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).

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 8 setups

  Has reproduction · 80

  After ~2 decades of ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin, especially centromeric/peri-centromeric satellite and micro-satellite DNA

  pbmc single cd4 pbmc-derived flip-seq mip-seq prip-seq

• Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

  PMID 41620470 · PMC12963367 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  A three-step RAMPAGE-based pipeline can systematically identify TE-derived transcription start sites (TSSs) genome-wide, distinguishing them from autonomous TE transcription and background noise.

  biosamples same k562 genomic rampage rna-seq h3k4me3

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

  Full-text index only

  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

  PMID 41844163 · PMC13030975 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Cell lysis (CL) nuclei isolation yields substantially more nuclei and less biased immune cell proportions than mechanical separation (MS)

  frozen paxgene cl-derived thawed single-nucleus confocal brightfield

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

  PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

  pbmc fetal pancreas gse149683 matched unmatched cross-protocol

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups

  Has reproduction · 90

  EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition

  evs matched plasma cell-line small differential adapter

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Exploration of RNA-binding proteins identified RPS27 as a potential regulator associated with Kaposi's sarcoma development.

  PMID 40016701 · PMC11866810 · BMC cancer · 2025 · 6 claims · 8 setups

  Full-text index only

  48 RBP genes are differentially expressed in KS tissue (3 upregulated: PCBP3, L1TD1, PEG10; 45 downregulated, mostly ribosomal protein genes including RPS27)

  matched lesion huvecs rna-sequencing rna-seq irip-seq

• Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

  PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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  A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

  larc scrna-seq scissor+ single-cell bulk pseudotime

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

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  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

  PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

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  PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

  gtex encode wi-38 thp-1 bulk eqtl variant-flowfish

• Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

  PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups

  Full-text index only

  446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways

  carotid degs six bulk kegg logistic

• A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches.

  PMID 41714633 · PMC13031279 · Nature communications · 2026 · 8 claims · 6 setups

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  GBM exhibits distinct cellular and molecular patterns organized by anatomical niche, with malignant, vascular, and immune compartments showing region-specific spatial associations

  gbm glioma single-cell scrna-seq cite-seq spatial

• FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.

  PMID 41704564 · PMC12907730 · NAR genomics and bioinformatics · 2026 · 6 claims · 1 setups

  Full-text index only

  FragmentFinder (FF) is a user-friendly, Windows-executable tool that identifies and characterizes short RNAs excised from any noncoding RNA precursor, requiring no computational background

  pancreatic sncrna