bioRxiv

Showing 3151 to 3160 of 4993 articles

Generanno: A Genomic Foundation Model for Metagenomic Annotation

bioRxiv Jan 1, 2025
The rapid growth of genomic and metagenomic data has underscored the pressing need for advanced computational tools capable of deciphering complex biological sequences. In this study, we introduce Generanno, a compact yet powerful genomic foundation ...
View on bioRxiv DOI

A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors

bioRxiv Jan 1, 2025
The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how binding specificity is achieved, which is essenti...
View on bioRxiv DOI

Design of peptides with non-canonical amino acids using flow matching

bioRxiv Jan 1, 2025
The canonical vocabulary of twenty amino acids limits the chemical space available to proteins and peptides. Expanding this vocabulary to hundreds of non-canonical amino acids allows the engineering of proteins with novel function and activity, and i...
View on bioRxiv DOI

Reengineering the antigen optimization process for superior neoantigen vaccine design

bioRxiv Jan 1, 2025
Identifying effective neoantigen sequences is essential for enhancing anti-tumor immunity. However, the vast sequence space (>109 possible peptides) and limited accuracy of existing immunogenicity predictors hinder efficient vaccine design for patien...
View on bioRxiv DOI

Predicting individual learning trajectories in zebrafish via the free-energy principle

bioRxiv Jan 1, 2025
The free-energy principle has been proposed as a unified theory of brain function, and recent evidence from in vitro experiments supports its validity. However, its empirical application to in vivo neuronal dynamics during active decision-making rema...
View on bioRxiv DOI

Uncovering executive function profiles within interindividual variability: A data driven clustering exploration of design fluency in school-aged children

bioRxiv Jan 1, 2025
This study applied unsupervised machine learning to performances on a design fluency task, to identify distinct executive function (EF) profiles among 113 neurotypical Canadian children (62% female, 74% White, aged 7-13). By tracking design, repetiti...
View on bioRxiv DOI

PrimateFace: A Machine Learning Resource for Automated Face Analysis in Human and Non-human Primates

bioRxiv Jan 1, 2025
Machine learning has revolutionized human face analysis, but equivalent tools for non-human primates remain limited and species-specific, hindering progress in neuroscience, anthropology, and conservation. Here, we present PrimateFace, a comprehensiv...
View on bioRxiv DOI

An Agentic AI Framework for Ingestion and Standardization of Single-Cell RNA-seq Data Analysis

bioRxiv Jan 1, 2025
The proliferation of publicly available single-cell RNA sequencing (scRNA-seq) data has created significant opportunities in biomedical research. However, the reuse of these resources is constrained by a series of preparatory steps, including metadat...
View on bioRxiv DOI

scMomer: A modality-aware pretraining framework for single-cell multi-omics modeling under missing modality conditions

bioRxiv Jan 1, 2025
Foundation models offer new opportunities to capture cellular behavior from large-scale single-cell data. However, their development has been greatly constrained due to the limited availability of multi-omics profiles. Consequently, most models are d...
View on bioRxiv DOI

Hypergraph Neural Networks Reveal Spatial Domains from Single-cell Transcriptomics Data

bioRxiv Jan 1, 2025
Spatial transcriptomics enables the measurement of gene expression while preserving spatial context within tissue samples. A key challenge is detecting spatial domains of biologically meaningful cell clusters, typically addressed using graph-based mo...
View on bioRxiv DOI
Popular Topics
Popular Journals