):605-7. doi: 10.1093/bioinformatics/btv638. Epub 2015 Oct 29.

PMID:
26515820
15.

Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.

Ding X, Cao CC, Sun X.

J Theor Biol. 2014 Jul 21;353:9-18. doi: 10.1016/j.jtbi.2014.02.039. Epub 2014 Mar 11.

PMID:
24631045
16.

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.

Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG.

Bioinformatics. 2016 Sep 15;32(18):2760-7. doi: 10.1093/bioinformatics/btw312. Epub 2016 Jun 3.

PMID:
27259541
17.

Estimating the composition of species in metagenomes by clustering of next-generation read sequences.

Seok HS, Hong W, Kim J.

Methods. 2014 Oct 1;69(3):213-9. doi: 10.1016/j.ymeth.2014.07.009. Epub 2014 Jul 27.

PMID:
25072168
18.

Advances in computational analysis of metagenome sequences.

Davenport CF, Tümmler B.

Environ Microbiol. 2013 Jan;15(1):1-5. doi: 10.1111/j.1462-2920.2012.02843.x. Epub 2012 Aug 8.

PMID:
22882611
19.

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities.

Suenaga H.

Environ Microbiol. 2012 Jan;14(1):13-22. doi: 10.1111/j.1462-2920.2011.02438.x. Epub 2011 Mar 1. Review.

PMID:
21366818
20.

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

Pride DT, Schoenfeld T.

BMC Genomics. 2008 Sep 17;9:420. doi: 10.1186/1471-2164-9-420.

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