Deciphering the impact of genomic variation on function

Code of Conduct Committee (alphabetical by last name … - Nature, 2024‏ - nature.com
Our genomes influence nearly every aspect of human biology—from molecular and cellular
functions to phenotypes in health and disease. Studying the differences in DNA sequence …

Graph machine learning for integrated multi-omics analysis

NA Valous, F Popp, I Zörnig, D Jäger… - British journal of …, 2024‏ - nature.com
Multi-omics experiments at bulk or single-cell resolution facilitate the discovery of hypothesis-
generating biomarkers for predicting response to therapy, as well as aid in uncovering …

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

I Rauluseviciute, R Riudavets-Puig… - Nucleic acids …, 2024‏ - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …

LIANA+ provides an all-in-one framework for cell–cell communication inference

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier… - Nature Cell …, 2024‏ - nature.com
The growing availability of single-cell and spatially resolved transcriptomics has led to the
development of many approaches to infer cell–cell communication, each capturing only a …

Federated learning for healthcare applications

A Chaddad, Y Wu, C Desrosiers - IEEE internet of things …, 2023‏ - ieeexplore.ieee.org
Due to the fast advancement of artificial intelligence (AI), centralized-based models have
become critical for healthcare tasks like in medical image analysis and human behavior …

An open source knowledge graph ecosystem for the life sciences

TJ Callahan, IJ Tripodi, AL Stefanski, L Cappelletti… - Scientific Data, 2024‏ - nature.com
Translational research requires data at multiple scales of biological organization.
Advancements in sequencing and multi-omics technologies have increased the availability …

Drugst. One—a plug-and-play solution for online systems medicine and network-based drug repurposing

A Maier, M Hartung, M Abovsky… - Nucleic Acids …, 2024‏ - academic.oup.com
In recent decades, the development of new drugs has become increasingly expensive and
inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly …

Revolutionizing immune research with organoid-based co-culture and chip systems

D Papp, T Korcsmaros, I Hautefort - Clinical and Experimental …, 2024‏ - academic.oup.com
The intertwined interactions various immune cells have with epithelial cells in our body
require sophisticated experimental approaches to be studied. Due to the limitations of …

Molecular causality in the advent of foundation models

S Lobentanzer, P Rodriguez-Mier, S Bauer… - Molecular Systems …, 2024‏ - embopress.org
Correlation is not causation: this simple and uncontroversial statement has far-reaching
implications. Defining and applying causality in biomedical research has posed significant …

LIANA+: an all-in-one cell-cell communication framework

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez Mier… - BioRxiv, 2023‏ - biorxiv.org
The growing availability of single-cell and spatially-resolved transcriptomics has led to the
rapidly growing popularity of methods to infer cell-cell communication. Many approaches …