Macha Nikolski

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 3

Top Topics

Microscopy Images

Phase Contrast Images

Metabolic Pathways

Top Venues

Frontiers Bioinform.

Publications

Emmanuel Bouilhol, Edgar Lefevre, Thierno Barry, Florian Levet, Anne Beghin, Virgile Viasnoff, Xareni Galindo, Rémi Galland, Jean-Baptiste Sibarita, Macha Nikolski
SalienceNet: An Unsupervised Image-to-Image Translation Method for Nuclei Saliency Enhancement in Microscopy Images. BIOIMAGING (2023)
Edgar Lefevre, Emmanuel Bouilhol, Antoine Chauvière, Wilfried Souleyreau, Marie-Alix Derieppe, Aurélien J. Trotier, Sylvain Miraux, Andreas Bikfalvi, Emeline J. Ribot, Macha Nikolski
Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images. Frontiers Bioinform. 2 (2022)
Grigorii Sukhorukov, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais-Colombel, Macha Nikolski
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data. Frontiers Bioinform. 2 (2022)
Anita Burgun, Dina V. Oksen, Wolfgang Kuchinke, Hans-Ulrich Prokosch, Thomas Ganslandt, Iain E. Buchan, Tjeerd Pieter van Staa, James A. Cunningham, Marianne L. Gjerstorff, Jean-Charles Dufour, Jean-François Gibrat, Macha Nikolski, Pierre Verger, Anne Cambon-Thomsen, Cristina Masella, Emanuele Lettieri, Paolo Bertele, Marjut Salokannel, Rodolphe Thiébaut, Charles Persoz, Geneviève Chêne, Christian Ohmann
Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA). MedInfo (2015)
Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 31 (19) (2015)
Thomas Hume, Hayssam Soueidan, Macha Nikolski, Guillaume Blin
Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem. SOFSEM (2015)
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinform. 30 (1) (2014)
Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, Macha Nikolski
Finishing bacterial genome assemblies with Mix. BMC Bioinform. 14 (S-15) (2013)
Anasua Sarkar, Macha Nikolski, Pascal Durrens
The family based variability in protein family expansion. Int. J. Bioinform. Res. Appl. 9 (2) (2013)
Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7 (4) (2011)
Géraldine Jean, Macha Nikolski
SyDiG: uncovering Synteny in Distant Genomes. Int. J. Bioinform. Res. Appl. 7 (1) (2011)
Anasua Sarkar, Hayssam Soueidan, Macha Nikolski
Identification of conserved gene clusters in multiple genomes based on synteny and homology. BMC Bioinform. 12 (S-9) (2011)
Hayssam Soueidan, Grégoire Sutre, Macha Nikolski
Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models. CMSB (2009)
Macha Nikolski, David James Sherman
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 25 (17) (2009)
Géraldine Jean, David James Sherman, Macha Nikolski
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. J. Comput. Biol. 16 (9) (2009)
Nikolay Vyahhi, Adrien Goëffon, Macha Nikolski, David James Sherman
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios. GECCO (2009)
David James Sherman, Tiphaine C. Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Pascal Durrens, Macha Nikolski, David James Sherman
Fusion and Fission of Genes Define a Metric between Fungal Genomes. PLoS Comput. Biol. 4 (10) (2008)
Adrien Goëffon, Macha Nikolski, David James Sherman
An efficient probabilistic population-based descent for the median genome problem. GECCO (2008)
Macha Nikolski, David James Sherman
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 23 (2) (2007)
Géraldine Jean, Macha Nikolski
Genome rearrangements: a correct algorithm for optimal capping. Inf. Process. Lett. 104 (1) (2007)
David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res. 34 (Database-Issue) (2006)
Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman
ProViz: protein interaction visualization and exploration. Bioinform. 21 (2) (2005)
David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res. 32 (Database-Issue) (2004)