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).

• Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

  PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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  DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

  nsclc matched lung quantitative pcr genomic

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

  PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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  Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

  a549 nsclc expansion wst-1 flow

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

  PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

  Has reproduction · 68

  Arg1 expression is induced in lung CD4+ T cells during in vivo influenza infection, ranking among the most highly induced genes.

  flow-sorted cd3 lung cd4+ bulk flow western

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time

• Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

  PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

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  Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

  serum resected plasma lower microarray two-dimensional proteomic

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  Autoencoder networks based on 266 shared DEGs reveal a comorbidity (positive) relationship between Alzheimer's disease and lung cancer.

  brain lung integrated shared microarray differential autoencoder

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.

  micro-dissected dissected e9.5 xenopus bulk rt-qpcr whole-mount

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.

  PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Has reproduction · 74

  SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.

  pairs nanostring st-sc osmfish_zeisel st-sc 5-fold spatially

• Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

  PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups

  Has reproduction · 81

  SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains

  pan-cancer pc9 451lu a375 bulk scrna-seq computational

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• Network-assisted protein identification and data interpretation in shotgun proteomics.

  PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

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  Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

  yeast organs mammary organ shotgun clique-enrichment microarray

• A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

  PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups

  Has reproduction · 100

  Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.

  pcrc mli mirna-seq mirna mirna qpcr differential

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

  PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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  A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

  dog predicted ace3 panel blast sequence homology