Search filters

List of works by Andrei Zinovyev

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis

scientific article published on 3 August 2015

A comprehensive modular map of molecular interactions in RB/E2F pathway

scientific article published on 4 March 2008

A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures

scientific article published on 22 October 2019

A review of computational approaches detecting microRNAs involved in cancer

scientific article

Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells

Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma

scientific article

Application of Atlas of Cancer Signalling Network in preclinical studies

scientific article published on 01 March 2019

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals

Assessing reproducibility of matrix factorization methods in independent transcriptomes

scientific article published on 01 November 2019

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

scientific article

Basic, simple and extendable kinetic model of protein synthesis

scientific article published on 01 July 2019

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

scientific article

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

scientific article published on 16 November 2007

Biologie des systèmes appliqués aux cancers

scientific article published on 01 June 2009

Blind source separation methods for deconvolution of complex signals in cancer biology

scientific article published on 19 December 2012

Cell death and life in cancer: mathematical modeling of cell fate decisions

scientific article published in January 2012

Classification of gene signatures for their information value and functional redundancy

scientific article published on 19 December 2017

Classification of microarray data using gene networks

scientific article

Codon adaptation index as a measure of dominating codon bias

scientific article published in November 2003

Codon bias signatures, organization of microorganisms in codon space, and lifestyle

scientific article published on 10 November 2004

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

scientific article published on 18 February 2020

Community-driven roadmap for integrated disease maps

scientific article published on 23 April 2018

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

scientific article published on 17 April 2020

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases

scientific article published on 8 December 2017

Constructive methods of invariant manifolds for kinetic problems

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

scientific article

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

scientific article published on 01 March 2019

Data complexity measured by principal graphs

article published in 2013

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts

scientific article

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients

scientific article published on 18 September 2019

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome

scientific article published on June 2015

Determining the optimal number of independent components for reproducible transcriptomic data analysis

scientific article

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors

scientific article

Dynamical modeling of microRNA action on the protein translation process

scientific article

ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma

scientific article published on 01 October 2019

Elastic Principal Graphs and Manifolds and their Practical Applications

article published in 2005

Exact solving and sensitivity analysis of stochastic continuous time Boolean models

scientific article published on 11 June 2020

Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer

scientific article

From a biological hypothesis to the construction of a mathematical model

scientific article published in January 2013

Geometrical Complexity of Data Approximators

How Cell Decides Between Life and Death: Mathematical Modeling of Epigenetic Landscapes of Cellular Fates

How much non-coding DNA do eukaryotes require?

scientific article

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

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

scientific article published on 01 March 2019

Identification of shortened 3' untranslated regions from expression arrays ⬇️

scientific article published on April 1, 2012

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

scientific article published on 07 September 2019

Independent component analysis provides clinically relevant insights into the biology of melanoma patients

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

scientific article published on 13 November 2014

Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks

scientific article

Interpreting pathways to discover cancer driver genes with Moonlight

scientific article published on 03 January 2020

Invariant Grids: Method of Complexity Reduction in Reaction Networks

article

Invariant grids for reaction kinetics

Kinetic signatures of microRNA modes of action

scientific article

Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets

scientific article published on 01 January 2019

MaBoSS 2.0: an environment for stochastic Boolean modeling

scientific article published in July 2017

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

scientific article published on 3 November 2015

Mathematical modeling of microRNA-mediated mechanisms of translation repression

scientific article published on January 2013

Mathematical modelling of cell-fate decision in response to death receptor engagement

scientific article

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets

scientific article published on 11 November 2020

Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways

scientific article

Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response

scientific article published on 02 December 2020

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization

scientific article published on 26 June 2019

Moonlight: a tool for biological interpretation and driver genes discovery

article

Multiscale model of the different modes of cancer cell invasion

scientific article published in 2023

NaviCell Web Service for network-based data visualization

scientific article

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

scientific article

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

scientific article

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.

scientific article

Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures.

scientific article

Network biology elucidates metastatic colon cancer mechanisms

scientific article published in July 2015

Network-based approaches for drug response prediction and targeted therapy development in cancer

scientific article published on 15 June 2015

OCSANA: optimal combinations of interventions from network analysis

article

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.

scientific article

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning. ⬇️

scientific article

Practical use of BiNoM: a biological network manager software

scientific article published in January 2013

Predicting genetic interactions from Boolean models of biological networks

scientific article published on 11 May 2015

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

scientific article published on 06 July 2018

Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Principal manifolds and graphs in practice: from molecular biology to dynamical systems

scientific article published in June 2010

ROMA: Representation and Quantification of Module Activity from Target Expression Data

scientific article

Reduction of dynamical biochemical reactions networks in computational biology

scientific article

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

scientific article published on 04 March 2020

Robust simplifications of multiscale biochemical networks

scientific article

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation

scientific article published on 20 October 2021

Signalling maps in cancer research: construction and data analysis

scientific article published in January 2018

Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

scientific article published on 20 May 2020

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

scientific article published on 23 April 2019

Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps

scientific article

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

scientific article published on 08 August 2013

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

scientific article published on 2 June 2018

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

scientific article

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

article

The mystery of two straight lines in bacterial genome statistics

scientific article published on 19 June 2007

The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease

scientific article

The shortest path is not the one you know: application of biological network resources in precision oncology research

scientific article

Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data

scientific article published on 01 November 2020

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

scientific article published on 01 February 2020

Understanding Different Types of Cell Death Using Systems Biology

article

Universal Seven-Cluster Structure of Genome Fragment Distribution: Basic Symmetry in Triplet Frequencies

[Biological network modelling and precision medicine in oncology]

scientific article published on 01 June 2014

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

scientific article published on 06 January 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

scientific article published on 31 October 2020

Paulina is supported by:

About Paulina

Help