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).

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

  pbmcs sorted expanded cancer multiparameter receptor targeted

• Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

  PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 49

  ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

  ptc degs key bulk kegg weighted

• A need for a 'whole-istic functional genomics' approach in complex human diseases: arthritis.

  PMID 12718747 · PMC165036 · Arthritis research & therapy · 2003 · 8 claims · 6 setups

  Full-text index only

  A systems ('whole-istic') functional genomics approach integrating multiple technologies and biological levels (cell, tissue, organ, organism) is necessary to understand complex diseases like arthritis.

  oa-affected cartilage type zebrafish gene differential genetic

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

  Full-text index only

  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

  PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.

  aortic gene computational normalized bulk ppi connectivity

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 45

  Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

  tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

  Full-text index only

  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative

• Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.

  PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups

  Has reproduction · 30

  BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors

  tur matched nmibc relapsed whole-exome sequencing immune

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC

  hct116 crc tumor chip-seq bulk single

• 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

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

  PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts

  tcga paired thbs2+ scrna-seq wgcna scrna-seq gsea

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

  PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 20

  AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

  ipf common key rats microarray network protein-protein

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

  Full-text index only

  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher