bioRxiv: Bioinformatics Preprints

Do Larger Models Really Win in Drug Discovery?A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

biorxiv.org·

spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

biorxiv.org·

DPLM: Dynamics-aware Protein Language Model via contrastive learning between sequence and molecular dynamics simulation trajectory

biorxiv.org·

Reference-Based Library Construction Improves Performance in low-input diaPASEF Workflows

biorxiv.org·

Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction

biorxiv.org·

Interpretable sequence-based machine learning consolidates candidate H3N2 hemagglutinin antigenic sites

biorxiv.org·

Scan Cluster: A versatile database-independent prediction tool for multi-genome identification of homologous gene clusters.

biorxiv.org·

From Generalist to Specialist: Evolution of PS2 α-integrins and Implications for Drug Targeting

biorxiv.org·

Modeling healthy proteomic profiles for anomaly detection using subspace learning based one-class classification

biorxiv.org·

SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

biorxiv.org·

Single nucleus transcriptome analysis of Arabidopsis thaliana roots infected with Phytophthora. capsici

biorxiv.org·

OmniAge: a compendium of aging omic biomarkers links mitotic clocks to clonal hematopoiesis and causality

biorxiv.org·

TorchLIMIX: GPU-accelerated multivariate genome-wideassociation studies

biorxiv.org·

NeuroCDS: Integrating Local and Global Neural Network Representations via Structural Constrained Viterbi Decoding for Robust CDS Annotation

biorxiv.org·

Systematic benchmarking of small variant calling pipelines for long-read RNA sequencing data

biorxiv.org·

A 37-million-particle dataset from over 250 experiments to accelerate data-driven cryo-EM analysis

biorxiv.org·

Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree

biorxiv.org·

Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets

biorxiv.org·

DoFormer: Causal Transformer for Gene Perturbation

Do Larger Models Really Win in Drug Discovery?A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

DPLM: Dynamics-aware Protein Language Model via contrastive learning between sequence and molecular dynamics simulation trajectory

Reference-Based Library Construction Improves Performance in low-input diaPASEF Workflows

Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction

Interpretable sequence-based machine learning consolidates candidate H3N2 hemagglutinin antigenic sites

Scan Cluster: A versatile database-independent prediction tool for multi-genome identification of homologous gene clusters.

From Generalist to Specialist: Evolution of PS2 α-integrins and Implications for Drug Targeting

Modeling healthy proteomic profiles for anomaly detection using subspace learning based one-class classification

SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

Single nucleus transcriptome analysis of Arabidopsis thaliana roots infected with Phytophthora. capsici

OmniAge: a compendium of aging omic biomarkers links mitotic clocks to clonal hematopoiesis and causality

TorchLIMIX: GPU-accelerated multivariate genome-wideassociation studies

NeuroCDS: Integrating Local and Global Neural Network Representations via Structural Constrained Viterbi Decoding for Robust CDS Annotation

Systematic benchmarking of small variant calling pipelines for long-read RNA sequencing data

A 37-million-particle dataset from over 250 experiments to accelerate data-driven cryo-EM analysis

Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree

Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets

A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata