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Concept

Network medicine

Related publications (27)

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

Network Alignment With Holistic Embeddings

Quoc Viet Hung Nguyen, Thành Tâm Nguyên, Chi Thang Duong, Thanh Trung Huynh

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. Howeve ...

IEEE COMPUTER SOC2023

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Opinion Formation over Adaptive Networks

Virginia Bordignon

An adaptive network consists of multiple communicating agents, equipped with sensing and learning abilities that allow them to extract meaningful information from measurements. The objective of the network is to solve a global inference problem in a decent ...

EPFL2022

Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Vassily Hatzimanikatis, Anastasia Sveshnikova, Homa Mohammadi Peyhani

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line w ...

Zenodo2022

Bringing Functional Context to Emerging Proximity-mapping Proteomics Tools

Yimon Aye

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current st ...

SWISS CHEMICAL SOC2022

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

Oxford University Press2021

Recent advances in trajectory inference from single-cell omics data

Bart Deplancke, Wouter Jozef L Saelens

Trajectory inference methods have emerged as a novel class of single-cell bioinformatics tools to study cellular dynamics at unprecedented resolution. Initial development focused on adapting methods based on clustering or graph traversal, but recent advanc ...

ELSEVIER2021

Is planning still political? The politicization of high-speed rail in Spain (1986–2016)

Ander Audikana Arriola

Post-political debate has stimulated a vigorous research agenda about the role of politics in regional and urban planning. It warns of a depoliticization process leading to the emergence of a consensual social order and the retreat of the properly politica ...

2021

Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks

Barbara Bravi

We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g., protein interaction networks involving complex formation and dissociation reactions. We propose the use of model reduction strategies t ...

AMER INST PHYSICS2020

Modeling biochemical reaction networks in complex intracellular environments

Daniel Robert Weilandt

Whether one aims to design treatments for diseases such as cancer or diabetes, engineer cells to produce valuable biochemicals sustainably, or to grasp the behavior of living organisms, it is essential to understand how cells react to genetic, environmenta ...

EPFL2020

Modeling, predicting and mining metabolism at atom-level resolution

Jasmin Maria Hafner

Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...

EPFL2020

Optimization methods and objective functions for analysis of metabolic network models

Zhaleh Hosseini

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...

EPFL2020

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye, Alexandra Krina Van Hall-Beauvais

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Clofarabine Commandeers the RNR-alpha-ZRANB3 Nuclear Signaling Axis

Yimon Aye, Yi Zhao

Ribonucleotide reductase (RNR) is an essential enzyme in DNA biogenesis and a target of several chemotherapeutics. Here, we investigate how antileukemic drugs (e.g., clofarabine [CIF]) that target one of the two subunits of RNR, RNR-alpha, affect noncanoni ...

CELL PRESS2020

Triple Network Model Dynamically Revisited: Lower Salience Network State Switching in Pre-psychosis

Dimitri Nestor Alice Van De Ville, Thomas William Arthur Bolton

Emerging evidence has attributed altered network coordination between the default mode, central executive, and salience networks (DMN/CEN/SAL) to disturbances seen in schizophrenia, but little is known for at-risk psychosis stages. Moreover, pinpointing im ...

2020

Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth

Sarah Wehrle

Plant reproduction relies on the highly regulated growth of the pollen tube for sperm delivery. This process is controlled by secreted RALF signaling peptides, which have previously been shown to be perceived by Catharanthus roseus RLK1-like (CrRLK1Ls) mem ...

National Academy of Sciences2020

Brain networks and their relevance for stroke rehabilitation

Friedhelm Christoph Hummel, Philipp Johannes Koch

Stroke has long been regarded as focal disease with circumscribed damage leading to neurological deficits. However, advances in methods for assessing the human brain and in statistics have enabled new tools for the examination of the consequences of stroke ...

2019

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Savoglidis, Milenko Tokic

Analysis of the dynamic and steady-state properties of biochemical networks hinges on information about the parameters of enzyme kinetics. The lack of experimental data characterizing enzyme activities and kinetics along with the associated uncertainties i ...

2019

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Dani Or, Vassily Hatzimanikatis, Meriç Ataman

Natural soil is characterized as a complex habitat with patchy hydrated islands and spatially variable nutrients that is in a constant state of change due to wetting-drying dynamics. Soil microbial activity is often concentrated in sparsely distributed hot ...

2019