Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.

  PMID 41663439 · PMC12996591 · Nature communications · 2026 · 7 claims · 7 setups

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  Aggregating peaks from 624 high-quality bulk ATAC-seq datasets defines ~1.4 million observed consensus peaks (cPeaks) covering ~30% of the genome.

  bulk scatac-seq cnn gm12878 bulk scatac-seq deep

• Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

  PMID 41526189 · PMC12951969 · Genome research · 2026 · 8 claims · 6 setups

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  Early feature extraction (via ConvNeXt V2 blocks), rather than downstream architecture type, is the primary determinant of prediction accuracy in high-resolution chromatin accessibility prediction.

  lines cancer sets gm12878 atac-seq peak input-shift

• Chromatin state architecture governs transcription factor accessibility across plant genomes.

  PMID 41570051 · PMC12867329 · PLoS genetics · 2026 · 8 claims · 8 setups

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  Chromatin states show a large degree of functional conservation between Arabidopsis thaliana and Marchantia polymorpha across more than 450 million years of land plant evolution

  arabidopsis marchantia chromhmm atac-seq antibody-based

• Statistical framework for calling allelic imbalance in high-throughput sequencing data.

  PMID 39966391 · PMC11836314 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 89

  MIXALIME is a versatile computational framework for calling allele-specific variants (ASVs) from diverse high-throughput omics data

  wa01 left heart chip-seq rna-seq cage-seq

• ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.

  PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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  ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.

  pc9 paired-end sorted atac-seq quality read

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

  Has reproduction · 90

  A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

  monocytes natural hematopoietic leukemia atac-seq hierarchical

• Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.

  PMID 41738836 · PMC13154841 · GigaScience · 2026 · 8 claims · 6 setups

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  Detection accuracy of eccDNA/circRNA tools is highly influenced by sequencing depth, alignment algorithm, and experimental enrichment protocol

  genome transcriptome muscle dnase1l3 simulated circle-seq atac-seq

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq

• RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

  PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups

  Has reproduction · 63

  RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data

  embryonic cd34+ shared promoter rna-seq atac-seq gsea

• Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

  PMID 41535307 · PMC12913623 · Nature communications · 2026 · 8 claims · 8 setups

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  e2MPRA, combining lentiviral integration-based MPRA with CUT&Tag or ATAC-seq, enables simultaneous measurement of regulatory activity, protein binding, and epigenetic modification of the same synthetic CRE sequences.

  hepg2 lentimpra atac-seq h3k27ac

• Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

  PMID 41664139 · PMC12888363 · Molecular horticulture · 2026 · 7 claims · 7 setups

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  Red-fleshed and orange-fleshed Guanxi pomelo arose from two independent somatic mutation events from the same white-fleshed wild type

  pomelo wild-type rt-qpcr carotenoid genome

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

  PMID 41826793 · PMC13020910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Pre-generated Blacklist exclusion sets were difficult to reproduce due to sensitivity to input BAM data, aligner choice, and read length

  hg38 gm12878 gse235167 syo-1 chip-seq rna-seq atac-seq

• CircleBase V2: an eccDNA annotation platform across cancers and species.

  PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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  CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

  raw eccdna tissues cancer circle-seq motif gene

• Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.

  PMID 41668146 · PMC12892563 · Molecular horticulture · 2026 · 6 claims · 5 setups

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  Regulatory differences in sRNAs between the two F1 hybrids are mainly driven by maternal inheritance, with Hybrid-sh showing more maternal influence and Hybrid-yh showing transgressive regulation

  brassica s70 small strand-specific atac-seq

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

  PMID 41547832 · PMC12914055 · Nature communications · 2026 · 8 claims · 8 setups

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  Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

  recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation

• Transcription and potential functions of a novel XIST isoform in male peripheral glia.

  PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

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  XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

  heart skeletal atlas peripheral scrna-seq aggregated scatac-seq