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List of selected publications

Bioinformatics

G. Jean and M. Nikolski, SyDiG:Uncovering Synteny in Distant Genomes, International Journal of Bioinformatics Research and Application (IJBRA), vol. 7(1), pp. 43-62, 2011

H. Ferry-Dumazet, L. Gil, C. Deborde,A. Moing, S. Bernillon, D. Rolin, M. Nikolski, A. de Daruvar and D. Jacob, MeRy-B: a web knowledgebase for the storage, visualization,analysis and annotation of plant 1H-NMR metabolomic profiles. BMC Plant Biology 11:104, 2011

A. Sarkar and H. Soueidan and M. Nikolski, Identification of conserved gene clusters in multiple genomes based on synteny and homology, BMC Bioinformatics, vol 12 (Suppl 9), S18, 2011

A. Sarkar, U. Maulik and M. Nikolski, Spectral clustering on neighborhood kernels with modified symmetry for remote homology detection, proceedings of EAIT Second International Conference on Emerging Applications of Information Technology, pp. 269-272, 2011

D. Waltemath, R. Adams, D. Beard, F. Bergmann, U. Bhalla, R. Britten, V. Chelliah, M. Cooling, J. Cooper,E. Crampin, A. Garny, S. Hoops,M. Hucka, P. Hunter, E. Klipp,C. Laibe, A. Miller, I. Moraru,D. Nickerson, P. Nielsen, M. Nikolski,S. Sahle, H. Sauro, H. Schmidt,J. Snoep, D. Tolle, O. Wolkenhauer, N. LeNovere, Minimum Information About a Simulation Experiment (MIASE), PLoS Computational Biology, vol. 7 (4), 2011, e1001122. doi:10.1371/journal.pcbi.1001122

H. Soueidan, G. Sutre and M. Nikolski, Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models, CMSB'09, Lecture Notes in Computer Science 5688 (ISBN 978-3-642-03844-0), pp. 313--327

The Genolevures Consortium, Comparative genomics of Protoploid Saccharomycetaceae , Genome Research, 2009 Oct;19(10):1696-709. Epub 2009 Jun 12.

G. Jean, D. Sherman and M. Nikolski, Mining the semantics of genome super-blocks to infer ancestral architectures, Journal of Computational Biology, 2009 Sep;16(9):1267-84.

N. Vyahhi, A. Goeffon, M. Nikolski and D. Sherman, Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios, GECCO 2009, pp 241-246 , ISBN:978-1-60558-325-9

D. Sherman, David, T. Martin, M. Nikolski, C. Cayla, J.L. Souciet and P. Durrens, Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes, Nucleic Acids Researc 2009, Vol. 37, Database issue D550-D554

M. Cvijovic, H. Soueidan, D. Sherman, E. Klipp and M. Nikolski, Exploratory Simulation of Cell Ageing Using Hierarchical Models, Proceedings of GIW 2008, Genome Informatics vol. 21, pp. 114-125, 2008

P. Durrens, M. Nikolski and D. Sherman, Fusion and Fission of Genes Define a Metric between Fungal Genomes, Plos Computational Biology, 4(10) 2008: e1000200 doi:10.1371/journal.pcbi.1000200

A. Goeffon, M. Nikolski and D. Sherman, An Efficient Probabilistic Population-Based Descent for the Median Gen\ ome Problem, Proceedings of GECCO 2008 (ISBN:978-1-60558-130-9), pp. 315-322

G. Jean and M. Nikolski, Genome rearrangements: a correct algorithm for optimal capping, Information Processing Letters, 2007, vol. 104(1), pp. 14-20

F. Iragne, M. Nikolski and D. Sherman, Extrapolation of metabolic pathways as an aid to modelling completely sequenced non-Saccharomyces yeasts, FEMS Yeast Res. 2007.

M. Nikolski and D. Sherman, Family relationships: should consensus reign ? - consensus clustering for protein families, Bioinformatics 2007 23(2):e71-e76

H. Soueidan, D.J. Sherman and M. Nikolski BioRica: A multi model description and simulation system, Proceedings of the 2nd Foundations of Systems Biology in Engineering (FOSBE) 2007, pp. 279-287, Fraunhofer IRB Verlag, ISBN 978-3-8167-7436-5

D. Sherman, P. Durrens, E. Beyne, M. Nikolski and J.-L. Souciet, Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts, Nucleic Acids Research, 2006, 34(Database Issue), D432-D435

F. Iragne, M. Nikolski, B. Mathieu, D. Auber, and D. Sherman, ProViz: protein interaction visualization and exploration, Bioinformatics 2005, vol. 21: 272-274

Collective work, Genome Evolution in Yeasts, Nature, 2004, 430(6995), pp. 35-44, July

Collective work (authors list), The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data, Nature Biotechnology 2004 Feb, 22(2): 177-83

D. Sherman, P. Durrens, E. Beyne, M. Nikolski, and J.-L. Souciet, G?nolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts, Nucleic Acids Res. 2004 January 1, 32 (Database issue): D315-D318

M. Nikolskaia Timed automata vs. hybrid systems for gene regulation. Jobim 2001.

BDDs and formal verification papers

M. Nikolskaia and L. Nikolskaia. Size of OBDD representation of 2-level redundancies functions. Theoretical Computer Science, 255(1-2):615-625, 2001.

M. Nikolskaia, A. Rauzy, P. Williams. Bypassing BDD construction for reliability analysis. Information Processing Letters, 75(1-2):85-89, 2000.

M. Nikolskaia and A. Rauzy. Heuristics for BDD handling of sum-of-products formulae. In Balkema, editor, Proceedings of the European Safety and Reliability Association Conference, ESREL'98, Trondheim, June 1998.

M. Nikolskaia, A. Rauzy, and D. J. Sherman. Almana: A BDD minimization tool integrating heuristic and rewriting methods. In Ganesh Gopalakrishnan and Phillip Windley, editors, Formal Methods in Computer-Aided Design, Second International Conference, FMCAD'98, Palo Alto, California, November 1998. Springer-Verlag LNCS 1522.

M. Nikolskaia and A. Rauzy. Fine-tuning of boolean formulae preprocessing techniques. In Balkema, editor, Proceedings of the European Safety and Reliability Association Conference, ESREL'99, Munich, September 1999.

M. Nikolskaia. A systematic study of heuristic analysis. In Proc. of Mathematical Methods in Reliability Conference, MMR 2000, pages 203-206, 2000

M. Nikolskaia and A. Rauzy Application des Diagrammes Binaires d'Expression au Traitement d'Arbres de D?faillance In Proc. Lambda-Mu 2000, pages 363-367, 2000

M. Nikolskaia. Experimental results on the size of OBDD representation of 2-level redundancies functions. LaBRI Technical Report 1208-98.

M. Nikolskaia and D. Sherman. Editable DAG (eDAG) Specification. LaBRI Technical Report 1198-97.

Misc

M. Nikolskaia, D. Sherman and P. Williams. Unifying Two Formula Rewriting Techniques for Circuit Verification and Risk Assessment. Tech. Report TR-1293-03, LaBRI, University of Bordeaux-1, 2001.