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Computational Biology and Bioinformatics, IBGC - CNRS

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Scopus Author ID: 6506606989
Loop profile: 70776

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Works (31)

Mobilization of an ICEclc-Like Element as a Potential Mechanism for the Spread of IMP-13 Carbapenemase in Pseudomonas aeruginosa

Journal of Global Antimicrobial Resistance
2025-03 | Journal article
DOI: 10.1016/j.jgar.2024.12.006
Contributors: Léa Bientz; Ulysse Guyet; Jennifer Guiraud; Mathieu Metifiot; Mikeldi Moulieras; Sabine Aillerie; Laure Coulange-Mayonnove; Bachir Boureima-Abdou; Alexis Groppi; Macha Nikolski et al.
Source: check_circle
Crossref

SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat

2024-12-17 | Preprint
DOI: 10.1101/2024.12.16.628691
Contributors: Florian Specque; Aurélien Barré; Macha Nikolski; Domitille Chalopin
Source: check_circle
Crossref

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data

Bioinformatics
2024-05-02 | Journal article
DOI: 10.1093/bioinformatics/btae282
Contributors: Johanna Galvis; Joris Guyon; Benjamin Dartigues; Helge Hecht; Björn Grüning; Florian Specque; Hayssam Soueidan; Slim Karkar; Thomas Daubon; Macha Nikolski et al.
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Crossref

Roadmap for a European cancer data management and precision medicine infrastructure

Nature Cancer
2024-02-06 | Journal article
DOI: 10.1038/s43018-023-00717-6
Contributors: Macha Nikolski; Eivind Hovig; Fatima Al-Shahrour; Niklas Blomberg; Serena Scollen; Alfonso Valencia; Gary Saunders
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Crossref

Synthesis of Flavonol-Bearing Probes for Chemoproteomic and Bioinformatic Analyses of Asteraceae Petals in Search of Novel Flavonoid Enzymes

International Journal of Molecular Sciences
2023-06-03 | Journal article
DOI: 10.3390/ijms24119724
Contributors: Karl Kempf; Oxana Kempf; Yoan Capello; Christian Molitor; Claire Lescoat; Rana Melhem; Stéphane Chaignepain; Elisabeth Génot; Alexis Groppi; Macha Nikolski et al.
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Crossref
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Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis

EMBO Molecular Medicine
2022 | Journal article
DOI: 10.15252/emmm.202115343
HAL: hal-03827725
Contributors: Joris Guyon; Ignacio Fernandez-Moncada; Claire Larrieu; Cyrielle Bouchez; Antonio Pagano Zottola; Johanna Galvis; Tiffanie Chouleur; Audrey Burban; Kevin Joseph; Vidhya Ravi et al.
Source: Self-asserted source
Macha Nikolski via HAL

SalienceNet: an unsupervised Image-to-Image translation method for nuclei saliency enhancement in microscopy images

2022-11-25 | Working paper
DOI: 10.1101/2022.10.27.514030
HAL: hal-03872294
Contributors: Bouilhol Emmanuel; Edgar Lefevre; Thierno Barry; Florian Levet; Anne Beghin; Virgile Viasnoff; Xareni Galindo; Rémi Galland; Jean-Baptiste Sibarita; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

Genetic and epigenetic interplay allows rapid transgenerational adaption to metal pollution in zebrafish

Environmental Epigenetics
2022-10-22 | Journal article
DOI: 10.1093/eep/dvac022
DOI: 10.1093/eep/dvac022
HAL: hal-03832262
Contributors: Fabien Pierron; Débora Heroin; Guillemine Daffe; Flore Daramy; Aurélien Barré; Olivier Bouchez; Alicia Romero-Ramirez; Patrice Gonzalez; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

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

Frontiers in Bioinformatics
2022-10-12 | Journal article
DOI: 10.3389/fbinf.2022.999700
DOI: 10.3389/fbinf.2022.999700
HAL: hal-03821458
Contributors: Edgar Lefevre; Emmanuel Bouilhol; Antoine Chauvière; Wilfried Souleyreau; Marie-Alix Derieppe; Aurélien Trotier; Sylvain Miraux; Andreas Bikfalvi; Emeline Ribot; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

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

Frontiers in Bioinformatics
2022-05-13 | Journal article
DOI: 10.3389/fbinf.2022.867111
DOI: 10.3389/fbinf.2022.867111
HAL: hal-03671482
PMID: 36304258
Contributors: Grigorii Sukhorukov; Maryam Khalili; Olivier Gascuel; Thierry Candresse; Armelle Marais; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images

Biological Imaging
2022-04-19 | Journal article
DOI: 10.1017/S2633903X22000034
HAL: hal-03659677
Contributors: Emmanuel Bouilhol; Anca Flavia Savulescu; Edgar Lefevre; Benjamin Dartigues; Robyn Brackin; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

Experimental and computational modeling for signature and biomarker discovery of renal cell carcinoma progression

Molecular Cancer
2021-12 | Journal article
DOI: 10.1186/s12943-021-01416-5
HAL: hal-03390517
PMC: PMC8527701
PMC: PMC8527701
Contributors: Lindsay Cooley; Justine Rudewicz; Wilfried Souleyreau; Andrea Emanuelli; Arturo Alvarez-Arenas; Kim Clarke; Francesco Falciani; Maeva Dufies; Diether Lambrechts; Elodie Modave et al.
Source: Self-asserted source
Macha Nikolski via HAL

Baseline co-medications may alter the anti-tumoural effect of checkpoint inhibitors as well as the risk of immune-related adverse events

European Journal of Cancer
2021-11 | Journal article
DOI: 10.1016/j.ejca.2021.08.036
Contributors: Marie Kostine; Eleonora Mauric; Alice Tison; Thomas Barnetche; Aurélien Barre; Macha Nikolski; Léa Rouxel; Caroline Dutriaux; Léa Dousset; Sorilla Prey et al.
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Crossref
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Prediction of RNA subcellular localization: learning from heterogeneous data sources

iScience
2021-10 | Journal article
DOI: 10.1016/j.isci.2021.103298
HAL: hal-03388153
PMC: PMC8571491
PMC: PMC8571491
Contributors: Anca Flavia Savulescu; Emmanuel Bouilhol; Nicolas Beaume; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via HAL

Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH

Cell Reports Methods
2021-09 | Journal article
DOI: 10.1016/j.crmeth.2021.100068
HAL: hal-03349483
PMC: PMC9017151
PMID: 35474672
PMC: PMC9017151
Contributors: Anca Savulescu; Robyn Brackin; Emmanuel Bouilhol; Benjamin Dartigues; Jonathan Warrell; Mafalda Pimentel; Nicolas Beaume; Isabela Fortunato; Stephane Dallongeville; Mikaël Boulle et al.
Source: Self-asserted source
Macha Nikolski via HAL

Population genomics of apricots unravels domestication history and adaptive events

Nature Communications
2021-06-25 | Journal article
DOI: 10.1038/s41467-021-24283-6
DOI: 10.1038/s41467-021-24283-6
HAL: hal-03282504
PMID: 34172741
Contributors: Alexis Groppi; Shuo Liu; A. Cornille; David Tricon; Quynh Trang Bui; Corinne Cruaud; Sandrine Arribat; Caroline Belser; William Marande; Jérôme Salse et al.
Source: Self-asserted source
Macha Nikolski via HAL

Antibodies against HLA cross-reactivity groups: From single antigen bead assay to immunoinformatics interpretation of epitopes

Molecular Immunology
2021-05 | Journal article
DOI: 10.1016/j.molimm.2021.02.020
HAL: hal-03169872
Contributors: Cédric Usureau; Edgar Lefèvre; Isabelle Top; Macha Nikolski; Pauline Varlet; Gabriel Choukroun; Judith Desoutter; Nicolas Guillaume
Source: Self-asserted source
Macha Nikolski via HAL

FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins

Scientific Reports
2020-11-17 | Journal article
DOI: 10.1038/s41598-020-75814-y
HAL: hal-03010357
Contributors: Matthieu Lagardère; Ingrid Chamma; Emmanuel Bouilhol; Macha Nikolski; Olivier Thoumine
Source: Self-asserted source
Macha Nikolski via HAL

ELA/APELA precursor cleaved by furin displays tumor suppressor function in renal cell carcinoma through mTORC1 activation

JCI Insight
2020-07-23 | Journal article
DOI: 10.1172/jci.insight.129070
DOI: 10.1172/jci.insight.129070
HAL: hal-03084443
Contributors: Fabienne Soulet; Clément Bodineau; Katarzyna Hooks B.; Jean Descarpentrie; Isabel D. Alves; Marielle Dubreuil; Amandine Mouchard; Malaurie Eugenie; Jean-Luc Hoepffner; José‑juan Lopez‑rubio et al.
Source: Self-asserted source
Macha Nikolski via HAL

A community effort to create standards for evaluating tumor subclonal reconstruction

Nature Biotechnology
2020-01 | Journal article
DOI: 10.1038/s41587-019-0364-z
DOI: 10.1038/s41587-019-0364-z
HAL: hal-02438695
Contributors: Adriana Salcedo; Maxime Tarabichi; Shadrielle Melijah G. Espiritu; Amit Deshwar; Matei David; Nathan Wilson; Stefan Dentro; Jeff Wintersinger; Lydia Liu; Minjeong Ko et al.
Source: Self-asserted source
Macha Nikolski via HAL

The invasive proteome of glioblastoma revealed by laser-capture microdissection

Neuro-Oncology Advances
2019 | Journal article
DOI: 10.1093/noajnl/vdz029
DOI: 10.1093/noajnl/vdz029
HAL: hal-02347439
Contributors: Thomas Daubon; Joris Guyon; Anne-Aurélie Raymond; Benjamin Dartigues; Justine Rudewicz; Zakaria Ezzoukhry; Jean-William Dupuy; John Herbert; Frédéric Saltel; Rolf Bjerkvig et al.
Source: Self-asserted source
Macha Nikolski via HAL

Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn’s-Like Microbiota Disturbances

Journal of Clinical Medicine
2019-05 | Journal article | Author
DOI: 10.3390/jcm8050645
Contributors: Raphaël Enaud; Katarzyna B. Hooks; Aurélien Barre; Thomas Barnetche; Christophe Hubert; Marie Massot; Thomas Bazin; Haude Clouzeau; Bui Stephanie; Michael Fayon et al.
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Multidisciplinary Digital Publishing Institute
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Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures

Life Science Alliance
2018-10-30 | Journal article
HAL: hal-01944573
Contributors: Anaïs Soula; Mélissa Valere; María-José López-González; Vicky Ury-Thiery; Alexis Groppi; Marc Landry; Macha Nikolski; Alexandre Favereaux
Source: Self-asserted source
Macha Nikolski via HAL

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study

Scientific reports
2018-04-03 | Journal article
DOI: 10.1038/s41598-018-23571-4
DNB: 1160228132
URN: urn:nbn:de:1111-201805288852
Contributors: Thomas Bazin; Katarzyna B. Hooks; Thomas Barnetche; Marie-Elise Truchetet; Raphaël Enaud; Christophe Richez; Maxime Dougados; Christophe Hubert; Aurélien Barré; Macha Nikolski et al.
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)
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A Peptide Targeting Inflammatory CNS Lesions in the EAE Rat Model of Multiple Sclerosis

Inflammation
2018-03-07 | Journal article
DOI: 10.1007/s10753-018-0748-0
DNB: 1159454531
URN: urn:nbn:de:1111-2018051212074
Contributors: Claudine Boiziau; Macha Nikolski; Elodie Mordelet; Justine Aussudre; Karina Vargas-Sanchez; Klaus G. Petry
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)
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Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk

Hepatology
2017 | Journal article
DOI: 10.1002/hep.29336
HAL: hal-01550711
Contributors: E Henriet; Aa Hammoud; Jw Dupuy; B Dartigues; Z Ezzoukry; N Dugot-Senant; T Leste-Lasserre; N Pallares-Lupon; M Nikolski; B Le Bail et al.
Source: Self-asserted source
Macha Nikolski via HAL

Data standards can boost metabolomics research, and if there is a will, there is a way

Metabolomics
2015-11-17 | Journal article
DOI: 10.1007/s11306-015-0879-3
DNB: 1112888233
URN: urn:nbn:de:1111-2016090410204
Contributors: Philippe Rocca-Serra; Reza Salek; Masanori Arita; Elon Correa; Saravanan Dayalan; Alejandra González-Beltrán; Tim Ebbels; Royston Goodacre; Janna Hastings; Kenneth Haug et al.
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Metabolomics
2015-05-26 | Journal article
DOI: 10.1007/s11306-015-0810-y
DNB: 1137755407
URN: urn:nbn:de:1111-2017080413849
Contributors: Reza Salek; Steffen Neumann; Daniel Schober; Jan Hummel; Kenny Billiau; Joachim Kopka; Elon Correa; Theo Reijmers; Antonio Rosato; Leonardo Tenori et al.
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)

Finishing bacterial genome assemblies with Mix

BMC bioinformatics
2013-10-15 | Journal article
DOI: 10.1186/1471-2105-14-S15-S16
DNB: 1082815837
URN: urn:nbn:de:1111-2016021742806
Contributors: Hayssam Soueidan; Florence Maurier; Alexis Groppi; Pascal Sirand-Pugnet; Florence Tardy; Christine Citti; Virginie Dupuy; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)

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

BMC bioinformatics
2011-10-05 | Journal article
DOI: 10.1186/1471-2105-12-S9-S18
DNB: 108279323X
URN: urn:nbn:de:1111-2016021732212
Contributors: Anasua Sarkar; Hayssam Soueidan; Macha Nikolski
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

BMC plant biology
2011-06-13 | Journal article
DOI: 10.1186/1471-2229-11-104
DNB: 1096474662
URN: urn:nbn:de:1111-2016041421192
Contributors: Hélène Ferry-Dumazet; Laurent Gil; Catherine Deborde; Annick Moing; Stéphane Bernillon; Dominique Rolin; Macha Nikolski; Antoine de Daruvar; Daniel Jacob
Source: Self-asserted source
Macha Nikolski via Deutsche Nationalbibliothek (DNB)
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