User profiles for A. Zinovyev

Andrei Zinovyev

In silico R&D Evotec
Verified email at evotec.com
Cited by 11724

Constructive methods of invariant manifolds for kinetic problems

AN Gorban, IV Karlin, AY Zinovyev - Physics Reports, 2004 - Elsevier
The concept of the slow invariant manifold is recognized as the central idea underpinning a
transition from micro to macro and model reduction in kinetic theories. We present the …

[HTML][HTML] Applications of single-cell and bulk RNA sequencing in onco-immunology

…, M Aglave, FX Danlos, A Marabelle, A Zinovyev… - European Journal of …, 2021 - Elsevier
The rising interest for precise characterization of the tumour immune contexture has recently
brought forward the high potential of RNA sequencing (RNA-seq) in identifying molecular …

[PDF][PDF] Fibroblast heterogeneity and immunosuppressive environment in human breast cancer

…, C Bonneau, M Kondratova, I Kuperstein, A Zinovyev… - Cancer cell, 2018 - cell.com
Carcinoma-associated fibroblasts (CAF) are key players in the tumor microenvironment.
Here, we characterize four CAF subsets in breast cancer with distinct properties and levels of …

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

…, PT Vuong, LP El Assal, I Kuperstein, A Zinovyev… - Nature protocols, 2019 - nature.com
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …

[HTML][HTML] Independent component analysis for unraveling the complexity of cancer omics datasets

…, F Radvanyi, A Gorban, U Kairov, A Zinovyev - International Journal of …, 2019 - mdpi.com
Independent component analysis (ICA) is a matrix factorization approach where the signals
captured by each individual matrix factors are optimized to become as mutually independent …

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

…, C Bonneau, A Guyard, K Tarte, A Zinovyev… - Cancer discovery, 2020 - AACR
Our work provides a significant advance in characterizing and understanding FAP + CAF in
cancer. We reached a high resolution at single-cell level, which enabled us to identify …

[BOOK][B] Principal manifolds for data visualization and dimension reduction

AN Gorban, B Kégl, DC Wunsch, AY Zinovyev - 2008 - Springer
In 1901, Karl Pearson [1] explained to the scientific community that the problem of data
approximation is (i) important and (ii) nice, and (iii) differs from the regression problem. He …

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

…, M Krueger, I Kuperstein, A Zinovyev… - Nucleic acids …, 2019 - academic.oup.com
A multitude of factors contribute to complex diseases and can be measured with ‘omics’
methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe …

[HTML][HTML] Classification of microarray data using gene networks

F Rapaport, A Zinovyev, M Dutreix, E Barillot, JP Vert - BMC bioinformatics, 2007 - Springer
Background Microarrays have become extremely useful for analysing genetic phenomena,
but establishing a relation between microarray analysis results (typically a list of genes) and …

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

V Boeva, A Zinovyev, K Bleakley, JP Vert… - …, 2011 - academic.oup.com
We present a tool for control-free copy number alteration (CNA) detection using deep-sequencing
data, particularly useful for cancer studies. The tool deals with two frequent problems …