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).
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From genomics to chemical genomics: new developments in KEGG.
PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups
KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.
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KEGG for linking genomes to life and the environment.
PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups
KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.
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Has reproduction
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
m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow
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LMPD: LIPID MAPS proteome database.
PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups
LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.
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Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups
Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).
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A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups
The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.
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Has reproduction · 73
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.
PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.
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The Edinburgh human metabolic network reconstruction and its functional analysis.
PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups
EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Columba: an integrated database of proteins, structures, and annotations.
PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups
COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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Has reproduction · 33
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.
PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups
C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory
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Investigating hookworm genomes by comparative analysis of two Ancylostoma species.
PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups
Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum
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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
FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data
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Has reproduction · 68
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.
PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups
Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla
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miRGator: an integrated system for functional annotation of microRNAs.
PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups
miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs
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DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
PMID 17576678 · PMC1933169 · Nucleic acids research · 2007 · 8 claims · 4 setups
The DAVID Gene Concept uses a single-linkage method to agglomerate tens of millions of gene/protein identifiers from NCBI, PIR, UniProt and other resources into unified DAVID genes.
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Has reproduction · 30
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups
MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.