bioRxiv: Bioinformatics Preprints

Building an open ecosystem for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative

biorxiv.org·

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

biorxiv.org·

SaVanache: indexing and visualizing pangenome variation graphs

biorxiv.org·

LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing

biorxiv.org·

TopoFuseNet: Hierarchical Graph Representation Learning with Multi-Scale Topological Features for Accurate Drug Synergy Prediction

biorxiv.org·

Allosteric Protein Chemical Shift Perturbations are Ubiquitous

biorxiv.org·

Efficient Stochastic Trace Generation for Transcription

biorxiv.org·

RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2

biorxiv.org·

MUSE enables cross-species multi-omics integration that incorporates transcriptional regulatory modules

biorxiv.org·

QuadStack: Specialized convolutional blocks enable in vivo BG4-binding motif prediction and highlight discrepancies with in vitro G-quadruplexes.

biorxiv.org·

Denoised MDS-UPDRS Part-III Scores Yield New Patterns of Progression Heterogeneity in Early Stage Parkinson's Disease

biorxiv.org·

A Differentiable dFBA Simulator for Scalable Bayesian Inference over Microbial Metabolic Models

biorxiv.org·

PromptBio-Bench: Benchmarking LLM-based Bioinformatics Agents for End-to-End Data Analysis

biorxiv.org·

Open-Rosalind: Tool-First Biomedical LLM Agents with Process-Aware Benchmarking

biorxiv.org·

vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisation

biorxiv.org·

Structural bias in machine learning-guided peptide design

biorxiv.org·

BART-spatial unravels biologically significant transcriptional regulators from spatial omics data

biorxiv.org·

Beyond Pathway Boundaries: A Degree-Aware Network Clustering Test for Gene Sets

biorxiv.org·

A Fractal-Dimension Framework for Quantifying Self-Similarity in Chromatin Folding

Building an open ecosystem for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

SaVanache: indexing and visualizing pangenome variation graphs

LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing

TopoFuseNet: Hierarchical Graph Representation Learning with Multi-Scale Topological Features for Accurate Drug Synergy Prediction

Allosteric Protein Chemical Shift Perturbations are Ubiquitous

Efficient Stochastic Trace Generation for Transcription

RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2

MUSE enables cross-species multi-omics integration that incorporates transcriptional regulatory modules

QuadStack: Specialized convolutional blocks enable in vivo BG4-binding motif prediction and highlight discrepancies with in vitro G-quadruplexes.

Denoised MDS-UPDRS Part-III Scores Yield New Patterns of Progression Heterogeneity in Early Stage Parkinson's Disease

A Differentiable dFBA Simulator for Scalable Bayesian Inference over Microbial Metabolic Models

PromptBio-Bench: Benchmarking LLM-based Bioinformatics Agents for End-to-End Data Analysis

Open-Rosalind: Tool-First Biomedical LLM Agents with Process-Aware Benchmarking

vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisation

Structural bias in machine learning-guided peptide design

BART-spatial unravels biologically significant transcriptional regulators from spatial omics data

Beyond Pathway Boundaries: A Degree-Aware Network Clustering Test for Gene Sets

Steering Sequence Generation in Protein Language Models through Iterative Lookback Monte Carlo Sampling