Publications associées à Biologie des systèmes

MPGM: Scalable and Accurate Multiple Network Alignment

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

Yimon Aye, Yi Zhao

Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools th ...

ROYAL SOC CHEMISTRY2020

The emergence and promise of single-cell temporal-omics approaches

Gioele La Manno, Alex Russell Lederer

Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes ...

CURRENT BIOLOGY LTD2020

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Vassily Hatzimanikatis, Sofia Tsouka

Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...

OXFORD UNIV PRESS2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

2020

Homogeneous multifocal excitation for high-throughput super-resolution imaging

Pierre Gönczy, Suliana Manley, Kyle Michael Douglass, Khalid Ashraf Mohie Ibrahim, Davide Gambarotto, Paul Guichard, Virginie Hamel, Denis Fortun, Niccolo Banterle, Dora Mahecic

Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for fie ...

NATURE PUBLISHING GROUP2020

Modeling Network Populations via Graph Distances

Sofia Charlotta Olhede

This article introduces a new class of models for multiple networks. The core idea is to parameterize a distribution on labeled graphs in terms of a Frechet mean graph (which depends on a user-specified choice of metric or graph distance) and a parameter t ...

AMER STATISTICAL ASSOC2020

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Vassily Hatzimanikatis, Ljubisa Miskovic, Milenko Tokic

Background: Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for impro ...

2020

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Biologie des systèmes

MPGM: Scalable and Accurate Multiple Network Alignment

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

The emergence and promise of single-cell temporal-omics approaches

Monobodies as enabling tools for structural and mechanistic biology

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Homogeneous multifocal excitation for high-throughput super-resolution imaging

Modeling Network Populations via Graph Distances

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

From turbulence to landscapes: Logarithmic mean profiles in bounded complex systems

Graph Chatbot

Chattez avec Graph Search

MPGM: Scalable and Accurate Multiple Network Alignment

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

The emergence and promise of single-cell temporal-omics approaches

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Monobodies as enabling tools for structural and mechanistic biology

Homogeneous multifocal excitation for high-throughput super-resolution imaging

Modeling Network Populations via Graph Distances

From turbulence to landscapes: Logarithmic mean profiles in bounded complex systems

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies