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).

• Human CRAMP1 specifically promotes the expression of histone H1 genes.

  PMID 41663757 · PMC12979687 · EMBO reports · 2026 · 8 claims · 8 setups

  Full-text index only

  CRAMP1 is a selective regulator of histone H1 gene expression that does not significantly affect core histone gene expression

  cancer hek293t rpe1 genome-wide immunoprecipitation-mass western

• Omics-aided design genome editing strategy for challenging human immortalized cell models.

  PMID 41678468 · PMC12900285 · PloS one · 2026 · 6 claims · 4 setups

  Full-text index only

  Omics profiling identifies bottlenecks associated with poor precise KI efficiency in hard-to-engineer cells

  mcf7 deep-targeted bulk dia-based

• Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella.

  PMID 41684216 · PMC12902445 · Microbial biotechnology · 2026 · 7 claims · 5 setups

  Full-text index only

  Structured, recurrent promoter variation in epigenetically regulated operons is a novel layer of functional adaptation in Salmonella, complementing genetic and epigenetic mechanisms.

  complete annotated 220-nucleotide opvab comparative correlation blastn

• Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

  PMID 41792463 · PMC13084053 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

  Full-text index only

  Combining cfDNA methylome (EwingSign) and fragmentome analysis detects all clinically confirmed relapse events in EwS/CIC patients

  plasma cfdna t7-mbd-seq ichorcna fragment

• BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.

  PMID 41896736 · PMC13147680 · BMC microbiology · 2026 · 7 claims · 8 setups

  Full-text index only

  BaGPipe is an automated, reproducible Nextflow pipeline that integrates pre-processing, Pyseer-based association analysis, and downstream visualisation into a unified bacterial GWAS workflow

  streptococcus staphylococcus aureus pneumoniae bacterial read amr

• Loss of long-range co-expression is a common feature in cancer.

  PMID 41935098 · PMC13247121 · NPJ systems biology and applications · 2026 · 8 claims · 7 setups

  Full-text index only

  In cancer, the strongest co-expressed gene pairs (top MI values) are predominantly intra-chromosomal, unlike in normal tissue.

  tissues same bladder cancer bulk differential bootstrap

• SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.

  PMID 41993886 · PMC13082578 · Computational and structural biotechnology journal · 2026 · 6 claims · 6 setups

  Full-text index only

  SnakeAltPromoter is the first unified, reproducible Snakemake workflow that automates alternative promoter analysis from raw RNA-seq data using 3 complementary methods (ProActiv, Salmon, DEXSeq)

  heart brain gm12878 simulated bulk cage rna-seq

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• isoSeQL: comparing long-read isoforms across multiple datasets.

  PMID 41452740 · PMC12790818 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  isoSeQL enables comparison of long-read isoform profiles across multiple datasets by consolidating SQANTI3-annotated samples into a unified SQLite database with consistent isoform IDs

  gencode simulated gm12878 peripheral intron simulated long-read

• Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells.

  PMID 41507516 · PMC12880982 · Communications biology · 2026 · 8 claims · 6 setups

  Full-text index only

  Hypoxia induces a coordinated downregulation of mito-nuclear OXPHOS gene expression across most human cell lines tested

  hct-116 u87 h460 hif1α rna-seq qpcr chip-seq

• Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

  PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

  Full-text index only

  Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

  liver hepg2 293t serum bulk single-cell oil

• Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

  PMID 41528819 · PMC12958807 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

  Full-text index only

  Differential gene expression caused by disruption of daf-2/InsR during L1 starvation is daf-16-dependent.

  elegans bulk principal hierarchical

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• Reducing language barriers, promoting information absorption, and communication using fanyi.

  PMID 39039634 · PMC11332769 · Chinese medical journal · 2024 · 7 claims · 3 setups

  Has reproduction · 67

  The fanyi R package retrieves gene information from NCBI and translates it into multiple languages using AI-driven online translation services

  pbmcs airway gene single-cell bulk functional

• Lower incidence of K-ras codon 12 mutation in flat colorectal adenomas than in polypoid adenomas.

  PMID 8144396 · PMC5919417 · Japanese journal of cancer research : Gann · 1994 · 5 claims · 3 setups

  Full-text index only

  Flat colorectal adenomas have a significantly lower K-ras codon 12 mutation frequency than polypoid adenomas and cancers.

  flat polypoid colorectal k-ras

• Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

  PMID 8641976 · PMC5921130 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 3 setups

  Full-text index only

  Four of five Japanese VHL disease families showed germ line VHL gene mutations, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation

  blood-derived hemangioblastoma single-strand direct sscp

• Discrimination of double primary lung cancer from intrapulmonary metastasis by p53 gene mutation.

  PMID 10188905 · PMC2362717 · British journal of cancer · 1999 · 7 claims · 3 setups

  Full-text index only

  p53 mutation patterns can be used as a clonal marker to discriminate double primary lung cancer from intrapulmonary metastasis in synchronous double lung tumours.

  paraffin-embedded pcr lung pcr-single-strand sequencing extraction

• Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

  PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

  Full-text index only

  RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

  colorectal same pcr-based msi

• Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.

  PMID 16351744 · PMC1866390 · BMC bioinformatics · 2005 · 5 claims · 3 setups

  Full-text index only

  OMIM Clinical Synopsis free-text phenotype and location names can be normalized and hierarchically structured into a controlled vocabulary suitable for computational analysis

  omim gene text statistical gene