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).

• Sensitive detection of somatic mutations in GC-rich cancer gene promoters.

  PMID 42088607 · PMC13136893 · NAR cancer · 2026 · 8 claims · 8 setups

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  Gene promoters, due to high GC content (CpG islands, ~70% of promoters), are systematically undersampled and have poor coverage in whole cancer genomes, causing missed somatic mutation calls

  gm12878 cancer ffpe lines hybrid whole-genome dnase-seq

• Identification of Foxm1 as a critical regulator for metabolic dysfunction-associated steatotic liver disease by epigenomic and transcriptional profiling.

  PMID 42088639 · PMC13137179 · Cell insight · 2026 · 8 claims · 8 setups

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  Enhancer and polycomb chromatin regions progressively increase in genomic coverage during MASLD progression

  liver aml12 chip-seq bulk histological

• Bacillus velezensis EU07 suppresses Fusarium graminearum via transcriptomic reprogramming.

  PMID 42103992 · PMC13234024 · Applied microbiology and biotechnology · 2026 · 8 claims · 7 setups

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  EU07 exposure compromises fungal cellular integrity, causing severe hyphal distortion

  graminearum five apolipophorin dual rna-seq gene

• A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

  PMID 42111187 · PMC13157187 · iScience · 2026 · 8 claims · 8 setups

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  cfDNAanalyzer integrates feature extraction, feature processing/selection, and machine learning model building into a single one-command-line toolkit for cfDNA genomic sequencing data

  balanced breast healthy multi-cancer cfdna machine computational

• Reconstructing transcriptional regulatory networks through genomics data.

  PMID 20048387 · PMC3666560 · Statistical methods in medical research · 2009 · 7 claims · 5 setups

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  Location data (ChIP-chip/ChIP-seq) alone is insufficient for TRN inference because binding does not imply regulation, TF binding is dynamic across conditions/time, and TRNs involve combinatorial effects of multiple TFs not captured by single-TF ChIP experiments.

  yeast generic perturbations followed chip-chip chip-seq gene

• Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq.

  PMID 41313685 · PMC12702366 · STAR protocols · 2025 · 7 claims · 7 setups

  Has reproduction · 85

  Integrated ATAC-seq and RNA-seq protocol to profile JAK inhibitor sensitivity in IFN-γ-primed human macrophages

  thp-1-derived ifn-γ-primed thp-1 rheumatoid atac-seq rna-seq microarray

• Single-cell ATAC-seq analysis of human embryoid bodies reveals crucial transcription factor networks involved in early germ layer specification.

  PMID 41906160 · PMC13154528 · Cell & bioscience · 2026 · 7 claims · 7 setups

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  scATAC-seq of human EBs can classify cells into the three germ layers and, via pseudotime analysis, identify 'early committed cells' at the onset of each germ layer.

  embryoid embryonic hescs single-cell mesendoderm neural

• 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

• IMGT, the international ImMunoGeneTics information system.

  PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

  igh mhc pairs automated junction structure

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

  randomly single-cell single scrna-seq cell-type orthogonal

• Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data.

  PMID 29420797 · PMC5961211 · Nucleic acids research · 2018 · 7 claims · 5 setups

  Has reproduction · 68

  Octopus-toolkit is a stand-alone application that automatically retrieves and processes large sets of epigenomic and transcriptomic NGS data from GEO in a single step

  mammary liver saccharomyces chip-seq rna-seq

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups

  Has reproduction

  Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas

  alteromonas trichodesmium differential classical smrt

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

  Has reproduction · 95

  Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

  kidney live blood snrna-seq snatac-seq bulk

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 79

  CLSM6A is a set of CNN-based deep learning models that predict single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  hct116 a549 brain hek293t miclip m6a-clip-seq m6a-seq

• Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

  PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups

  Has reproduction · 73

  A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level

  jurkat rna-seq genome proteomics

• Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

  PMID 39300486 · PMC11414060 · Genome biology · 2024 · 8 claims · 8 setups

  Has reproduction · 78

  ZBTB48 physically interacts with the m6A/m6Am demethylase FTO

  hek293 inducible polyadenylated ap-ms co-immunoprecipitation clip

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier