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).

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

  PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups

  Has reproduction · 40

  DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.

  simulated real-world simulation scrna-seq-based

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

  PMID 16899448 · PMC1557808 · Nucleic acids research · 2006 · 7 claims · 4 setups

  Full-text index only

  3D VizStruct (DFT-based radial mapping + KLD as z-axis) can identify SNPs/polymorphic markers that are predictive of underlying biological class distinctions across diverse datasets

  lpl y-chromosome coral simulated snp aflp numerical

• SNP-VISTA: an interactive SNP visualization tool.

  PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets

  abo homologous acid snp multi-species blast-based

• COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

  PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

  Has reproduction · 84

  COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

  animal same coexpression gene rnaseq-based microarray-based pathway

• 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

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

  Full-text index only

  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

  PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups

  Has reproduction · 64

  VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction

  blood lists differentially individual differential pathway functional

• Narcisse: a mirror view of conserved syntenies.

  PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

  annotated genome pairwise pairs sequence nucleic-level conserved

• Ontological Discovery Environment: a system for integrating gene-phenotype associations.

  PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

  strains integrated bipartite phish gene differential pairwise

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 8 claims · 5 setups

  Has reproduction

  AOE integrates publicly available gene expression data from GEO, ArrayExpress, and GEA into a single searchable index.

  ebi ncbi sequence arrayexpress metadata cross-database visualization

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

• Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

  PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups

  Has reproduction · 75

  sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample

  simulated adipose gastrocnemius dnb numerical microarray protein-protein

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

  Full-text index only

  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• Visualizing the genome: techniques for presenting human genome data and annotations.

  PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

  Full-text index only

  Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

  flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation

• Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

  PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 6 setups

  Has reproduction · 94

  EiaD is a reproducible, versioned pan-eye and body RNA-seq transcriptome dataset built from 916 eye and 1375 GTEx samples via a Snakemake pipeline output as a single SQLite database.

  eye-related body eiad fetal bulk differential term