Nombre de documents

54

CV de Macha Nikolski


Communication dans un congrès21 documents

  • Thomas Hume, Hayssam Soueidan, Macha Nikolski, Guillaume Blin. Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem. Giuseppe F. Italiano. 41st International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM'15), Jan 2015, Pec pod Sněžkou, Czech Republic. LNCS, 8939, pp. 242-253, 2015. <hal-01056406>
  • Thomas Barnetche, Christophe Hubert, Aurélien Barré, Christophe Richez, Emilie Shipley, et al..  Identification and Characterization of A Synovial Fluid Microbial DNA in Rheumatoid Arthritis Patients. Annual European Congress of Rheumatology, Jun 2014, Paris, France. <10.1136/annrheumdis-2014-eular.4999>. <hal-01208393>
  • Thomas Hume, Hayssam Soueidan, Fabienne Wong Jun Tai, Antoine Vekris, Klaus Petry, et al.. Efficient mapping of short peptides on whole proteome database for biomarker discovery. JOBIM 2013, Jul 2013, France. <hal-00970511>
  • Anasua Sarkar, Macha Nikolski, Ujjwal Maulik. Spectral Clustering on Neighborhood Kernels with Modified Symmetry for Remote Homology Detection. International Conference on Emerging Applications of Information Technology, Feb 2011, India. pp.269-272, 2011, <10.1109/EAIT.2011.81>. <hal-00738255>
  • Hayssam Soueidan, Grégoire Sutre, Macha Nikolski. Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models. 21. Computational Methods in Systems Biology (CMSB'09), 2009, Bologna, Italy. Springer Verlag, 5688, pp.313--327, 2009, Lecture notes in BioInformatics. <hal-00408909>
  • Tiphaine Martin, Macha Nikolski, David James Sherman, Jean-Luc Souciet, Pascal Durrens. The Génolevures online database. Second German/ French/European/ Meeting Yeast and Filamentous Fungi, May 2009, Strasbourg, France. 2009. <inria-00409534>
  • Nikolay Vyahhi, Adrien Goëffon, David James Sherman, Macha Nikolski. Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios. Franz Rothlauf. ACM SIGEVO Conference on Genetic and evolutionary computation, 2009, Montréal, Canada. ACM, 2009. <inria-00407508>
  • Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens. The Génolevures website comparative genomic studies on hemiascomycetous yeasts. Comparative Genomics of Eukaryotic Microorganisms 2009, Oct 2009, San Feliu de Guixols, Spain. 2009. <inria-00524390>
  • Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens. Base de données Génolevures : génomique comparative des Hemiascomycetes. Eric Rivals and Irena Rusu. Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182, 2009. <inria-00401915>
  • Macha Nikolski. Mining the semantics of of genome super-blocks. 3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia. 2008. <inria-00350572>
  • Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, et al.. The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeasts. First German/French/European/ Meeting Yeast and Filamentous Fungi, May 2008, Strasbourg, France. 2008. <inria-00407631>
  • Adrien Goëffon, Macha Nikolski, David James Sherman. An Efficient Probabilistic Population-Based Descent for the Median Genome Problem. GECCO: Genetic And Evolutionary Computation Conference, Aug 2008, Atlanta, United States. ACM, pp.315-322, 2008. <hal-00341672>
  • Hayssam Soueidan, David James Sherman, Macha Nikolski. BioRica: A multi model description and simulation system. F0SBE, 2007, Germany. pp.279-287, 2007. <hal-00306550>
  • Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, et al.. The Génolevures online database. J.Micheal Cherry and Ian G. Macreadie. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. 24, pp.S135, 2007, Number S1; Yeast. <inria-00401921>
  • Pascal Durrens, Macha Nikolski, David James Sherman. Gene fusion and fission events in fungus genomes. 23rd international conference on yeast genetics and molecular biology, Jul 2007, Melbourne, Australia. Wiley, 24-S1, pp.S132, 2007, Yeast. <inria-00402220>
  • Géraldine Jean, David James Sherman, Macha Nikolski. Reconstruction and visualization of genome rearrangements within the Kuyveromyces. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Oct 2007, San Feliu de Guixols, Spain. pp.44, 2007. <inria-00350567>
  • Pascal Durrens, Macha Nikolski, David James Sherman. Gene Fusion and Fission Events in Fungal Genomes. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S132, 2007. <inria-00352592>
  • Hayssam Soueidan, Macha Nikolski, Grégoire Sutre. Model Checking AllTL Properties for Set Automata. MOVEP, 2006, Bordeaux, France. pp.203-209, 2006. <hal-00407478>
  • Aurélien Barré, Vincent Jouffe, Macha Nikolski, Antoine De Daruvar, Alain Blanchard, et al.. Annotation transfer based on orthology relationships: reannotation of mycoplasma genomes from the Pneumoniae group. JOBIM, Jul 2006, Bordeaux, France. 2006. <inria-00407480>
  • Macha Nikolski. Protein families within Hemiascomycetes. Yeast Genome 10th Anniversary, Sep 2006, Brussels, Belgium. 2006. <inria-00407496>
  • Macha Nikolski, Pascal Ferraro, Pascal Durrens, Michel Aigle. Saccharomyces Siliceus. First International Workshop on Systems Biology of Yeast, Nov 2003, United States. pp.électronique, 2003. <hal-00307128>

Autre publication1 document

  • Macha Nikolski. Consensus clustering for protein families. Invited seminar at Saint Petersburg State University, Saint Petersburg, Russia. 2006. <inria-00407494>

Article dans une revue29 documents

  • Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, et al.. MICADo - Looking for mutations in targeted PacBio cancer data: an alignment-free method. Frontiers in Genetics, Frontiers, 2016, <10.3389/fgene.2016.00214>. <hal-01409750>
  • Eric Dausse, Aurélien Barré, Aimé Ahissan, Alexis Groppi, Alain Rico, et al.. Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation. Biosensors and Bioelectronics, Elsevier, 2016. <hal-01269677>
  • Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus Dittrich, et al.. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, Oxford University Press (OUP), 2015, 31 (19), <10.1093/bioinformatics/btv316>. <hal-01248545>
  • Nathalie Quenel-Tueux, Marc Debled, Justine Rudewicz, Gaetan Macgrogan, Marina Pulido, et al.. Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated for large operable or locally advanced hormone-receptor-positive breast cancer.. British Journal of Cancer, Cancer Research UK, 2015, pp.bjc.2015.247. <10.1038/bjc.2015.247>. <hal-01180992>
  • Hayssam Soueidan, Louise-Amélie Schmitt, Thierry Candresse, Macha Nikolski. Finding and identifying the viral needle in the metagenomic haystack: Trends and Challenges. Frontiers in microbiology, Frontiers Research Foundation, 2014, pp.5:739. <10.3389/fmicb.2014.00739>. <hal-01100888>
  • Macha Nikolski, Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, et al.. Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinformatics, Oxford University Press (OUP), 2013, pp.10.1093/bioinformatics/btt256. <10.1093/bioinformatics/btt256>. <hal-00848263>
  • Anasua Sarkar, Macha Nikolski, Pascal Durrens. The family based variability in protein family expansion.. International Journal of Bioinformatics Research and Applications, Inderscience, 2013, 9 (2), pp.121-33. <http://inderscience.metapress.com/content/nr688l207137g0q3/fulltext.pdf>. <10.1504/IJBRA.2013.052473>. <hal-00857374>
  • Lucía Manso-Silván, Florence Tardy, Eric Baranowski, Aurélien Barré, Alain Blanchard, et al.. Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle. Genome Announcements, American Society for Microbiology, 2013, 1 (3), pp.e00348-13. <10.1128/genomeA.00348-13>. <hal-00907454>
  • Virginie Dupuy, Pascal Sirand-Pugnet, Eric Baranowski, Aurélien Barré, Marc Breton, et al.. Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats. Genome Announcements, American Society for Microbiology, 2013, 1 (3), pp.e00354-13. <10.1128/genomeA.00354-13>. <hal-00907450>
  • Emilie Dordet-Frisoni, Eric Baranowski, Aurélien Barré, Alain Blanchard, Marc Breton, et al.. Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae. Genome Announcements, American Society for Microbiology, 2013, 1 (3), epub ahead of print. <10.1128/genomeA.00280-13>. <hal-00907449>
  • Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, et al.. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics, BioMed Central, 2013, pp.doi:10.1186/1471-2105-14-S15-S16. <hal-00879163>
  • Géraldine Jean, Macha Nikolski. SyDiG: uncovering Synteny in Distant Genomes. Int. J. of Bioinformatics Research and Applications, 2011, pp.43-62. <10.1504/IJBRA.2011.039169>. <hal-00737390>
  • Dagmar Waltemath, Richard Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, et al.. Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology, Public Library of Science, 2011, 7 (4), pp.e1001122. <10.1371/journal.pcbi.1001122>. <hal-00772491>
  • H. Ferry-Dumazet, L. Gil, C. Deborde, A. Moing, S. Bernillon, et al.. MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant 1H-NMR metabolomic profiles. BMC Plant Biology, BioMed Central, 2011, 11:104, pp.10.1186/1471-2229-11-104. <hal-00648167>
  • Hélène Ferry-Dumazet, Laurent Gil, Catherine Deborde, Annick Moing, Stéphane Bernillon, et al.. MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.. BMC Plant Biology, BioMed Central, 2011, 11, pp.104. <10.1186/1471-2229-11-104>. <hal-00645944>
  • Anasua Sarkar, Hayssam Soueidan, Macha Nikolski. Identification of conserved gene clusters in multiple genomes based on synteny and homology. BMC Bioinformatics, BioMed Central, 2011, 12, pp.S18. <10.1186/1471-2105-12-S9-S18>. <hal-00737346>
  • Jean-Luc Souciet, Bernard Dujon, Claude Gaillardin, Mark Johnston, Philippe V Baret, et al.. Comparative genomics of protoploid Saccharomycetaceae.. Genome Research, Cold Spring Harbor Laboratory Press, 2009, 19, pp.1696-1709. <10.1101/gr.091546.109>. <inria-00407511>
  • David James Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, et al.. Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2009, pp.D550-D554. <10.1093/nar/gkn859>. <inria-00341578>
  • Géraldine Jean, David James Sherman, Macha Nikolski. Mining the semantics of genome super-blocks to infer ancestral architectures. Journal of Computational Biology, Mary Ann Liebert, 2009, 16 (9), pp.1267-1284. <10.1089/cmb.2008.0046>. <inria-00414692>
  • Maria Cvijovic, Hayssam Soueidan, Edda Klipp, David James Sherman, Macha Nikolski. Exploratory Simulation of Cell Ageing Using Hierarchical Models. Genome Informatics, 2008, 21, pp.114--125. <hal-00407512>
  • Florian Iragne, Macha Nikolski, David James Sherman. Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts.. FEMS Yeast Research, Oxford University Press (OUP), 2008, 8 (1), pp.132-9. <10.1111/j.1567-1364.2007.00290.x>. <inria-00202723>
  • Pascal Durrens, Macha Nikolski, David James Sherman. Fusion and fission of genes define a metric between fungal genomes.. PLoS Computational Biology, Public Library of Science, 2008, 4 (10), pp.e1000200. <10.1371/journal.pcbi.1000200>. <inria-00341569>
  • Florian Iragne, Macha Nikolski, David Sherman. Extrapolation of metabolic pathways as an aid to modelling completely sequenced. FEMS Yeast Research, Oxford University Press (OUP), 2007, pp.132-139. <hal-00306592>
  • Géraldine Jean, Macha Nikolski. Genome rearrangements: a correct algorithm for optimal capping. Information Processing Letters, Elsevier, 2007, 104 (1), pp.14-20. <10.1016/j.ipl.2007.04.011>. <inria-00274291>
  • Macha Nikolski, David James Sherman. Family relationships: should consensus reign?- consensus clustering for protein families. Bioinformatics, Oxford University Press (OUP), 2007, 23, pp.e71--e76. <10.1093/bioinformatics/btl314>. <inria-00202434>
  • David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, et al.. Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2006, 34 (Database issue), pp.D432-5. <10.1093/nar/gkj160>. <hal-00118142>
  • Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman. ProViz: protein interaction visualization and exploration. Bioinformatics, Oxford University Press (OUP), 2005, 21 (2), pp.272-274. <10.1093/bioinformatics/bth494>. <inria-00202436>
  • Bernard Dujon, David Sherman, Gilles Fischer, Pascal Durrens, Serge Casaregola, et al.. Genome evolution in yeasts.. Nature, Nature Publishing Group, 2004, 430 (6995), pp.35-44. <10.1038/nature02579>. <hal-00104411>
  • David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet. Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2004, 32 (Database issue), pp.D315-8. <10.1093/nar/gkh091>. <inria-00407519>

Poster2 documents

  • Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Richard Iggo, Jonas Bergh, et al.. Looking for mutations in PacBio cancer data: an alignment-free method. JOBIM 2015, Jul 2015, Clermont-Ferrand, France. <hal-01254846>
  • Justine Rudewicz, Hayssam Soueidan, Audrey Gros, Gaetan Macgrogan, Hervé Bonnefoi, et al.. Bioinformatics methods for analyzing anti-hormonal treatment resistance in breast cancer. BCBB 2014 (Bordeaux Computational Biology and Bioinformatics), Nov 2014, Bordeaux, France. <hal-01120049>

HDR1 document

  • Macha Nikolski. From Genomic to Functional models. Computer Science [cs]. Université Sciences et Technologies - Bordeaux I, 2009. <tel-01086142>