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Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS

 Remi Trimbour , Ina Maria Deutschmann , Laura Cantini
2023
Pré-publication, Document de travail hal-04237756v1
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Assessing reproducibility of matrix factorization methods in independent transcriptomes

 Laura Cantini , Ulykbek Kairov , Aurélien de Reyniès , Emmanuel Barillot , François Radvanyi , et al.
Bioinformatics, In press, ⟨10.1093/bioinformatics/btz225/5426054⟩
Article dans une revue hal-02095317v1
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Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

 Nicolas Sompairac , Petr V Nazarov , Urszula Czerwinska , Laura Cantini , Anne Biton , et al.
International Journal of Molecular Sciences, 2019, 20 (18), pp.4414. ⟨10.3390/ijms20184414⟩
Article dans une revue hal-02343412v1

Evaluating the reproducibility of single-cell gene regulatory network inference algorithms

 Yoonjee Kang , Denis Thieffry , Laura Cantini
2020
Pré-publication, Document de travail hal-03000601v1
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Interpreting pathways to discover cancer driver genes with Moonlight

 Antonio Colaprico , Catharina Olsen , Matthew Bailey , Gabriel Odom , Thilde Terkelsen , et al.
Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-019-13803-0⟩
Article dans une revue hal-03001026v1
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Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments

 Elisa Reale , Daniela Taverna , Laura Cantini , Loredana Martignetti , Matteo Osella , et al.
Epigenomics, 2019, 11 (14), pp.1581-1599. ⟨10.2217/epi-2019-0050⟩
Article dans une revue hal-03001049v1
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Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors

 Geert-Jan Huizing , Laura Cantini , Gabriel Peyré
Proceedings of the 39th International Conference on Machine Learning,, Jul 2022, Baltimore, United States
Communication dans un congrès hal-03828733v1
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Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

 Andrei Zinovyev , Urszula Czerwinska , Laura Cantini , Emmanuel Barillot , Klaus M. Frahm , et al.
PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007652⟩
Article dans une revue hal-02114063v1
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Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization

 Alessandro Greco , Jon Sanchez Valle , Vera Pancaldi , Anaïs Baudot , Emmanuel Barillot , et al.
International Journal of Molecular Sciences, 2019, 20 (13), pp.3114. ⟨10.3390/ijms20133114⟩
Article dans une revue hal-02277045v2
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Paired single-cell multi-omics data integration with Mowgli

 Geert-Jan Huizing , Ina Maria Deutschmann , Gabriel Peyré , Laura Cantini
2023, ⟨swh:1:dir:ae39daf96a574fdd1da1737b2d30cd33ada5bbf1;origin=https://hal.archives-ouvertes.fr/hal-04186802;visit=swh:1:snp:8e03c5df57d39d486cc3a4f16bc59de9dae8af08;anchor=swh:1:rel:ca5735ff4d7d2a0d4b9ead6f773dcdef4ad34ef7;path=/⟩
Logiciel hal-04186802v1
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Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer

 Laura Cantini , Pooya Zakeri , Céline Hernandez , Aurelien Naldi , Denis Thieffry , et al.
Nature Communications, 2021, 12, ⟨10.1038/s41467-020-20430-7⟩
Article dans une revue hal-03102088v1

Optimal Transport improves cell-cell similarity inference in single-cell omics data

 Geert-Jan Huizing , Gabriel Peyré , Laura Cantini
Bioinformatics, 2022, ⟨10.1093/bioinformatics/btac084⟩
Article dans une revue hal-03365157v1

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer

 Laura Cantini , Gloria Bertoli , Claudia Cava , Thierry Dubois , Andrei Zinovyev , et al.
Nucleic Acids Research, 2019, 47 (5), pp.2205-2215. ⟨10.1093/nar/gkz016⟩
Article dans une revue hal-02129600v1

Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data

 Laura Cantini , Michele Caselle
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-018-36744-y⟩
Article dans une revue hal-02129598v1

Unsupervised Ground Metric Learning using Wasserstein Eigenvectors

 Geert-Jan Huizing , Laura Cantini , Gabriel Peyré
Proceedings of the 39th International Conference on Machine Learning, Jul 2022, Baltimore, United States
Communication dans un congrès hal-03387865v1
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Optimal transport improves cell–cell similarity inference in single-cell omics data

 Geert-Jan Huizing , Gabriel Peyré , Laura Cantini
Bioinformatics, 2022, 38 (8), pp.2169-2177. ⟨10.1093/bioinformatics/btac084⟩
Article dans une revue hal-03828714v1

MOTL: enhancing multi-omics matrix factorization with transfer learning

 David Hirst , Morgane Térézol , Laura Cantini , Paul Villoutreix , Matthieu Vignes , et al.
2024
Pré-publication, Document de travail hal-04538968v1
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Benchmarking joint multi-omics dimensionality reduction approaches for cancer study

 Laura Cantini , Pooya Zakeri , Céline Hernandez , Aurelien Naldi , Denis Thieffry , et al.
2020
Pré-publication, Document de travail hal-02998156v1
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Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms

 Yoonjee Kang , Denis Thieffry , Laura Cantini
Frontiers in Genetics, 2021, 12, ⟨10.3389/fgene.2021.617282⟩
Article dans une revue hal-03358193v1
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Determining the optimal number of independent components for reproducible transcriptomic data analysis

 Ulykbek Kairov , Laura Cantini , Alessandro Greco , Askhat Molkenov , Urszula Czerwinska , et al.
BMC Genomics, 2017, 18 (1), pp.712. ⟨10.1186/s12864-017-4112-9⟩
Article dans une revue inserm-02064099v1

Classification of gene signatures for their information value and functional redundancy

 Laura Cantini , Laurence Calzone , Loredana Martignetti , Mattias Rydenfelt , Nils Blüthgen , et al.
npj Systems Biology and Applications, 2018, 4 (1), ⟨10.1038/s41540-017-0038-8⟩
Article dans une revue hal-02129604v1
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An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids

 Karla Fabiola Corral-Jara , Laura Cantini , Nathalie Poupin , Tao Ye , Jean-Paul Rigaudière , et al.
Nutrients, 2020, 12 (12), pp.3864. ⟨10.3390/nu12123864⟩
Article dans une revue hal-03100700v1

Optimal transport improves cell–cell similarity inference in single-cell omics data

 Geert-Jan Huizing , Gabriel Peyré , Laura Cantini
Bioinformatics, 2022, ⟨10.1093/bioinformatics/btac084⟩
Article dans une revue hal-03623386v1
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Paired single-cell multi-omics data integration with Mowgli

 Geert-Jan Huizing , Ina Maria Deutschmann , Gabriel Peyré , Laura Cantini
2023
Pré-publication, Document de travail hal-04237733v1
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