Search - Archive ouverte HAL Access content directly

Filter your results

111 Results
Image document

Optimal Bounds for Computing α-gapped Repeats

Maxime Crochemore , Roman Kolpakov , Gregory Kucherov
10th International Conference on Language and Automata Theory and Applications (LATA), , Mar 2016, Prague, Czech Republic. pp.245 - 255, ⟨10.1007/978-3-319-30000-9_19⟩
Conference papers hal-01577120v1

Multi-seed lossless filtration

Gregory Kucherov , Laurent Noé , Mikhail Roytberg
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005, 2 (1), pp.51--61. ⟨10.1109/TCBB.2005.12⟩
Journal articles inria-00000718v1
Image document

Optimal Reconstruction of Graphs Under the Additive Model

Vladimir Grebinski , Gregory Kucherov
[Research Report] RR-3171, INRIA. 1997
Reports inria-00073517v1
Image document

Finding approximate repetitions under Hamming distance

Roman Kolpakov , Gregory Kucherov
[Research Report] RR-4163, INRIA. 2001, pp.30
Reports inria-00072459v1
Image document

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

Gregory Kucherov , Laurent Noé , Mihkail Roytberg
Journal of Bioinformatics and Computational Biology, 2006, 4 (2), pp.553-69. ⟨10.1142/S0219720006001977⟩
Journal articles hal-00018114v2
Image document

NORINE: a database of nonribosomal peptides.

Ségolène Caboche , Maude Pupin , Valérie Leclère , Arnaud Fontaine , Philippe Jacques , et al.
Nucleic Acids Research, 2008, Database issue, 36 (Database issue), pp.D326-31. ⟨10.1093/nar/gkm792⟩
Journal articles inria-00281012v1
Image document

On the ground reducibility problem for word rewriting systems with variables

Gregory Kucherov , Michaël Rusinowitch
[Research Report] RR-1892, INRIA. 1993
Reports inria-00074779v1

On Maximal Repetitions in Words

Roman Kolpakov , Gregory Kucherov
Journal of Discrete Algorithms, 2000, 1 (1), pp.159-186
Journal articles inria-00099092v1
Image document

Maximal Repetitions in Words or How to Find all Squares in Linear Time

Roman Kolpakov , Gregory Kucherov
[Intern report] 98-R-227 || kolpakov98b, 1998, 22 p
Reports inria-00098737v1

Evolution of biosequence search algorithms: a brief survey

Gregory Kucherov
Bioinformatics, 2019, 35 (19), pp.3547-3552. ⟨10.1093/bioinformatics/btz272⟩
Journal articles hal-02414833v1

Efficient tree-structured categorical retrieval

Djamal Belazzougui , Gregory Kucherov
Preprints, Working Papers, ... hal-03049384v1
Image document

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

Fabrice Touzain , Sophie Schbath , Isabelle Debled-Rennesson , Bertrand Aigle , Gregory Kucherov , et al.
BMC Bioinformatics, 2008, 9 (73), pp.on line. ⟨10.1186/1471-2105-9-73⟩
Journal articles inria-00580657v1

Computer analysis of multiple repeats in bacteria

Alexey Vitreschak , Laurent Noé , Gregory Kucherov
The fourth International Conference on Bioinformatics of Genome Regulation and Structure - BGRS'2004, 2004, Novosibirsk, Russia, 5 p
Conference papers inria-00100088v1
Image document

Multi-seed lossless filtration (Extended abstract)

Gregory Kucherov , Laurent Noé , Mikhail A. Roytberg
Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching - CPM'2004, Jul 2004, Istambul, Turkey. pp.297-310, ⟨10.1007/11557067_21⟩
Conference papers inria-00001162v1

Improved hit criteria for DNA local alignment

Laurent Noé , Gregory Kucherov
Proceedings of the 5th Open Days in Biology, Computer Science and Mathematics - JOBIM'2004, 2004, Montreal, Canada, 11 p
Conference papers inria-00099999v1

Identification of Transcription Factor Binding Sites in Streptomyces coelicolor A3(2) by Phylogenetic Comparison

Fabrice Touzain , Patricia Lavigne , Isabelle Debled-Rennesson , Bertrand Aigle , Pierre Leblond , et al.
European Conference for Computer Biology - ECCB'2003, 2003, Paris, France
Conference papers inria-00099608v1

On repetition-free binary words of minimal density

Roman Kolpakov , Gregory Kucherov , Yuri Tarannikov
Theoretical Computer Science, 1999, 218 (1), pp.161--175. ⟨10.1016/S0304-3975(98)00257-6⟩
Journal articles inria-00098854v1
Image document

On relationship between term rewriting systems and regular tree languages

Gregory Kucherov
[Research Report] RR-1273, INRIA. 1990
Reports inria-00075286v1
Image document

RNF: a general framework to evaluate NGS read mappers

Karel Brinda , Valentina Boeva , Gregory Kucherov
Bioinformatics, 2016, 32 (1), pp.136-139. ⟨10.1093/bioinformatics/btv524⟩
Journal articles hal-01220199v2

Full-fledged Real-Time Indexing for Constant Size Alphabets

Gregory Kucherov , Yakov Nekrich
ICALP'13, Jul 2013, Riga, Latvia. pp.650-660
Conference papers hal-00790316v1

Spaced seeds improve k-mer-based metagenomic classification

Karel Brinda , Maciej Sykulski , Gregory Kucherov
Journal articles hal-01250752v1

Approximate String Matching using a Bidirectional Index

Gregory Kucherov , Dekel Tsur
Reports hal-00824706v1
Image document

On-Line Construction of Position Heaps

Gregory Kucherov
18th International Symposium on String Processing and Information Retrieval (SPIRE 2011), Oct 2011, Pisa, Italy. pp.326-337, ⟨10.1007/978-3-642-24583-1_32⟩
Conference papers hal-00681855v1
Image document

Simplitigs as an efficient and scalable representation of de Bruijn graphs

Karel Brinda , Michael Baym , Gregory Kucherov
Genome Biology, 2021, 22 (96), ⟨10.1101/2020.01.12.903443⟩
Journal articles hal-03049400v1

How many square occurrences must a binary sequence contain?

Gregory Kucherov , Pascal Ochem , Michael Rao
The Electronic Journal of Combinatorics, 2003, 10 (1), 11 p. ⟨10.37236/1705⟩
Journal articles inria-00099596v1

The complexity of some complementation problems

David Plaisted , Gregory Kucherov
Information Processing Letters, 1999, 71 (3-4), pp.159-165
Journal articles inria-00098851v1

Absent words in a sliding window with applications

Maxime Crochemore , Alice Héliou , Gregory Kucherov , Laurent Mouchard , Solon Pissis , et al.
Information and Computation, 2019, pp.104461. ⟨10.1016/j.ic.2019.104461⟩
Journal articles hal-02414839v1
Image document

Rapid heuristic inference of antibiotic resistance and susceptibility by genomic neighbor typing

Karel Brinda , Alanna Callendrello , Kevin C Ma , Derek R Macfadden , Themoula Charalampous , et al.
Preprints, Working Papers, ... hal-02414869v1
Image document

Efficient Tree-Structured Categorical Retrieval

Djamal Belazzougui , Gregory Kucherov
31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020), Jun 2020, Copenhagen, Denmark. ⟨10.4230/LIPIcs.CPM.2020.4⟩
Conference papers hal-03049420v1
Image document

Dynamic read mapping and online consensus calling for better variant detection

Karel Brinda , Valentina Boeva , Gregory Kucherov
Preprints, Working Papers, ... hal-01323188v1