Bibliography

Major publications by the team in recent years

[1]

I. Debled-Rennesson, J.-L. Rémy, J. Rouyer-Degli.
Detection of the Discrete Convexity of Polyominoes, in: Discrete Applied Mathematics, January 2003, vol. 125, n^o 1, p. 115-133.

[2]

R. Kolpakov, G. Bana, G. Kucherov.
mreps : efficient and flexible detection of tandem repeats in DNA, in: Nucleic Acids Research, July 2003, vol. 31, n^o 13, p. 3672-3678.

Publications of the year

Articles in refereed journals and book chapters

[3]

A. Braquelaire, B. Kerautret.
Reconstruction of Lambertian Surfaces by Discrete Equal Height Contours and Regions Propagation, in: Image and Vision Computing, February 2005, vol. 23, n^o 2, p. 177-189.

[4]

I. Debled-Rennesson, J.-L. Rémy, J. Rouyer-Degli.
Linear Segmentation of Discrete Curves into Fuzzy Segments, in: Discrete Applied Mathematics, October 2005, vol. 151, n^o 1-3, p. 122–137.

[5]

I. Debled-Rennesson, S. Tabbone, L. Wendling.
Multiorder polygonal approximation of digital curves, in: Electronic Letters on Computer Vision and Image Analysis, Special Issue on Document Analysis, August 2005, vol. 5, n^o 2, p. 98–110.

[6]

H. Dörksen-Reiter, I. Debled-Rennesson.
Convex and Concave Parts of Digital Curves, in: Geometric Properties from Incomplete Data, R. Klette, R. Kozera, L. Noakes, J. Weickert (editors), Computational Imaging and Vision, Springer-Verlag, January 2005, vol. 31.

[7]

Y. Gérard, I. Debled-Rennesson, P. Zimmermann.
An elementary digital plane recognition algorithm, in: Discrete Applied Mathematics, October 2005, vol. 151, n^o 1-3, p. 169–183.

[8]

B. Kerautret, A. Braquelaire.
A Reversible and Statistical Method for Discrete Surfaces Smoothing, in: Computer & Graphics, (in press), 2006, vol. 30, n^o 1.

[9]

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.

[10]

G. Kucherov, L. Noé, M. Roytberg.
Multi-seed lossless filtration, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, January-March 2005, vol. 2, n^o 1, p. 51–61.

[11]

L. Noé, G. Kucherov.
YASS: enhancing the sensitivity of DNA similarity search, in: Nucleic Acid Research, 2005, vol. 33, p. W540-W543.

Publications in Conferences and Workshops

[12]

M. Bouvel, V. Grebinski, G. Kucherov.
Combinatorial search on graphs motivated by bioinformatics applicaitons: a brief survey, in: Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG), Metz (France), June 23-25, 2005, D. Kratsch (editor), Lecture Notes in Computer Science, Springer Verlag, 2005, vol. 3787, p. 16–27.

[13]

I. Debled-Rennesson, F. Feschet, J. Rouyer-Degli.
Blurred Segments Decomposition in Linear Time, in: Proceedings of the 12th International Conference on Discrete Geometry for Computer Imagery, Poitiers, France, E. Andres, G. Damiand, P. Lienhardt (editors), LNCS, Springer-Verlag, April 2005, vol. 3429, p. 371-382.

[14]

B. Kerautret, A. Braquelaire.
A Statistical Approach for Geometric Smoothing of Discrete Surfaces, in: Proceeding of the International Conference on Discrete Geometry for Computer Imagery, Poitiers, France, E. Andres, G. Damiand, P. Lienhardt (editors), LNCS, Springer-Verlag, April 2005, vol. 3429, p. 405-414.

[15]

B. Kerautret, X. Granier, A. Braquelaire.
Intuitive Shape Modeling by Shading Design, in: Proceedings of the 5th International Symposium on Smart Graphics, Frauenwoerth Cloister, Germany, LNCS, Springer-Verlag, August 2005, n^o 3638, p. 163-174.

[16]

G. Kucherov, L. Noé, M. Roytberg.
A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds, in: Proceedings of the 5th Workshop on Algorithms in Bioinformatics (WABI), Mallorca (Spain), October 3-6, 2005, R. Casadio, G. Myers (editors), Lecture Notes in Computer Science, Springer-Verlag, 2005, vol. 3692, p. 251–263.

[17]

F. Touzain, S. Schbath, I. Debled-Rennesson, B. Aigle, P. Leblond, G. Kucherov.
SIGffRid : Programme de recherche des sites de fixation des facteurs de transcription par approche comparative, in: JOBIM, 2005, p. 417-425.

Miscellaneous

[18]

T. Nguyen.
Optimisation du calcul de la courbure de l'ADN, DPEA report, IFI, October 2005.

[19]

L. Provot.
Reconnaissance de morceaux de plans discrets bruités, DEA report, LORIA, June 2005.

References in notes

[20]

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang, W. Miller, D. Lipman.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, in: Nucleic Acids Research, 1997, vol. 25, n^o 17, p. 3389–3402.

[21]

T. Atlung, H. Ingmer.
H-NS: a modulator of environmentally regulated gene expression, in: Mol Microbiol, April 1997, vol. 24, n^o 1, p. 7-17.

[22]

A. Bolshoy, P. McNamara, P. Harrington, E. Trifonov.
Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles, in: Proc. Natl. Acad. Sci. USA, 1991, vol. 88, p. 2312-6.

[23]

B. Brejova, D. Brown, T. Vinar.
Vector seeds: an extension to spaced seeds allows substantial improvements in sensitivity and specificity, in: Proceedings of the 3rd International Workshop in Algorithms in Bioinformatics (WABI), Budapest (Hungary), G. Benson, R. Page (editors), Lecture Notes in Computer Science, Springer, September 2003, vol. 2812.

[24]

J. Buhler, U. Keich, Y. Sun.
Designing seeds for similarity search in genomic DNA, in: Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), Berlin (Germany), ACM Press, April 2003, p. 67-75.

[25]

S. Burkhardt, J. Kärkkäinen.
Better filtering with gapped q-grams, in: Fundamenta Informaticae, 2003, vol. 56, n^o 1-2, p. 51-70.

[26]

J.-M. Chassery, A. Montanvert.
Géométrie discrète en imagerie, Hermès , Paris, 1991.

[27]

D. Coeurjolly, L. Tougne, Y. Gérard, J.-P. Reveillès.
An Elementary Algorithm for Digital Arc Segmentation, in: Electronic Notes in Theoretical Computer Science, 2001, vol. 46.

[28]

M. Crochemore, C. Hancart, T. Lecroq.
Algorithmique du texte, Vuibert Informatique, 2001.

[29]

M. Crochemore, W. Rytter.
Jewels of Stringology, World Scientific, 2002.

[30]

M. Crochemore, W. Rytter.
Text algorithms, Oxford University Press, 1994.

[31]

I. Debled-Rennesson.
Estimation of Tangents to a Noisy Discrete Curve, in: Vision Geometry XII, Electronic Imaging, San Jose, California, USA, L. J. Latecki, D. M. Mount, A. Y. Wu (editors), Proceedings of the SPIE, January 2004, vol. 5300, p. 117-126.

[32]

I. Debled-Rennesson, J.-L. Rémy, J. Rouyer-Degli.
Detection of the Discrete Convexity of Polyominoes, in: Discrete Applied Mathematics, January 2003, vol. 125, n^o 1, p. 115-133.

[33]

M. Dlakic, R. Harrington.
DIAMOD: display and modeling of DNA bending, in: Bioinformatics, 1998, vol. 14, p. 326-331.

[34]

C. Dorman, P. Deighan.
Regulation of gene expression by histone-like proteins in bacteria, in: Curr Opin Genet Dev, April 2003, vol. 13, n^o 2, p. 179-84.

[35]

D. Gusfield.
Algorithms on Strings, Trees, and Sequences, Cambridge University Press, 1997.

[36]

F. Hommais, E. Krin, C. Laurent-Winter, O. Soutourina, A. Malpertuy, J.-P. Le Caer, A. Danchin, P. Bertin.
Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS, in: Mol Microbiol, April 2001, vol. 40, n^o 1, p. 20-36.

[37]

R. Kolpakov, G. Bana, G. Kucherov.
mreps : efficient and flexible detection of tandem repeats in DNA, in: Nucleic Acids Research, July 2003, vol. 31, n^o 13, p. 3672-3678.

[38]

S. Kurtz, J. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich.
REPuter: the manifold applications of repeat analysis on a genomic scale, in: Nucleic Acids Res., November 15 2001, vol. 29, n^o 22, p. 4633-42.

[39]

A. Lefebvre, T. Lecroq, H. Dauchel, J. Alexandre.
FORRepeats: detects repeats on entire chromosomes and between genomes, in: Bioinformatics, February 12 2003, vol. 19, n^o 3, p. 319-26.

[40]

B. Ma, J. Tromp, M. Li.
PatternHunter: Faster and more sensitive homology search, in: Bioinformatics, 2002, vol. 18, n^o 3, p. 440-445.

[41]

L. Noé, G. Kucherov.
Improved hit criteria for DNA local alignment, in: BMC Bioinformatics, October 2004, vol. 5, n^o 149.

[42]

F. Rapaport.
Calcul du rayon de courbure d'une séquence d'ADN, Stage de DEA, June 2004
http://www.loria.fr/publications/2004/A04-R-276/A04-R-276.ps.

[43]

E. Shpigelman, E. Trifonov, A. Bolshoy.
CURVATURE: software for the analysis of curved DNA, in: Comput Appl Biosci, 1993, vol. 9, n^o 4, p. 435-40.

[44]

A. Vincens, C. André, S. Hazout.
D-ASSIRC: distributed program for finding sequence similarities in genomes, in: Bioinformatics, March 2002, vol. 18, n^o 3, p. 446-51.

[45]

W. Wan, J. A. Ventura.
Segmentation of Planar Curves into Straight-Line Segments and Elliptical Arcs, in: Graphical Models and Image Processing, 1997, vol. 59, p. 484–494.