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Author Details

Andrei Zinovyev
INSERM U, Institut Curie, PSL Research University
2003
102
35
Antoine Forget (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37380559Proteogenomic Characterization of Bladder Cancer Reveals Sensitivity to Apoptosis Induced by Tumor Necrosis Factor-related Apoptosis-inducing Ligand in FGFR3-mutated Tumors.Eur Urol2024
36879200scEvoNet: a gradient boosting-based method for prediction of cell state evolution.BMC Bioinformatics2023
37600970Omics data integration in computational biology viewed through the prism of machine learning paradigms.Front Bioinform2023
37289551Multiscale model of the different modes of cancer cell invasion.Bioinformatics2023
37448589<i>Transmorph</i>: a unifying computational framework for modular single-cell RNA-seq data integration.NAR Genom Bioinform2023
34871374Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data.Bioinformatics2022
35561190BIODICA: a computational environment for Independent Component Analysis of omics data.Bioinformatics2022
36673174Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution Data.Entropy (Basel)2022
36352218ClustMMRA v2: A Scalable Computational Pipeline for the Identification of MicroRNA Clusters Acting Cooperatively on Tumor Molecular Subgroups.Adv Exp Med Biol2022
33326111Systems Biology Analysis for Ewing Sarcoma.Methods Mol Biol2021
33866228Applications of single-cell and bulk RNA sequencing in onco-immunology.Eur J Cancer2021
33889829The multilayer community structure of medulloblastoma.iScience2021
34682092Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation.Entropy (Basel)2021
34795689Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis.Front Genet2021
34088607Adaptation through the lens of single-cell multi-omics data: Comment on "Dynamic and thermodynamic models of adaptation" by A.N. Gorban et al.Phys Life Rev2021
32434947Single-Cell Analysis Reveals Fibroblast Clusters Linked to Immunotherapy Resistance in Cancer.Cancer Discov2020
31998109Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets.Front Neurorobot2020
31900418Interpreting pathways to discover cancer driver genes with Moonlight.Nat Commun2020
32049009Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.Cell Rep2020
32069277Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.PLoS Comput Biol2020
33146381cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.Bioinformatics2020
33287042Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets.Entropy (Basel)2020
33276543Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response.Cancers (Basel)2020
33241287Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data.Gigascience2020
32527218Exact solving and sensitivity analysis of stochastic continuous time Boolean models.BMC Bioinformatics2020
29237040Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.Brief Bioinform2019
31698578Basic, simple and extendable kinetic model of protein synthesis.Math Biosci Eng2019
31641119A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.Nat Commun2019
30169736PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.Bioinformatics2019
31533822Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients.BMC Med Genomics2019
31500324Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.Int J Mol Sci2019
31577941ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma.Cell Rep2019
31247897Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.Int J Mol Sci2019
31015418Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.Nat Commun2019
30999838Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.BMC Bioinformatics2019
30938767Assessing reproducibility of matrix factorization methods in independent transcriptomes.Bioinformatics2019
30787451Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nat Protoc2019
30657980Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer.Nucleic Acids Res2019
30371894The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.Nucleic Acids Res2019
29726961Application of Atlas of Cancer Signalling Network in preclinical studies.Brief Bioinform2019
29688273Community-driven roadmap for integrated disease maps.Brief Bioinform2019
29370181Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks.PLoS One2018
29971009The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.Front Physiol2018
30034343Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial).Front Physiol2018
29872544Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.NPJ Syst Biol Appl2018
29688383Signalling maps in cancer research: construction and data analysis.Database (Oxford)2018
29455927Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer.Cancer Cell2018
27559053Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors.Clin Cancer Res2017
28415074NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.Database (Oxford)2017
28410145A review of computational approaches detecting microRNAs involved in cancer.Front Biosci (Landmark Ed)2017
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Collaborators

Emmanuel Barillot
Institut Curie, Universite PSL
Co-authored papers 56
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 26
Loredana Martignetti
Institut Curie, PSL Research University
Co-authored papers 11
Laura Cantini
Institut Pasteur, Universite Paris Cite, CNRS UMR 3738
Co-authored papers 9
Olivier Delattre
PSL Research University, Institut Curie Research Center, INSERM U, Institut Curie
Co-authored papers 6
Denis Thieffry
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 4
Franck Tirode
Cancer Center of Lyon
Co-authored papers 4
Didier Surdez
Balgrist University Hospital, University of Zurich (UZH)
Co-authored papers 3
Aur??lien Naldi
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 3
Arnau Montagud
Institut Curie, PSL Research University
Co-authored papers 3
Charles Auffray
European Institute for Systems Biology and Medicine
Co-authored papers 3
Ugur Dogrusoz
Bilkent University
Co-authored papers 3
Reinhard Schneider
Co-authored papers 3
Michele Caselle
University of Turin and INFN
Co-authored papers 2
Heinrich Kovar
St. Anna Children's Cancer Research Institute (CCRI), Medical University Vienna
Co-authored papers 2
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 2
Claudine Chaouiya
Aix Marseille University CNRS
Co-authored papers 2
Alfonso Valencia
Josep Carreras Leukaemia Research Institute (IJC)
Co-authored papers 2
Alessandra Carbone
Co-authored papers 2
Stephan Gebel
Co-authored papers 2
Thomas G P Gr??newald
German Cancer Research Center
Co-authored papers 2
Atul J Butte
Bakar Computational Health Sciences Institute, University of California san francisco
Co-authored papers 1
Nathan Sheffield (CM4AI)
University of Virginia
Co-authored papers 1
Peter J Houghton
The University of Texas Health Science Center at San Antonio
Co-authored papers 1
E Alejandro Sweet-Cordero
University of California San Francisco
Co-authored papers 1
B. E. Snaar-Jagalska
Institute of Biology, Leiden University
Co-authored papers 1
Stefan Burdach
Technische Universitat Munchen
Co-authored papers 1
Jaume Mora
Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu
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Branka Radic-Sarikas
St. Anna Children's Cancer Research Institute (CCRI), Medical University of Vienna
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Antoine Forget (CM4AI)
University of California San Francisco
Co-authored papers 1
Release 1.2