Concept

Network medicine

Publications associées (90)

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

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

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

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

Networks with correlated edge processes

Sofia Charlotta Olhede, Mária Süveges

This article proposes methods to model non-stationary temporal graph processes motivated by a hospital interaction data set. This corresponds to modelling the observation of edge variables indicating interactions between pairs of nodes exhibiting dependenc ...

OXFORD UNIV PRESS2023

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

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

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova

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 ...

EPFL Infoscience2022

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 UNIV PRESS2021

Recent advances in trajectory inference from single-cell omics data

Bart Deplancke, Wouter 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

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Wouter Saelens

We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...

NATURE RESEARCH2021

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