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).

• baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.

  PMID 41526967 · PMC12888418 · Genome biology · 2026 · 8 claims · 7 setups

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  baal-nf is a nextflow-based pipeline that infers allele-specific binding (ASB) from ChIP-seq data by integrating BaalChIP with de novo (NoPeak) and known (JASPAR) motif mapping to identify motif-disrupting variants

  genotyped chip-seq heterozygous high-quality chip-seq motif evolutionary

• Stress testing reveals selective vulnerabilities in protein homeostasis.

  PMID 41575849 · PMC13040462 · Cell reports · 2026 · 8 claims · 8 setups

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  Tn-seq fitness profiling across strains lacking major chaperones/proteases under proteotoxic stress reveals stress- and strain-specific fitness determinants otherwise masked by redundancy

  caulobacter transposon growth sequencing

• Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

  PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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  48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

  tcga tssb blca mirna-seq bulk kegg

• Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.

  PMID 41680899 · PMC12903587 · Genome medicine · 2026 · 7 claims · 6 setups

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  A novel batch-effect correction method (log-normal gene usage modeling, Z-score normalization, and roulette-wheel resampling) allows combining AIRR-seq data from different batches and protocols.

  blood peripheral batch-corrected airr-seq airr-seq hla tcrβ

• Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

  PMID 41729083 · PMC12956012 · JCI insight · 2026 · 8 claims · 7 setups

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  A clonally expanded CD8+GZMK+IFNG+ T cell population (subdivided into IFNGhi and IFNGint groups) is enriched in the EM lesion and shows an inflammatory, tissue-resident phenotype (GZMBlo/PRF1-) resembling tissue-enriched GZMK+ TteK cells

  whole-skin cd8+gzmk+ifnghi identified skin scrna-seq pseudobulk immune

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• BCR::ABL1-Induced Enhancer Reprogramming Uncovers Hypersensitivity of Ph+B-ALL Cells to Enhancer-Targeting Drugs.

  PMID 41764406 · PMC13137836 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  BCR::ABL1-induced malignant transformation and transcriptional reprogramming of B-cell precursors is accompanied by genome-wide enhancer (non-promoter H3K27ac) activation

  b-cell ph+b-all tom-1 lines rna-seq promoter-capture western

• RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations.

  PMID 25236449 · PMC4174954 · Genetics · 2014 · 8 claims · 7 setups

  Has reproduction · 50

  Genetic variants distinguishing an individual genome from the reference cause read misalignment and biased transcript abundance estimates, and fine-tuning of alignment algorithms does not correct this problem.

  liver genomic cast simulated bulk high-density rna-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

• Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.

  PMID 41839849 · PMC12992920 · Nature communications · 2026 · 8 claims · 8 setups

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  274,682 enhancers and 25,975 promoters were characterized across 24 tissues from an adult female sheep using ChIP-seq, ATAC-seq, CAGE-seq, RRBS, WGBS, and RNA-seq.

  tissues sheep pig chip-seq atac-seq cage-seq

• Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

  PMID 41904529 · PMC13217986 · Cell communication and signaling : CCS · 2026 · 8 claims · 7 setups

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  MITF knockdown and IFNγ stimulation each produce substantial but distinct changes in chromatin accessibility in 624Mel melanoma cells

  624mel melanoma atac-seq western motif

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

  PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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  Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

  bimaculatus prothoracic differentially gbig rna-seq genome differential

• Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

  PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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  Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

  zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly

• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

  PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

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  scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

  pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality

• Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.

  PMID 40811813 · PMC12830129 · Blood advances · 2026 · 6 claims · 8 setups

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  Bex1 (and to a lesser extent Bex4) is ectopically expressed in Pten-deficient mouse T-ALL blasts

  thymocytes thymocyte t-all normal scrna-seq rt-qpcr bulk

• Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.

  PMID 41037662 · PMC12877751 · Cancer discovery · 2026 · 8 claims · 7 setups

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  ATAC-seq profiling of osteosarcoma patient samples, PDXs, and PDX-CLs reveals two distinct chromatin accessibility subtypes: early osteoblast-derived (EOD) and late osteoblast-derived (LOD)

  n=8 pdx-derived pdx osteosarcoma atac-seq bulk h3k27ac

• CTCF's loop-independent functions prevail over chromatin looping in the acute degradation system.

  PMID 41191909 · PMC13107559 · Protein & cell · 2026 · 8 claims · 8 setups

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  CTCF regulates Ppa2 and Zbtb39 expression through mechanisms independent of chromatin looping

  ctcf-aid mescs rna-seq chip-seq western

• TEDD: a comprehensive database for translation efficiency dynamics.

  PMID 41217970 · PMC12807600 · Nucleic acids research · 2026 · 8 claims · 4 setups

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  TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) spanning 24 tissues/cell types, 74 cell lines, and 52 conditions.

  tissues reference rna-seq ribo-seq rnc-seq

• Deep-Learning Tool ScVital Enables Species-Agnostic Integration of Cancer Cell States.

  PMID 41223329 · PMC13053053 · Cancer research · 2026 · 7 claims · 7 setups

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  scVital is a variational autoencoder with an adversarially trained discriminator that embeds scRNA-seq data from different species into a species-agnostic latent space to overcome batch effect.

  pbmc normal pancreatic lung scrna-seq