Team sequoia

Members
Overall Objectives
Scientific Foundations
Software
New Results
Contracts and Grants with Industry
Other Grants and Activities
Dissemination
Bibliography

Bibliography

Major publications by the team in recent years

[1]
S. Caboche, M. Pupin, V. Leclère, A. Fontaine, P. Jacques, G. Kucherov.
NORINE: a database of nonribosomal peptides, in: Nucleic Acids Research, 2008, vol. Database Issue, Vol. 36, p. D326–331
http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D326.
[2]
M. Defrance, H. Touzet.
Predicting transcription factor binding sites using local over-representation and comparative genomics, in: BMC Bioinformatics, 2006
http://www.biomedcentral.com/1471-2105/7/396/abstract.
[3]
G. Didier, I. Laprevotte, M. Pupin, A. Henaut.
Local decoding of sequences and alignment-free comparison., in: Journal of Computational Biology, 2006, vol. 13, no 8, p. 1465–1476
http://dx.doi.org/10.1089/cmb.2006.13.1465.
[4]
S. Dulucq, H. Touzet.
Decomposition algorithms for the tree edit distance problem, in: Journal of Discrete Algorithms, 2005, p. 448-471
http://dx.doi.org/10.1016/j.jda.2004.08.018.
[5]
M. Figeac, J.-S. Varré.
Sorting By Reversals with Common Intervals, in: Proceedings of the 4th International Workshop Algorithms in Bioinformatics (WABI 2004), Bergen, Norway, September 17-21, 2004, Lecture Notes in Computer Sciences, Springer Verlag, 2004, vol. 3240, p. 26-37.
[6]
R. Kolpakov, G. Kucherov.
Identification of periodic structures in words, in: Applied combinatorics on words, J. Berstel, D. Perrin (editors), Lothaire books, Cambridge University Press, 2005, vol. Encyclopedia of Mathematics and its Applications, vol. 104, chap. 8, p. 430–477
http://www-igm.univ-mlv.fr/~berstel/Lothaire/index.html.
[7]
G. Kucherov, L. Noé, M. Roytberg.
Multi-seed lossless filtration, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, January-March 2005, vol. 2, no 1, p. 51–61.
[8]
D. Lavenier, M. Giraud.
Bioinformatics Applications, in: Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays, Springer, 2005
http://dx.doi.org/10.1007/0-387-26106-0_8.
[9]
A. Liefooghe, H. Touzet, J.-S. Varré.
Large Scale Matching for Position Weight Matrices., in: Proceedings 17th Annual Symposium on Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science, Springer Verlag, 2006, vol. 4009, p. 401–412
http://www.springerlink.com/content/7113757vj6205067/.
[10]
L. Noé, G. Kucherov.
YASS: enhancing the sensitivity of DNA similarity search, in: Nucleic Acid Research, 2005, vol. 33, p. W540-W543.
[11]
H. Touzet, J.-S. Varré.
Efficient and accurate P-value computation for Position Weight Matrices, in: Algorithms for Molecular Biology, 2007, vol. 2, no 15.

Publications of the year

Doctoral Dissertations and Habilitation Theses

[12]
S. Caboche.
Mise en place d'une plateforme logicielle pour l'analyse des peptides non-ribosomiaux, Université de Lille 1, 2009, Ph. D. Thesis.
[13]
A. Fontaine.
Classification d'ARN codants et d'ARN non-codants, Université de Lille 1, 2009
http://www2.lifl.fr/~fontaina/These.pdf, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

[14]
S. Caboche, M. Pupin, V. Leclère, P. Jacques, G. Kucherov.
Structural pattern matching of nonribosomal peptides, in: BMC Structural Biology, March 18 2009, vol. 9:15
http://www.biomedcentral.com/1472-6807/9/15.
[15]
A. Fontaine, H. Touzet.
Computational identification of protein-coding sequences by comparative analysis, in: International Journal of Data Mining and Bioinformatics, 2009, vol. 3, no 2, p. 160–176
http://www.inderscience.com/search/index.php?action=record&rec_id=24849.
[16]
M. Giraud.
Asymptotic behavior of the number of runs and microruns, in: Information and Computation, 2009, vol. 207, no 11, p. 1221-1228
http://dx.doi.org/10.1016/j.ic.2009.02.007.
[17]
R. Kolpakov, G. Kucherov.
Searching for gapped palindromes, in: Theoretical Computer Science, 2009, vol. 410, no 51, p. 5365–5373.
[18]
A. Ouangraoua, P. Ferraro.
A constrained edit distance algorithm between semi-ordered trees, in: Theor. Comput. Sci., 2009, vol. 410, no 8-10, p. 837-846.
[19]
A. Ouangraoua, P. Ferraro.
A new constrained edit distance between quotiented ordered trees, in: J. Discrete Algorithms, 2009, vol. 7, no 1, p. 78-89.
[20]
M. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, G. Kucherov.
On subset seeds for protein alignment, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, vol. 6, no 3, p. 483–494
http://www.lifl.fr/~noe/files/pp_TCBB09_preprint.pdf.

International Peer-Reviewed Conference/Proceedings

[21]
M. Giraud, J.-S. Varré.
Parallel Position Weight Matrices Algorithms, in: Proceedings of the 8th International Symposium on Parallel and Distributed Computing, ISPDC'09, 2009, p. 65-69
http://dx.doi.org/10.1109/ISPDC.2009.31.
[22]
M. Gîrdea, G. Kucherov, L. Noé.
Back-translation for discovering distant protein homologies, in: Proceedings of the 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia (USA), S. Salzberg, T. Warnow (editors), Lecture Notes in Computer Science, Springer Verlag, September 2009, vol. 5724, p. 108–120
http://www.springerlink.com/content/3236004m84465n7j/.
[23]
E. Harris, T. Lecroq, G. Kucherov, S. Lonardi.
CPM's 20th Anniversary: A Statistical Retrospective, in: Proceedings of the 20th Annual Combinatorial Pattern Matching Symposium (CPM), Lille (France), June 22-24, 2009, Lecture Notes in Computer Science, Springer Verlag, 2009, vol. 5577, p. 1-11.
[24]
A. Liefooghe, H. Touzet, J.-S. Varré.
Self-overlapping occurrences and Knuth-Morris-Pratt algorithm for weighted matching, in: Proceedings of the 3rd International Conference on Language and Automata Theory and Applications, April 2-8, 2009 - Tarragona, Spain, 2009, vol. 5457, p. 481–492
http://www.springerlink.com/content/p6q458l886880v45/.
[25]
P. Steffen, R. Giegerich, M. Giraud.
GPU Parallelization of Algebraic Dynamic Programming, in: Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 09), 2009, to appear.

National Peer-Reviewed Conference/Proceedings

[26]
A. Darracq, J.-S. Varré, P. Touzet.
A Study of Genomic Rearrangements in Maize Mitochondrial Genomes, in: Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2009), 2009, poster.
[27]
A. Saffarian, M. Giraud, H. Touzet.
Paysage d'énergie et structures localement optimales d'un ARN, in: Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2009) (poster), 2009, poster.

Workshops without Proceedings

[28]
A. Darracq, J.-S. Varré, P. Touzet.
A Study of Genomic Rearrangements in Maize Mitochondrial Genomes, in: The 17th annual meeting of the Society for Molecular Biology and Evolution (SMBE 2009), 2009, poster.
[29]
M. Gîrdea, L. Noé, G. Kucherov.
Read Mapping Tool for AB SOLiD Data, in: 9th Workshop on Algorithms in Bioinformatics (WABI), Philadelphia (USA), September 12-13, 2009, September 2009
http://www.lifl.fr/~noe/files/poster_WABI09.abstract.pdf, poster.
[30]
R. Uricaru, C. Michotey, L. Noé, H. Chiapello, É. Rivals.
Improved sensitivity and reliability of anchor based genome alignment, in: Proceedings of the 10th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 9-11, 2009, Nantes (France), 2009, p. 31–36
http://www.lirmm.fr/~uricaru/articles/jobim26.pdf.
[31]
J.-S. Varré, S. Janot, M. Giraud.
Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics, in: Bioinformatics Open Source Conference (BOSC), 2009.

Books or Proceedings Editing

[32]
G. Kucherov, E. Ukkonen (editors)
Combinatorial Pattern Matching: 20th Annual Symposium (CPM), Lille (France), June 2009. Proceedings, Lecture Notes in Computer Science, Springer, 2009, vol. 5577.

References in notes

[33]
B. O. Bachmann, J. Ravel.
Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data, in: Methods in Enzymology, 2009, vol. 458, p. 181–217.
[34]
H. Berman, K. Henrick, H. Nakamura, J. L. Markley.
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data, in: Nucleic Acids Research, 2007, vol. 35, no Database issue, p. D301–303.
[35]
G. Blin, A. Denise, S. Dulucq, C. Herrbach, H. Touzet.
Alignment of RNA structures, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008.
[36]
G. Blin, H. Touzet.
How to Compare Arc-Annotated Sequences: The Alignment Hierarchy, in: 13th International Symposium on String Processing and Information Retrieval (SPIRE), Lecture Notes in Computer Science, Springer Verlag, 2006, vol. 4209, p. 291–303
http://www.springerlink.com/content/4k37q116j2720832/.
[37]
D. G. Brown.
A survey of seeding for sequence alignments, in: Bioinformatics Algorithms: Techniques and Applications, I. Mandoiu, A. Zelikovsky (editors), J. Wiley and Sons, 2008.
[38]
S. Burkhardt, J. Kärkkäinen.
Better Filtering with Gapped q-Grams, in: Proceedings of CPM'01, LNCS, Springer-Verlag, 2001, vol. 2089, p. 73–85
http://www.springerlink.com/index/GYKW51MPJQNWRMQX.pdf.
[39]
M. Charalambous, P. Trancoso, A. Stamatakis.
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, in: Adv. in Informatics, 2005, p. 415–425.
[40]
UniProt. Consortium.
The Universal Protein Resource (UniProt) 2009, in: Nucleic Acids Research, 2009, vol. 37, no Database issue, p. D169–74.
[41]
A. Fontaine, A. de Monte, H. Touzet.
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences, in: Nucleic Acids Research, 2008, vol. Web Server Issue, Vol 36, no suppl 2, p. W14-W18
http://nar.oxfordjournals.org/cgi/content/full/gkn321.
[42]
E. Freyhult, J. Bollback, P. Gardner.
Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA, in: Genome Research, 2007, vol. 17, p. 117 – 125.
[43]
P. Gardner, R. Giegerich.
A comprehensive comparison of comparative RNA structure prediction approaches, in: BMC Bioinformatics, 2004, vol. 5(140).
[44]
P. Gelsinger.
Microprocessors for the New Millennium: Challenges, Opportunities, and New Frontiers, in: IEEE International Solid State Circuits Conference (ISSCC 2001), 2001, p. 22-25.
[45]
G. Kucherov, L. Noé, M. Roytberg.
A unifying framework for seed sensitivity and its application to subset seeds, in: Journal of Bioinformatics and Computational Biology, 2006, vol. 4, no 2, p. 553–569
http://www.worldscinet.com/jbcb/04/0402/S0219720006001977.html.
[46]
G. Kucherov, L. Noé, M. Roytberg.
Subset Seed Automaton, in: 12th International Conference on Implementation and Application of Automata (CIAA 07), Lecture Notes in Computer Science, Springer Verlag, 2007, vol. 4783, p. 180–191
http://www.springerlink.com/content/y824l20554002756/.
[47]
F. Lipmann, W. Gevers, H. Kleinkauf, R. J. Roskoski.
Polypeptide synthesis on protein templates: the enzymatic synthesis of gramicidin S and tyrocidine., in: Adv Enzymol Relat Areas Mol Biol, 1971, vol. 35, p. 1–34.
[48]
W. Liu, B. Schmidt, G. Voss, W. Müller-Wittig.
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, in: High Performance Computing (HiPC 2006), LNCS 4297, 2006, p. 363-374.
[49]
B. Ma, J. Tromp, M. Li.
PatternHunter: Faster and more sensitive homology search, in: Bioinformatics, 2002, vol. 18, no 3, p. 440–445
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/440.
[50]
A. Machado-Lima, H. Portillo, A. Durham.
Computational methods in noncoding RNA research, in: Journal of Mathematical Biology, 2008, vol. 56 (1-2), p. 15-49.
[51]
S. A. Manavski, G. Valle.
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, in: BMC Bioinformatics, 2008, vol. 9 (S2), S10 p.
[52]
E. S. Nawrocki EP.
Query-dependent banding (QDB) for faster RNA similarity searches, in: PLoS Comput Biology, 2007, vol. 3(3):e56.
[53]
L. Noé, G. Kucherov.
YASS: Similarity Search in DNA Sequences, INRIA, 2003, no RR-4852, Technical report.
[54]
A. Ouangraoua, P. Ferraro, L. Tichit, S. Dulucq.
Local similarity between quotiented ordered trees, in: J. Discrete Algorithms, 2007, vol. 5, no 1, p. 23-35.
[55]
P. Peterlongo, L. Noé, D. Lavenier, G. les Georges, J. Jacques, G. Kucherov, M. Giraud.
Protein similarity search with subset seeds on a dedicated reconfigur able hardware, in: Parallel Processing and Applied Mathematics / Parallel Biocomputi ng Conference (PPAM / PBC 07), R. Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski (editors), Lecture Notes in Computer Science (LNCS), 2008, vol. 4967, p. 1240-1248
http://www.lifl.fr/~giraud/publis/peterlongo-pbc-07.pdf.
[56]
P. Peterlongo, L. Noé, D. Lavenier, V. H. Nguyen, G. Kucherov, M. Giraud.
Optimal neighborhood indexing for protein similarity search, in: BMC Bioinformatics, 2008, vol. 9, no 534
http://www.biomedcentral.com/1471-2105/9/534.
[57]
M. Pop, S. Salzberg.
Bioinformatics challenges of new sequencing technology, in: Trends Genetics, 2008, vol. 24(3), p. 142-9.
[58]
G. Rizk, D. Lavenier.
GPU accelerated RNA folding algorithm, in: Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science (ICCS 2009), 2009.
[59]
M. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, G. Kucherov.
Efficient seeding techniques for protein similarity search, in: Proceedings of the 2nd Workshop on Algorithms in Molecular Biology (ALBIO'08), Vienna (Austria), July 7-9, 2008, M. Elloumi, J. Küng, M. Linial, R. Murphy, K. Schneider, C. Toma (editors), Communications in Computer and Information Science, Springer Verlag, 2008, vol. 13, p. 466–478
http://www.springerlink.com/content/m3560l36r573xjr5/.
[60]
M. Schatz, C. Trapnell, A. Delcher, A. Varshney.
High-throughput sequence alignment using Graphics Processing Units., in: BMC Bioinformatics, 2007, vol. 8, 474 p.
[61]
A. Starcevic, J. Zucko, J. Simunkovic, P. F. Long, J. Cullum, D. Hranueli.
ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures, in: Nucleic Acids Res., 2008, vol. 36, p. 6882–6892.
[62]
H. Touzet.
Comparative analysis of RNA genes: the CaRNAc software, Humana Press, 2007, vol. Methods in Molecular Biology, Special issue on comparative genomic s I, p. 465-473
http://hal.archives-ouvertes.fr/docs/00/17/85/57/PDF/comparativerna.pdf.
[63]
H. Touzet.
Comparing similar ordered trees in linear-time, in: Journal of Discrete Algorithms, 2007, vol. 5, no 4, p. 696-705
http://linkinghub.elsevier.com/retrieve/pii/S1570866706000700.
[64]
H. Touzet.
Looking for RNA motifs, fast and well, in: ARENA – non-coding RNA bioinformatics (Toulouse), 2008, (talk).

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