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).

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

  Has reproduction · 90

  A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

  monocytes natural hematopoietic leukemia atac-seq hierarchical

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• Correcting scale distortion in RNA sequencing data.

  PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)

  tcga su2c gse47774 gtex bulk computational d'agostino

• Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

  PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

  quiescent satellite regenerating situ atac-seq rna-seq motif

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Detection of p53 mutations in precancerous gastric tissue.

  PMID 14520466 · PMC2394306 · British journal of cancer · 2003 · 8 claims · 6 setups

  Full-text index only

  p53 mutations can be detected in precancerous gastritis and intestinal metaplasia tissue using the restriction site mutation (RSM) assay

  gastric enzyme-resistant gastritis pylori-positive restriction sequencing electron

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

  Full-text index only

  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

  Full-text index only

  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

  PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

  Full-text index only

  K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

  a549 western proliferation clonogenic

• Patterns of somatic mutation in human cancer genomes.

  PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

  Full-text index only

  Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

  cancers additional computational combined targeted follow-up statistical

• Proteomic profiling of the amniotic fluid to detect inflammation, infection, and neonatal sepsis.

  PMID 17227133 · PMC1769412 · PLoS medicine · 2007 · 8 claims · 8 setups

  Full-text index only

  Higher MR scores (severe, 3-4) are associated with significantly shorter amniocentesis-to-delivery intervals than minimal (1-2) or no (0) inflammation

  amniotic placental blood seldi-tof elisa clinical

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

  Full-text index only

  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Of mice and men: comparative proteomics of bronchoalveolar fluid.

  PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

  Full-text index only

  Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

  pooled oxidative unpooled balf shotgun functional protein-protein

• In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

  PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups

  Full-text index only

  2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy

  sickle excised patients 2d-dige tandem immunoblot

• The 32nd Annual Congress of the Society of Critical Care Medicine, 28 January - 2 February 2003, San Antonio, USA.

  PMID 12720569 · PMC270663 · Critical care (London, England) · 2003 · 8 claims · 8 setups

  Full-text index only

  Proteomics is more useful than genomics for identifying regulatory pathways and druggable targets in disease because transcriptional responses to different stimuli often converge while protein interaction networks reveal distinct regulatory nodes

  macrophages patients animal ards gene histological mechanical

• Human genome research in China.

  PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

  Full-text index only

  China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

  genome chinese high-risk nb4 large-scale mutation positional

• PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

  PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 8 claims · 8 setups

  Has reproduction · 76

  Drug repurposing screen of the LINCS transcriptional signature database identified PI3K/mTOR/Akt inhibitors as the most prominent pharmacological class capable of repressing REDD1/FKBP51 expression.

  keratinocytes hacat skin ear computational rt-pcr western

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only