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).

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification.

  gene gse6186 time short convolutional

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 8 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirmed a positive association between DED and DEP occurrence

  patients taiwan biobank twb meta-analysis genome-wide score

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 6 setups

  Has reproduction

  D2H2 is a web-based portal integrating hundreds of curated diabetes-relevant transcriptomics datasets with bioinformatics tools for gene/gene set queries

  brain top curated d2h2 differential gene bulk

• snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.

  PMID 34900230 · PMC8637247 · F1000Research · 2021 · 8 claims · 4 setups

  Has reproduction · 67

  snpQT is a scalable, stand-alone software pipeline using nextflow and BioContainers for comprehensive, reproducible, interactive QC of human genomic data.

  synthetic amyotrophic user snp-array gwas population

• Bioinformatic mapping of AlkB homology domains in viruses.

  PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

  ncbi 146-sequence representative hel psi-blast pfam profile

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

  Full-text index only

  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

  PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

  Full-text index only

  SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

  sidcon real mixtures snp re-analysis

• An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.

  PMID 32425511 · PMC7218276 · Bioinformatics and biology insights · 2020 · 8 claims · 6 setups

  Has reproduction · 84

  An integrated methodology combining nonnegative matrix factorization (NMF), the WebGestalt functional enrichment tool, and an ad hoc gene extraction procedure automatically identifies informative gene subsets from microarray data matrices that differ in number of genes (rows) and patients (columns)

  caf bone extracted microarray functional

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• FOXM1 inhibitor, RCM‑1, enhances venetoclax mediated apoptosis through downregulation of ATP2B4 in rhabdomyosarcoma.

  PMID 41789627 · PMC12987556 · International journal of oncology · 2026 · 8 claims · 8 setups

  Has reproduction · 10

  Combination therapy of RCM-1 and venetoclax inhibits RMS tumor growth more efficiently than venetoclax alone in an animal model by decreasing proliferation and inducing apoptosis

  rms injected muscle cck-8 caspase subcutaneous

• miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 6 claims · 5 setups

  Has reproduction

  miRge3.0 with 12 CPUs consistently has the best execution speed compared to miRge2.0, Chimira and sRNAbench

  sra synthetic qiagen small small umi differential

• High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

  PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups

  Has reproduction · 69

  NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.

  mycobacterium tuberculosis chip-seq input strand-specific

• Dcode.org anthology of comparative genomic tools.

  PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

  dlx1 hoxa prothrombin gene comparative multi-species phylogenetic

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

  Full-text index only

  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Pathways to injury in chronic pancreatitis: decoding the role of the high-risk SPINK1 N34S haplotype using meta-analysis.

  PMID 18414673 · PMC2289874 · PloS one · 2008 · 6 claims · 7 setups

  Full-text index only

  SPINK1 N34S is strongly associated with chronic pancreatitis overall

  chronic alcoholic idiopathic tropical meta-analysis genotyping publication