Macha Nikolski

28 papers A 2B 1Journal 21Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat.
Bioinform.
Florian Specque, Aurélien Barré, Macha Nikolski, Domitille Chalopin
2025 J jnl
TrialMatchAI: An End-to-End AI-powered Clinical Trial Recommendation System to Streamline Patient-to-Trial Matching.
CoRR
Majd Abdallah, Sigve Nakken, Mariska Bierkens, Johanna Galvis, Alexis Groppi, Slim Karkar, Lana Meiqari, Maria Alexandra Rujano, Steve Canham, Rodrigo Dienstmann, Remond J. A. Fijneman, Eivind Hovig, Gerrit Meijer, Macha Nikolski
2024 J jnl
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.
Bioinform.
Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn A. Grüning, Florian Specque, Hayssam Soueidan, Slim Karkar, Thomas Daubon, Macha Nikolski
2023 — conf
SalienceNet: An Unsupervised Image-to-Image Translation Method for Nuclei Saliency Enhancement in Microscopy Images.
BIOIMAGING
Emmanuel Bouilhol, Edgar Lefevre, Thierno Barry, Florian Levet, Anne Beghin, Virgile Viasnoff, Xareni Galindo, Rémi Galland, Jean-Baptiste Sibarita, Macha Nikolski
2022 J jnl
Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images.
Frontiers Bioinform.
Edgar Lefevre, Emmanuel Bouilhol, Antoine Chauvière, Wilfried Souleyreau, Marie-Alix Derieppe, Aurélien J. Trotier, Sylvain Miraux, Andreas Bikfalvi, Emeline J. Ribot, Macha Nikolski
2022 J jnl
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data.
Frontiers Bioinform.
Grigorii Sukhorukov, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais-Colombel, Macha Nikolski
2015 B conf
Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem.
SOFSEM
Thomas Hume, Hayssam Soueidan, Macha Nikolski, Guillaume Blin
2015 — conf
Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).
MedInfo
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
2015 J jnl
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform.
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
2014 J jnl
Further Steps in TANGO: improved taxonomic assignment in metagenomics.
Bioinform.
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
2013 J jnl
Finishing bacterial genome assemblies with Mix.
BMC Bioinform.
Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, Macha Nikolski
2013 J jnl
The family based variability in protein family expansion.
Int. J. Bioinform. Res. Appl.
Anasua Sarkar, Macha Nikolski, Pascal Durrens
2011 J jnl
Identification of conserved gene clusters in multiple genomes based on synteny and homology.
BMC Bioinform.
Anasua Sarkar, Hayssam Soueidan, Macha Nikolski
2011 J jnl
Minimum Information About a Simulation Experiment (MIASE).
PLoS Comput. Biol.
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
2011 J jnl
SyDiG: uncovering Synteny in Distant Genomes.
Int. J. Bioinform. Res. Appl.
Géraldine Jean, Macha Nikolski
2009 J jnl
Family relationships: should consensus reign? - consensus clustering for protein families.
Bioinform.
Macha Nikolski, David James Sherman
2009 — book
From Genomic to Functional models.
Macha Nikolski
2009 J jnl
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.
Nucleic Acids Res.
David James Sherman, Tiphaine C. Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens
2009 J jnl
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures.
J. Comput. Biol.
Géraldine Jean, David James Sherman, Macha Nikolski
2009 — conf
Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models.
CMSB
Hayssam Soueidan, Grégoire Sutre, Macha Nikolski
2009 A conf
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios.
GECCO
Nikolay Vyahhi, Adrien Goëffon, Macha Nikolski, David James Sherman
2008 A conf
An efficient probabilistic population-based descent for the median genome problem.
GECCO
Adrien Goëffon, Macha Nikolski, David James Sherman
2008 J jnl
Fusion and Fission of Genes Define a Metric between Fungal Genomes.
PLoS Comput. Biol.
Pascal Durrens, Macha Nikolski, David James Sherman
2007 J jnl
Family relationships: should consensus reign? - consensus clustering for protein families.
Bioinform.
Macha Nikolski, David James Sherman
2007 J jnl
Genome rearrangements: a correct algorithm for optimal capping.
Inf. Process. Lett.
Géraldine Jean, Macha Nikolski
2006 J jnl
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.
Nucleic Acids Res.
David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet
2005 J jnl
ProViz: protein interaction visualization and exploration.
Bioinform.
Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman
2004 J jnl
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.
Nucleic Acids Res.
David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski