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).
-
Has reproduction
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups
A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.
-
Has reproduction · 95
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.
PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups
Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism
-
Full-text index only
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.
-
Full-text index only
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.
PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups
A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.
-
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
-
Full-text index only
From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.
PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups
There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins
-
Full-text index only
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
-
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.
-
Full-text index only
An online database for brain disease research.
PMID 16594998 · PMC1489945 · BMC genomics · 2006 · 7 claims · 5 setups
SMRIDB is a comprehensive web-based database integrating gene expression data and clinical metadata to aid understanding of the genetic effects of brain disease (bipolar disorder, schizophrenia, depression)