Genomics

Explore the top 1% of genomics preprints on bioRxiv, ranked by QED Score for originality and validity. Find standout research in genome sequencing, single-cell genomics, functional genomics, epigenomics, and gene regulation, with each paper's claims and supporting evidence laid out clearly.

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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.

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Physiology

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Developmental Biology

Genomics

Whole-genome 3D architectural screen reveals modulators of brain DNA structure

Transcription factor collaboration enables precise T cell state engineering

Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing

Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

Enhancer hubs govern chromatin topology and Th17 cell identity

CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution

Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma

Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci

Quantitative prediction of nonsense-mediated mRNA decay across human genes by genomic language model and large-scale mutational scanning

In vivo interrogation of transcriptional and epigenetic regulators of lung epithelial regeneration

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq

Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors

A genome-wide atlas of meiotic recombination intermediates reveals distinct modes of DNA repair that direct crossovers away from transcriptionally marked genes

A Multispecies, Modality-Agnostic Scalable In Vivo Mosaic Screening Platform for Therapeutic Target Discovery

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart

Modeling mitochondrial inheritance enables high-precision single-cell lineage tracing in humans

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening

A haplotype-resolved view of human gene regulation

Enhancer Poising Enables Pathogenic Gene Activation by Noncoding Variants

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects

Spatial joint profiling of DNA methylome and transcriptome in mammalian tissues

Whole-genome single-cell multimodal history tracing to reveal cell identity transition

Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues

A complete diploid human genome benchmark for personalized genomics

A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting

Mouse Single-Cell Long-Read Splicing Atlas by Ouro-Seq

Multimodal foundation model predicts zero-shot functional perturbations and cell fate dynamics

A high-coverage genome from a 200,000-year-old Denisovan

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

Genome-wide Chromosome-specific Aneuploidy Engineering and Phenotypic Characterization with CRISPR-Taiji

Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

Protamine lacunae preserve the paternal chromatin landscape in sperm

Circulating chromatin reveals the effects of disease-associated variants on gene regulation

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

A complete diploid human genome benchmark for personalized genomics

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons

A genome-wide atlas of meiotic recombination intermediates reveals distinct modes of DNA repair that direct crossovers away from transcriptionally marked genes

A global view of human centromere variation and evolution

A haplotype-resolved view of human gene regulation

A high-coverage genome from a 200,000-year-old Denisovan

A Multispecies, Modality-Agnostic Scalable In Vivo Mosaic Screening Platform for Therapeutic Target Discovery

A scalable approach to resolving variants of uncertain significance

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

Circulating chromatin reveals the effects of disease-associated variants on gene regulation

CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution

Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors

Comprehensive perturbation of transcription factors in human cardiomyocytes reveals the regulatory architecture of congenital heart disease

Decoding the MYC locus reveals a druggable ultraconserved RNA element

Designing AI-programmable therapeutics with the EDEN family of foundation models

Early microglial priming in Alzheimer’s disease revealed by ME-seq

Enhancer hubs govern chromatin topology and Th17 cell identity

Enhancer Poising Enables Pathogenic Gene Activation by Noncoding Variants

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

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