Macha Nikolski

According to our database, Macha Nikolski authored at least 24 papers between 2004 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

SalienceNet: An Unsupervised Image-to-Image Translation Method for Nuclei Saliency Enhancement in Microscopy Images.

Emmanuel Bouilhol, Edgar Lefevre, Thierno Barry, Florian Levet, Anne Beghin, Virgile Viasnoff, Xareni Galindo, Rémi Galland, Jean-Baptiste Sibarita, Macha Nikolski

Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2023

2022

VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data.

Grigorii Sukhorukov, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais-Colombel, Macha Nikolski

Frontiers Bioinform., 2022

Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images.

Edgar Lefevre, Emmanuel Bouilhol, Antoine Chauvière, Wilfried Souleyreau, Marie-Alix Derieppe, Aurélien J. Trotier, Sylvain Miraux, Andreas Bikfalvi, Emeline J. Ribot, Macha Nikolski

Frontiers Bioinform., 2022

2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

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

Bioinform., 2015

Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem.

Thomas Hume, Hayssam Soueidan, Macha Nikolski, Guillaume Blin

Proceedings of the SOFSEM 2015: Theory and Practice of Computer Science, 2015

Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).

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

Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

2014

Further Steps in TANGO: improved taxonomic assignment in metagenomics.

Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente

Bioinform., 2014

2013

The family based variability in protein family expansion.

Anasua Sarkar, Macha Nikolski, Pascal Durrens

Int. J. Bioinform. Res. Appl., 2013

Finishing bacterial genome assemblies with Mix.

Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, Macha Nikolski

BMC Bioinform., 2013

2011

Minimum Information About a Simulation Experiment (MIASE).

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

PLoS Comput. Biol., 2011

SyDiG: uncovering Synteny in Distant Genomes.

Géraldine Jean, Macha Nikolski

Int. J. Bioinform. Res. Appl., 2011

Identification of conserved gene clusters in multiple genomes based on synteny and homology.

Anasua Sarkar, Hayssam Soueidan, Macha Nikolski

BMC Bioinform., 2011

2009

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

David James Sherman, Tiphaine C. Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens

Nucleic Acids Res., 2009

Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures.

Géraldine Jean, David James Sherman, Macha Nikolski

J. Comput. Biol., 2009

Swarming along the evolutionary branches sheds light on genome rearrangement scenarios.

Nikolay Vyahhi, Adrien Goëffon, Macha Nikolski, David James Sherman

Proceedings of the Genetic and Evolutionary Computation Conference, 2009

Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models.

Hayssam Soueidan, Grégoire Sutre, Macha Nikolski

Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

From Genomic to Functional models.

Macha Nikolski

, 2009

2008

Fusion and Fission of Genes Define a Metric between Fungal Genomes.

Pascal Durrens, Macha Nikolski, David James Sherman

PLoS Comput. Biol., 2008

An efficient probabilistic population-based descent for the median genome problem.

Adrien Goëffon, Macha Nikolski, David James Sherman

Proceedings of the Genetic and Evolutionary Computation Conference, 2008

2007

Genome rearrangements: a correct algorithm for optimal capping.

Géraldine Jean, Macha Nikolski

Inf. Process. Lett., 2007

Family relationships: should consensus reign? - consensus clustering for protein families.

Macha Nikolski, David James Sherman

Bioinform., 2007

2006

Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.

David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet

Nucleic Acids Res., 2006

2005

ProViz: protein interaction visualization and exploration.

Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman

Bioinform., 2005

2004

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski

Nucleic Acids Res., 2004