2. Saaidi, A., et al. An EM algorithm for mapping short reads in multiple RNA structure probing experiments. in {Matbio2017}. 2017. London, United Kingdom.

3. Becker, H.F., et al., High-Throughput Sequencing Reveals Circular Substrates for an Archaeal RNA ligase. {RNA Biology}, 2017. 14(8): p. 1075-1085.pdf

4. Régnier, M. and P. Chassignet, Accurate prediction of the statistics of repetitions in random sequences: a case study in Archaea genomes. Frontiers in Bioengineering and Biotechnology, 2016. 4: p. 35.online

5. Iakovishina, D., et al., SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Bioinformatics, 2016. 32(7): p. 984-992.PDF

6. Régnier, M., et al., Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models. Algorithms for Molecular Biology, 2014. 9: p. 25.

7. Régnier, M., B. Fang, and D. Iakovishina. Clump Combinatorics, Automata, and Word Asymptotics. in 2014 Proceedings of the Eleventh Workshop on Analytic Algorithmics and Combinatorics, {ANALCO} 2014, Portland, Oregon, USA, January 6, 2014. 2014. {SIAM}.

8. Bourdon, J. and M. Régnier, Large deviation properties for patterns. J. Discrete Algorithms, 2014. 24: p. 2-11.

9. Berillo, O., M. Regnier, and A. Ivashchenko, TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues. {Bioinformation}, 2014. 10(7): p. 472-473.

10. Berillo, O., M. Régnier, and A. Ivashchenko, Binding of intronic miRNAs to the mRNAs of host genes encoding intronic miRNAs and proteins that participate in tumourigenesis. Comp. in Bio. and Med., 2013. 43(10): p. 1374-1381.

11. Berillo, O., et al., Characteristics of binding sites of intergenic, intronic and exonic miRNAs with mRNAs of oncogenes coding intronic miRNAs. {African Journal of Biotechnology}, 2013. 12(10): p. 1016-1024.

12. Issabekova, A., et al., Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis. {Bioinformation}, 2012. 8(11): p. 513-518.

13. Saule, C., et al., Counting RNA Pseudoknotted Structures. Journal of Computational Biology, 2011. 18(10): p. 1339-1351.

14. Guais, A., et al., Toxicity of carbon dioxide: a review. Chem Res Toxicol, 2011. 24(12): p. 2061-70.

15. Saule, C., et al. Counting RNA pseudoknotted structures (extended abstract). in {22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010)}. 2010. San Francisco, United States: {Discrete Mathematics and Theoretical Computer Science}.

16. Regnier, M., et al., A Word Counting Graph, in {London Algorithmics 2008: Theory and Practice (Texts in Algorithmics)}, J.W.D. Joseph Chan and M.S. Rahman, Editors. 2009, {London College Publications}. p. 31.

17. Ivashchenko, A., et al., Using profiles based on hydropathy properties to define essential regions for splicing. {International Journal of Biological Sciences}, 2009. 5: p. 13-19.

18. Boeva, V., et al., Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms for Molecular Biology, 2007. 2.

19. Régnier, M. and M. Vandenbogaert, Comparison of Statistical Significance Criteria. J. Bioinformatics and Computational Biology, 2006. 4(2): p. 537-552.

20. Boeva, V., et al., Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics, 2006. 22(6): p. 676-684.

21. Tompa, M., et al., An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology, 2005. 23(1): p. 137 – 144.

22. Tahi, F., S. Engelen, and M. Régnier, P-dcfold or How to Predict all Kinds of Pseudoknots in RNA Secondary Structures. International Journal on Artificial Intelligence Tools, 2005. 14(5): p. 703-716.

23. Boeva, V., et al. Assessing the Significance of Sets of Words. in Combinatorial Pattern Matching, 16th Annual Symposium, {CPM} 2005, Jeju Island, Korea, June 19-22, 2005, Proceedings. 2005. Springer.

24. Régnier, M. and A. Denise, Rare Events and Conditional Events on Random Strings. Discrete Mathematics & Theoretical Computer Science, 2004. 6(2): p. 191-214.PDF

25. Régnier, M. Mathematical Tools for Regulatory Signals Extraction. in Bioinformatics of Genome Regulation and Structure. 2004. Kluwer Academic Publisher.

26. Lescot, M. and M. Régnier, Motif statistics on plants datasets. Biophysics, 2004. 48(1): p. 1–6.

27. Boeva, V., V. Makeev, and M. Régnier. SWAN: searching for highly divergent tandem repeats in DNA sequences and statistical significance. in JOBIM'04. 2004. Montréal: IEEE Computer Society.

28. Tahi, F., S. Engelen, and M. Régnier. A Fast Algorithm for RNA Secondary Structure Prediction Including Pseudoknots. in 3rd {IEEE} International Symposium on BioInformatics and BioEngineering {(BIBE} 2003), 10-12 March 2003, Bethesda, MD, {USA}. 2003. {IEEE} Computer Society.

29. Tahi, F., M. Gouy, and M. Régnier, Automatic RNA Secondary Structure Prediction with a Comparative Approach. Computers & Chemistry, 2002. 26(5): p. 521-530.

30. Papatsenko, D.A., et al., Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila/ Early Developmental Enhancers. Genome Research, 2002. 12(3): p. 470-481.

31. Lifanov, A., et al. Binding sites for transcription factors: what can tell an isolated segment of regulatory DNA? in BGRS’02. 2002. Novossibirsk.

32. Denise, A., M. Régnier, and M. Vandenbogaert. Assessing the Statistical Significance of Overrepresented Oligonucleotides. in Algorithms in Bioinformatics, First International Workshop, {WABI} 2001, Aarhus, Denmark, August 28-31, 2001, Proceedings. 2001. Springer-Verlag.

33. Régnier, M. and L. Mouchard. Periods and Quasiperiods Characterization. in Combinatorial Pattern Matching, 11th Annual Symposium, CPM 2000, Montreal, Canada, June 21-23, 2000, Proceedings. 2000.

34. Régnier, M., A. Lifanov, and V.J. Makeev. Three Variations on Word Counting. in Proceedings of the German Conference on Bioinformatics GCB 2000, Heidelberg, October 5-7, 2000. 2000. Logos-Verlag.

35. Régnier, M., A unified approach to word occurrence probabilities. Discrete Applied Mathematics, 2000. 104(1-3): p. 259-280.PDF

36. Régnier, M. Computational Complexity of Word Counting. in Computational Biology, First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000, Montpellier, France, May 3-5, 2000, Selected Papers. 2000. Springer.

37. Mahmoud, H.M., et al., Analytic Variations on Bucket Selection and Sorting. Acta Inf., 2000. 36(9/10): p. 735-760.

38. Hirschberg, D. and M. Régnier, Tight Bounds on the Number of String Subsequences. Journal of Discrete Algorithms, 2000. 1(1): p. 123-132.

39. Régnier, M. and W. Szpankowski. On the Approximate Pattern Occurrences in a Text. in Compression and Complexity of SEQUENCES 1997. 1998. IEEE Computer Society.

40. Régnier, M. and W. Szpankowski, On Pattern Frequency Occurrences in a Markovian Sequence. Algorithmica, 1998. 22(4): p. 631-649.

41. Régnier, M. and W. Szpankowski. Complexity of Sequential Pattern Matching Algorithms. in Randomization and Approximation Techniques in Computer Science, Second International Workshop, RANDOM'98, Barcelona, Spain, October 8-10, 1998, Proceedings. 1998. Springer.

42. Régnier, M. A unified approach to word statistics. in Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, RECOMB 1998, New York, NY, USA, March 22-25, 1998. 1998. ACM.

43. Régnier, M. and W. Szpankowski. On the Approximate Pattern Occurrences in a Text. in Compression and Complexity of SEQUENCES 1997. 1997.

44. Mahmoud, H.M., R.T. Smythe, and M. Régnier, Analysis of Boyer-Moore-Horspool string-matching heuristic. Random Struct. Algorithms, 1997. 10(1-2): p. 169-186.

45. Régnier, M. and L. Rostami. A Simple (but Optimal) 2D-Witness Algorithm. in Third South American Workshop on String Processing. 1996.

46. Régnier, M. and L. Rostami. A Unifying Look at d-Dimensional Periodicities and Space Coverings. in Combinatorial Pattern Matching, 4th Annual Symposium, {CPM} 93, Padova, Italy, June 2-4, 1993, Proceedings. 1993. Springer.

47. Fabret, F., M. Régnier, and E. Simon. An Adaptive Algorithm for Incremental Evaluation of Production Rules in Databases. in 19th International Conference on Very Large Data Bases, August 24-27, 1993, Dublin, Ireland, Proceedings. 1993. Morgan Kaufmann.

48. Baeza-Yates, R.A. and M. Régnier, Fast Two-Dimensional Pattern Matching. Inf. Process. Lett., 1993. 45(1): p. 51-57.

50. Régnier, M., Enumeration of bordered words. Le langage de la vache-qui-rit. {ITA}, 1992. 26: p. 303-318.pdf.

51. Régnier, M. A Language Approach to String Searching Evaluation. in Combinatorial Pattern Matching, Third Annual Symposium, CPM’92, Tucson, Arizona, USA, April 29 - May 1, 1992, Proceedings. 1992. Springer.

52. Fabret, F., M. Régnier, and E. Simon. Optimizing Incremental Computation of Datalog Programs with Non-deterministic Semantics. in Database Theory - ICDT'92, 4th International Conference, Berlin, Germany, October 14-16, 1992, Proceedings. 1992. Springer.

53. Baeza-Yates, R.A. and M. Régnier, Average Running Time of the Boyer-Moore-Horspool Algorithm. Theor. Comput. Sci., 1992. 92(1): p. 19-31.

54. Albert, L. and M. Régnier. Complexity of Recursive Production Rules Execution. in MFDBS 91, 3rd Symposium on Mathematical Fundamentals of Database and Knowledge Bases Systems, Rostock, Germany, May 6-9, 1991, Proceedings. 1991. Springer.

56. Baeza-, Y., Ricardo A. and M. Régnier. Fast Algorithms for Two Dimensional and Multiple Pattern Matching (Preliminary Version). in SWAT 90, 2nd Scandinavian Workshop on Algorithm Theory, Bergen, Norway, July 11-14, 1990, Proceedings. 1990. Springer.

58. Baeza-, Y., Ricardo A., G.H. Gonnet, and R\'e, gnier, Mireille. Analysis of Boyer-Moore-Type String Searching Algorithms. in Proceedings of the First Annual {ACM-SIAM} Symposium on Discrete Algorithms, 22-24 January 1990, San Francisco, California, {USA.}. 1990. {SIAM}.

59. Régnier, M. and E. Simon. Efficient evaluation of production rules in a DBMS. in Cinqui{\`{e}}mes Journ{\'{e}}es Bases de Donn{\'{e}}es Avanc{\'{e}}es, 26-28 Septembre 1989, Gen{\`{e}}ve, Suisse (Informal Proceedings). 1989.

60. Régnier, M. and P. Jacquet, New results on the size of tries. {IEEE} Trans. Information Theory, 1989. 35(1): p. 203-205.

61. Régnier, M., A Limiting Distribution for Quicksort. {ITA}, 1989. 23(3): p. 335-343.pdf.

62. Régnier, M. Knuth-Morris-Pratt Algorithm: An Analysis. in Mathematical Foundations of Computer Science 1989, MFCS'89, Porabka-Kozubnik, Poland, August 28 - September 1, 1989, Proceedings. 1989. Springer.pdf.

63. Luccio, F., M. Régnier, and R. Schott, ,. Discs and Other Related Data Structures. in Algorithms and Data Structures, Workshop {WADS} '89, Ottawa, Canada, August 17-19, 1989, Proceedings. 1989. Springer.

64. Régnier, M. Trie Hashing Analysis. in Proceedings of the Fourth International Conference on Data Engineering, February 1-5, 1988, Los Angeles, California, {USA}. 1988. Computer Society Press of IEEE.

65. Jacquet, P. and M. Régnier. Normal Limiting Distribution of the Size of Tries. in Performance '87, Proceedings of the 12th {IFIP} {WG} 7.3 International Symposium on Computer Performance Modelling, Measurement and Evaluation, Brussels, Belgium, 7-9 December 1987. 1987.pdf.

66. Jacquet, P. and M. Régnier. Trie Partitioning Process: Limiting Distributions. in CAAP'86, 11th Colloquium on Trees in Algebra and Programming, Nice, France, March 24-26, 1986, Proceedings. 1986. Springer.

67. Régnier, M., Analysis of Grid File Algorithms. {BIT}, 1985. 25(2): p. 335-357.

68. Flajolet, P., M. Régnier, and D. Sotteau, Algebraic Methods for trie statistics. #ADM#, 1985. 25: p. 145-188.

69. Flajolet, P., M. Régnier, and R. Sedgewick. Some Uses of the Mellin Integral Transform in the Analysis of Algorithms. in Combinatorial Algorithms on Words. 1985. Springer Verlag.

70. Régnier, M. Grid File Algorithms: An Analysis in the Biased Case. in Foundations of Software Technology and Theoretical Computer Science, Fourth Conference, Bangalore, India, December 13-15, 1984, Proceedings. 1984. Springer.

71. Régnier, M. Analyse de la taille de l'index du hachage dynamique sous des hypotheses poissoniennes. in CAAP'82. 1982. Lille: Springer Verlag.

72. Régnier, M. Linear Hashing with Groups of Reorganization: An Algorithms for Files without History. in {JCDKB}. 1982. Jerusalem.

73. Régnier, M., On the Average Height of Trees in Digital Search and Dynamic Hashing. Inf. Process. Lett., 1981. 13(2): p. 64-66.