Bioinformatics

Explore the top 1% of bioinformatics preprints on bioRxiv, ranked by QED Score for originality and validity. This collection highlights new computational methods, algorithms, software tools, and machine learning approaches for biological data, with a claim-by-claim breakdown of each paper's evidence.

15

papers in this category

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How the QED Score works

QED Score is a validated AI-based quality metric that evaluates life science papers on two dimensions: originality and validity. Each manuscript is anonymized, broken down into its claims and supporting evidence, and examined by specialized AI agents for statistical rigor, consistency across figures, and fit with the existing literature. Scores are percentile ranks, so they're comparable across fields. In blinded tests, expert professors sided with QED Score over journal rank in 75% of decisive cases.

Read the methodology

Physiology

Animal Behavior and Cognition

Plant Biology

Developmental Biology

Bioinformatics

Temporal AI model predicts drivers of cell state trajectories across human aging

Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix

Learning transcriptome architecture from sequence with a long-context RNA foundation model

Predicting how perturbations reshape cellular trajectories with PerturbGen

Decoding conformational heterogeneity across disordered proteomes

Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change

Stack: In-Context Learning of Single-Cell Biology

Predicting the Evolutionary and Functional Landscapes of Viruses with a Unified Nucleotide-Protein Language Model: LucaVirus

HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design

Predicting the Evolutionary and Functional Landscapes of Viruses with a Unified Nucleotide-Protein Language Model: LucaVirus

Stack: In-Context Learning of Single-Cell Biology

Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change

Decoding conformational heterogeneity across disordered proteomes

Predicting how perturbations reshape cellular trajectories with PerturbGen

Learning transcriptome architecture from sequence with a long-context RNA foundation model

Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix

Temporal AI model predicts drivers of cell state trajectories across human aging

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

Decoding conformational heterogeneity across disordered proteomes

Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design

Learning transcriptome architecture from sequence with a long-context RNA foundation model

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

Predicting how perturbations reshape cellular trajectories with PerturbGen

Predicting the Evolutionary and Functional Landscapes of Viruses with a Unified Nucleotide-Protein Language Model: LucaVirus

PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

Stack: In-Context Learning of Single-Cell Biology

Temporal AI model predicts drivers of cell state trajectories across human aging

How the QED Score works

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