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Results: 17

1.

Using cascading Bloom filters to improve the memory usage for de Brujin graphs.

Salikhov K, Sacomoto G, Kucherov G.

Algorithms Mol Biol. 2014 Feb 24;9(1):2. doi: 10.1186/1748-7188-9-2.

PMID:
24565280
[PubMed]
Free PMC Article
2.

Regular language constrained sequence alignment revisited.

Kucherov G, Pinhas T, Ziv-Ukelson M.

J Comput Biol. 2011 May;18(5):771-81. doi: 10.1089/cmb.2010.0291.

PMID:
21554020
[PubMed - indexed for MEDLINE]
3.

Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Noé L, Gîrdea M, Kucherov G.

Adv Bioinformatics. 2010. pii: 708501. doi: 10.1155/2010/708501. Epub 2010 Sep 16.

PMID:
20936175
[PubMed]
Free PMC Article
4.

Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.

Caboche S, Leclère V, Pupin M, Kucherov G, Jacques P.

J Bacteriol. 2010 Oct;192(19):5143-50. doi: 10.1128/JB.00315-10. Epub 2010 Aug 6.

PMID:
20693331
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Back-translation for discovering distant protein homologies in the presence of frameshift mutations.

Girdea M, Noe L, Kucherov G.

Algorithms Mol Biol. 2010 Jan 4;5(1):6. doi: 10.1186/1748-7188-5-6.

PMID:
20047662
[PubMed]
Free PMC Article
6.

On subset seeds for protein alignment.

Roytberg M, Gambin A, Noé L, Lasota S, Furletova E, Szczurek E, Kucherov G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):483-94. doi: 10.1109/TCBB.2009.4.

PMID:
19644175
[PubMed - indexed for MEDLINE]
7.

Structural pattern matching of nonribosomal peptides.

Caboche S, Pupin M, Leclère V, Jacques P, Kucherov G.

BMC Struct Biol. 2009 Mar 18;9:15. doi: 10.1186/1472-6807-9-15.

PMID:
19296847
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Optimal neighborhood indexing for protein similarity search.

Peterlongo P, Noé L, Lavenier D, Nguyen VH, Kucherov G, Giraud M.

BMC Bioinformatics. 2008 Dec 16;9:534. doi: 10.1186/1471-2105-9-534.

PMID:
19087280
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.

Touzain F, Schbath S, Debled-Rennesson I, Aigle B, Kucherov G, Leblond P.

BMC Bioinformatics. 2008 Jan 31;9:73. doi: 10.1186/1471-2105-9-73.

PMID:
18237374
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula.

Grzebelus D, Lasota S, Gambin T, Kucherov G, Gambin A.

BMC Genomics. 2007 Nov 9;8:409.

PMID:
17996080
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Reconsidering the significance of genomic word frequencies.

Csurös M, Noé L, Kucherov G.

Trends Genet. 2007 Nov;23(11):543-6. Epub 2007 Oct 26.

PMID:
17964682
[PubMed - indexed for MEDLINE]
12.

NORINE: a database of nonribosomal peptides.

Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G.

Nucleic Acids Res. 2008 Jan;36(Database issue):D326-31. Epub 2007 Oct 2.

PMID:
17913739
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Multiseed lossless filtration.

Kucherov G, Noé L, Roytberg M.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jan-Mar;2(1):51-61.

PMID:
17044164
[PubMed - indexed for MEDLINE]
14.

A unifying framework for seed sensitivity and its application to subset seeds.

Kucherov G, Noé L, Roytberg M.

J Bioinform Comput Biol. 2006 Apr;4(2):553-69.

PMID:
16819802
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

YASS: enhancing the sensitivity of DNA similarity search.

Noé L, Kucherov G.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W540-3.

PMID:
15980530
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Improved hit criteria for DNA local alignment.

Noé L, Kucherov G.

BMC Bioinformatics. 2004 Oct 14;5:149.

PMID:
15485572
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

mreps: Efficient and flexible detection of tandem repeats in DNA.

Kolpakov R, Bana G, Kucherov G.

Nucleic Acids Res. 2003 Jul 1;31(13):3672-8.

PMID:
12824391
[PubMed - indexed for MEDLINE]
Free PMC Article

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