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).

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

  PMID 33779545 · PMC8049744 · eLife · 2021 · 8 claims · 5 setups

  Has reproduction · 100

  The initial transcriptional response to amputation is identical during head and foot regeneration at 3 hpa

  hydra atac-seq rna-seq chromvar

• Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.

  PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups

  Has reproduction · 69

  Kidney xenografts show only modest/minimal growth after transplantation into NHP recipients

  cynomolgus kidney nhp clinical bulk serial

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative

• eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

  PMID 34019643 · PMC8218201 · Nucleic acids research · 2021 · 8 claims · 7 setups

  Has reproduction · 82

  eVITTA is a web-based toolbox with three integrated modules (easyGEO, easyGSEA, easyVizR) for GEO data access, functional profiling, and multi-dataset comparison

  nasopharyngeal elegans bulk pre-ranked microarray

• RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

  PMID 36429012 · PMC9688714 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 37

  RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression

  brain rna-edited brain-isolated naïve rna-seq pathway pcr

• Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.

  PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)

  sorted rna-seq periarticular bulk gene flow

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

  PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

  hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation

• A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.

  PMID 39423268 · PMC11488575 · Science advances · 2024 · 8 claims · 5 setups

  Full-text index only

  An unsupervised ML pipeline using the extended isolation forest (EIF) algorithm can reliably detect ribosome pausing sites from noisy, coverage-biased RiboSeq data across expression levels

  saccharomyces simulated yeast riboseq simulated comparative

• 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

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive colorectal cancer cell lines (NCI-H508, Caco2) but weakly expressed in cetuximab-resistant lines (KM12C, SW480)

  crc cetuximab-sensitive nf1 cetuximab-resistant western sirna dapi

• Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

  PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 8 claims · 5 setups

  Has reproduction · 77

  Microbial keystone species and gut microbiota composition are highly variable during pathological development of BPSD in AD

  appswe app gut 16s random open

• Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.

  PMID 20559924 · PMC4745893 · Journal of cardiovascular translational research · 2008 · 8 claims · 6 setups

  Full-text index only

  Molecular signature analysis (MSA) uses machine-learning/classification methods (e.g., PAM/nearest shrunken centroids) on gene expression patterns to classify samples by phenotype for diagnosis, prognosis, or therapy response.

  myocardial endomyocardial peripheral pbmcs microarray allomap gene