Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Challenges and opportunities in sharing microbiome data and analyses

C Huttenhower, RD Finn, AC McHardy - Nature Microbiology, 2023 - nature.com
Microbiome data, metadata and analytical workflows have become 'big'in terms of volume
and complexity. Although the infrastructure and technologies to share data have been …

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

D Szklarczyk, R Kirsch, M Koutrouli… - Nucleic acids …, 2023 - academic.oup.com
Much of the complexity within cells arises from functional and regulatory interactions among
proteins. The core of these interactions is increasingly known, but novel interactions …

[HTML][HTML] Effective drug combinations in breast, colon and pancreatic cancer cells

P Jaaks, EA Coker, DJ Vis, O Edwards, EF Carpenter… - Nature, 2022 - nature.com
Combinations of anti-cancer drugs can overcome resistance and provide new treatments,.
The number of possible drug combinations vastly exceeds what could be tested clinically …

Graph neural networks: foundation, frontiers and applications

L Wu, P Cui, J Pei, L Zhao, X Guo - … of the 28th ACM SIGKDD Conference …, 2022 - dl.acm.org
The field of graph neural networks (GNNs) has seen rapid and incredible strides over the
recent years. Graph neural networks, also known as deep learning on graphs, graph …

Improved prediction of protein-protein interactions using AlphaFold2

P Bryant, G Pozzati, A Elofsson - Nature communications, 2022 - nature.com
Predicting the structure of interacting protein chains is a fundamental step towards
understanding protein function. Unfortunately, no computational method can produce …

A proximity-dependent biotinylation map of a human cell

CD Go, JDR Knight, A Rajasekharan, B Rathod… - Nature, 2021 - nature.com
Compartmentalization is a defining characteristic of eukaryotic cells, and partitions distinct
biochemical processes into discrete subcellular locations. Microscopy and biochemical …

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes

J Schwartzentruber, S Cooper, JZ Liu… - Nature …, 2021 - nature.com
Genome-wide association studies have discovered numerous genomic loci associated with
Alzheimer's disease (AD); yet the causal genes and variants are incompletely identified. We …

Towards a structurally resolved human protein interaction network

DF Burke, P Bryant, I Barrio-Hernandez… - Nature Structural & …, 2023 - nature.com
Cellular functions are governed by molecular machines that assemble through protein-
protein interactions. Their atomic details are critical to studying their molecular mechanisms …

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

A Stukalov, V Girault, V Grass, O Karayel, V Bergant… - Nature, 2021 - nature.com
The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-
depth understanding of molecular functions of viral proteins and their interactions with the …