Pierre Nicodème's Publications

Pierre Nicodème's Publications

Bioinformatics

Group

LIX - Ecole polytechnique

Publications

Non-Refereed

Slides, etc

Publication List:

Counting occurrences for a finite set of words: an inclusion-exclusion approach, Frédérique Bassino, Julien Clément, Julien Fayolle and Pierre Nicodème, DMTCS Proceedings of the International Conference on Analysis of Algorithms AofA07, Juan-les-Pins, June 2007, pages 29--42, ps | pdf

Average profiles, from tries to suffix-trees, Pierre Nicodème (2005). International Conference on Analysis of Algorithms AofA05, Barcelona, June 2005, DMTCS proc. AD, 2005, pages 257--266, ps | pdf

q-gram analysis and urn models, Pierre Nicodème (2003). Proc. of Discrete Random Walks DRW2003, pages 243--258 ps | pdf

Regexpcount, a symbolic package for counting problems on regular expressions and words, Pierre Nicodème, Fundamenta Informaticae, vol. 56, num. 1-2, 2003, pages 71--88. (BibTeX reference). ps | pdf

Proteome Analysis Based on Motif Statistics, Pierre Nicodème, Tobias Doerks, and Martin Vingron, Bioinformatics, vol. 18, 2002, pages 161--171. - published as the proceedings of the First European Conference on Computational Biology ECCB02, Saarbrücken, October 2002.(BibTeX reference). Preliminary version: ps | pdf

Motif Statistics, Pierre Nicodème, Bruno Salvy, and Philippe Flajolet, Theoretical Computer Science, vol. 287, n°2, 2002, pages 593--618. - Extended version of an article published in the proceedings of 7th Annual European Symposium on Algorithms ESA'99, Prague, July 1999. Preliminary version [BW|Color postscript], (BibTeX reference).

Fast Approximate Motif Statistics, Pierre Nicodème (2001). Journal of Computational Biology, vol. 8, no. 3, p. 235-248. Preliminary version: abstract | ps | pdf

Regexpcount, a symbolic package for counting problems on regular expressions and words , Pierre Nicodème (2000). Proceedings of the 15th german conference on bioinformatics GCB00, p. 63-73. Preliminary version: abstract | ps | pdf

WWW-Access to the SYSTERS Protein sequence Cluster set, Antje Krause, Pierre Nicodème, Eric Bornberg-Bauer, Marc Rehmsmeier and Martin Vingron, (1998). Application Note accepted for the GCB Special Issue of Bioinformatics

SSMAL: similarity searching with alignment graphs, Pierre Nicodème (1998). Bioinformatics, vol. 14, no. 6, p. 508-515. Preliminary version: abstract | ps | pdf

Alignement avec des familles de séquences protéiques, Pierre Nicodème (1997). "Thèse universitaire", Université Paris VII. Defended on September 4, 1997. 184 pages. résumé | ps

Selecting Optimal Oligonucleotide Primers for Multiplex PCR, Pierre Nicodème and Jean-Marc Steyaert(1997). In: Proc. of Fifth Conference on Intelligent Systems for Molecular Biology ISMB97, p. 210-213. Preliminary version: abstract | ps | pdf

Compact Balanced Tries, Pierre Nicodème (1992). In: Proc. of IFIP Congress, Madrid, p. 477-483. Preliminary version: abstract | ps | pdf

Non-Refereed Publication List:

The Algorithms Project edits the proceedings of its bi-weekly research seminar. I contributed the following summaries.

Flajolet, P.: Analytic Urns. In: Algorithms Seminar, 2002-2004 (Avr. 2005), F. Chyzak, Ed., Research Report no. 5542, INRIA. p. 55-60.
Fayolle, J.: Suffix Trees and Simple Sources. In: Algorithms Seminar, 2002-2004 (Avr. 2005), F. Chyzak, Ed., Research Report no. 5542, INRIA. p. 65-70.
Durand, M.: A Probabilistic Counting Algorithm. In: Algorithms Seminar, 2002-2004 (Avr. 2005), F. Chyzak, Ed., Research Report no. 5542, INRIA. p. 93-96.
Dembo, A.: Cover Time and Favourite Points for Planar Random Walks. (With Christine Fricker.) In: Algorithms Seminar, 2000-2001 (Mar. 2002), F. Chyzak, Ed., Research Report no. 4406, INRIA. p. 121-126.
Banderier, C.: Classifying ECO-systems and random walks. In: Algorithms Seminar, 1999-2000 (Nov. 2000), F. Chyzak, Ed., Research Report no. 4056, INRIA. p. 35-38.
Bomboy, R.: Eigenring et réducibilité des équations aux différences finies. (With Frédéric Chyzak.) In: Algorithms Seminar, 1999-2000 (Nov. 2000), F. Chyzak, Ed., Research Report no. 4056, INRIA. p. 57-63.
Rivals, E.: Enumeration of Autocorrelations and Computation of Their Populations. In: Algorithms Seminar, 1999-2000 (Nov. 2000), F. Chyzak, Ed., Research Report no. 4056, INRIA. p. 115-118.
Lefebvre, F.: Grammaires et séquences biologiques. In: Algorithms Seminar, 1995-1996 (Sep. 1996), B. Salvy, Ed., Research Report no. 2992, INRIA. p. 23-28.
Gourdon, X.: Distance d'un point à une hypersurface algèbrique. In: Algorithms Seminar, 1995-1996 (Sep. 1996), B. Salvy, Ed., Research Report no. 2992, INRIA. p. 47-50.
Régnier, M.: Recherche de motifs : combinatoire et probabilités. In: Algorithms Seminar, 1995-1996 (Sep. 1996), B. Salvy, Ed., Research Report no. 2992, INRIA. p. 117-120.
Vallée, B.: The Gauss reduction algorithm. In: Algorithms Seminar, 1994-1995 (Oct. 1995), B. Salvy, Ed., Research Report no. 2669, INRIA. p. 87-90.
Flajolet, P.: Analytic Analysis of Algorithms. In: Algorithms Seminar, 1992-1993 (Dec. 1993), B. Salvy, Ed., Research Report no. 2130, INRIA. p. 115-120.
Golin, M.: Maxima in convex regions. In: Algorithms Seminar, 1991-1992 (Oct. 1992), P. Flajolet and P. Zimmermann, Ed., Research Report no. 1779, INRIA. p. 13-21.
Régnier, M.: Fast two dimensional pattern-matching In: P. Flajolet and P. Zimmermann, Ed., Research Report no. 1779, INRIA. p. 149-153.
Slides:
Counting occurrences for a finite set of words: an inclusion-exclusion approach, Pierre Nicodème, presented at ALEA07, Luminy, February 2007, joint work with Frédérique Bassino, Julien Clément and Julien Fayolle pdf
Average profiles, from tries to suffix-trees, Pierre Nicodème, presented in May 2006 at MIT; updated version of the Sep. 2005 talk at FU-Berlin, pdf
Motif statistics, Pierre Nicodème, joint work with Bruno Salvy and Philippe Flajolet (a slightly longer version of the ESA99 talk), presented in May 2006 at IWAP2006, Hartford, Connecticut, USA pdf
Motif statistics in the context of dynamical sources, Extract of a talk of Jeremie Bourdon and Brigitte Vallée (Latina, April 2006), presented in May 2006 at IWAP2006, Hartford, Connecticut, USA pdf
q-gram analysis and urn models, Pierre Nicodème (Sep. 2003) at Institut Henri Poincaré (Discrete Random Walks 2003): ps | pdf
Combinatorics and Biology, Pierre Nicodème (Sep. 2002) at FU Berlin (english version of the next item): ps | pdf
Combinatoire et Biologie, Pierre Nicodème (2002). Presented at a conference to secondary school teachers (Jan. 2002) at IHP: ps
Genomes comparison based on Motif statistics, Pierre Nicodème (2002). Presented at the workshop ALEA 2002: ps Shortened version of the next item.
Fast approximate motif statistics, Pierre Nicodème (2001). Presented at the seminar "Statistics and Genomes", Université d'Evry: ps
Statistics on words from Wojcech Szpankowski and Mireille Régnier, Pierre Nicodème (2001). Presented at the seminar of SSB (Versailles and Evry): ps
The symbolic package regexpcount, Pierre Nicodème (2000). Presented at the German Conference on Bioinformatics GCB'00 (Heidelberg): ps
Motif statistics, Pierre Nicodème (1999) (With Bruno Salvy and Philippe Flajolet.) Presented at ESA'99 (Prague): ps Shortened english version of the next item.
Statistiques de motifs, Pierre Nicodème (Feb. 1999) (With Bruno Salvy and Philippe Flajolet). Presented at the seminar of LRI-Orsay: ps

Publication List:

Non-Refereed Publication List:

Slides: