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).

• Atlas-guided discovery of transcription factors for T cell programming.

  PMID 41639465 · PMC13017511 · Nature · 2026 · 8 claims · 8 setups

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  A multi-omics atlas (Taiji pipeline) integrating RNA-seq and ATAC-seq across nine CD8+ T cell states can predict TF activity and identify state-selective versus multi-state TFs

  cd8+ lcmv p14 c57bl rna-seq pearson crispr

• Landscape of allele-specific transcription factor binding in the human genome.

  PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 82

  A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

  gtrd k562 mcf7 types chip-seq variant bayesian

• Methods for proteomic analysis of transcription factors.

  PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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  Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

  nuclear crude intact partially emsa southwestern systematic

• TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

  PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

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  TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

  drosophila combined motif chip-seq whole-animal

• Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.

  PMID 41650962 · PMC12985389 · Stem cell reports · 2026 · 8 claims · 8 setups

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  Analysis of 532 RNA-seq datasets constructed a high-resolution promoter activity landscape across hematopoietic lineages

  hematopoietic major monocytes candidate rna-seq h3k4me3 motif

• AmalgaMo: flexible DNA motif merging.

  PMID 41768281 · PMC12947577 · Bioinformatics advances · 2026 · 7 claims · 7 setups

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  AmalgaMo is a flexible command-line tool for merging highly similar DNA/RNA motifs, using five tunable parameters (t, m, r, s, a), accepting HOCOMOCO/JASPAR/MEME/CisBP formats.

  hocomoco paired chip-seq atac-seq motif regression-based bulk

• Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes.

  PMID 41898740 · PMC13026113 · International journal of molecular sciences · 2026 · 7 claims · 7 setups

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  Pigmented potato cultivars (DG26, DJ247) accumulate higher levels of flavonoids and linoleic acid derivatives than the white-fleshed cultivar (AG594)

  potato bioinformatic untargeted rna-seq rt-qpcr

• Exonic enhancers are a widespread class of dual-function regulatory elements.

  PMID 41927541 · PMC13216554 · Nature communications · 2026 · 8 claims · 8 setups

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  Many protein-coding exons possess enhancer activity across species, forming a class of candidate Exonic Enhancers (cEEs)

  coding k-562 cloned garre1 chip-seq dnase histone

• Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

  PMID 24696402 · PMC4007537 · Genome biology and evolution · 2014 · 7 claims · 7 setups

  Has reproduction · 68

  A de novo reference transcriptome for Heliocidaris erythrogramma spanning larval, metamorphic, and postmetamorphic stages provides a genomic resource for studying radial body plan evolution.

  sea heliocidaris panther novo rna-seq principal

• 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

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon

• SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.

  PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 78

  A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin

  injured normal p2-whgs oral bulk single-cell gene

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

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  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

  PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

  orthologous randomized high-score promoters pssm-based comparative motif

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation

• Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

  PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

  Has reproduction · 71

  A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

  luad tumor a549 single-cell infercnv pseudotime

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• TBP regulates transposable element expression in early mouse embryos.

  PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

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  The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

  single embryos computational embryonic rna-seq atac-seq motif