Pierre Nicodème's Publications

Pierre Nicodème's Publications

Publication List:

Counting occurrences for a finite set of words: combinatorial methods, Frédérique Bassino, Julien Clément and Pierre Nicodème, ACM Transactions on Algorithms, vol.8 (3). #31. pp. 349-373. 2013, pdf

Constant time estimation of ranking statistics by analytic combinatorics, Cyril Banderier and Pierre Nicodème, abstract at SMPGD 2011 (Statistical Methods for Post-Genomic Data), Jan. 27-28, 2011, 4 pages , pdf

Bounded Discrete Walks, Cyril Banderier and Pierre Nicodème, DMTCS Proceedings of AofA2010, 21st International Meeting on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms, Vienna, Austria, June 28 - July 2, 2010, pages 35-48, pdf

Profile of Tries, Gahyun Park, Hsien-Kuei Hwang, Pierre Nicodème and Wojciech Szpankowski, SIAM Journal on Computing, 38, 5, 2009, pages 1821-1880, pdf

Constructions for Clump Statistics, Frédérique Bassino, Julien Clément, Julien Fayolle and Pierre Nicodème, DMTCS Proceedings of the Fifth Colloquium on Mathematics and Computer Science, Blaubeuren, September 2008, pages 183-198, pdf

Profile of Tries, Gahyun Park, Hsien-Kuei Hwang, Pierre Nicodème and Wojciech Szpankowski, Abstract in Proc. LATIN 2008, LNCS 4957, 1-11, 2008, pdf

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.