Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks and generating re...

Histopathology plays a crucial role in the diagnosis of many diseases, especially cancers, for which the correct classification of tissue samples significantly influences treatments for patients. The ...

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

Background Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain ...

Artificial intelligence (AI) is revolutionizing scientific discovery because of its super capability, following the neural scaling laws, to integrate and analyze large-scale datasets to mine knowledge...

A key question in single-cell biology is how cells communicate and exchange information with neighboring cells in tissues. Here, the authors introduce NiCo to predict the downstream effect of cell-cel...

Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrast...

biVI models the biophysical processes generating nascent and mature single-cell transcriptomes using variational autoencoders.

Podcast Episode · Night Science · 11/25/2024 · 51m

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pret...

Abstract. The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure

Abstract. Ribosome profiling (Ribo-Seq) has revolutionised our understanding of translation, but the increasing complexity and volume of Ribo-Seq data pres

The effect of transcription factor binding on transcription initiation is dependent on the position of the transcription factor binding site.

Understanding tumor cell heterogeneity and plasticity is crucial for overcoming drug resistance. Single-cell technologies enable analyzing cell states at a given condition, but catenating static cell ...

Abstract. The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this n

AbstractBackground. Integrating artificial intelligence (AI) in healthcare settings has the potential to benefit clinical decision-making. Addressing chall

The rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, enabling researchers to gain deeper insights into the complex interactions between cells a...

Abstract. The development of spatially resolved transcriptomics (ST) technologies has made it possible to measure gene expression profiles coupled with cel

Abstract. The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely acce

Abstract. Pangenomes have emerged in response to limitations associated with traditional linear reference genomes. In contrast to a traditional reference t

Enformer Celltyping is a genomic deep learning model that predicts epigenetic signals in unseen cell types using distal DNA interactions and chromatin accessibility data. Here, authors show it general...

Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...

Various Foundation Models (FMs) have been built based on the pre-training and fine-tuning framework to analyze single-cell data with different degrees of success. In this manuscript, we propose a meth...

Code-based data visualization is a crucial tool for understanding and communicating experimental findings while ensuring scalability and reproducibility. However, complex programming interfaces pose a...

One person has died and others are in hospital after eating the carrots, officials say.