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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Full-text index only
Polymorphix: a sequence polymorphism database.
PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups
Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.
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Full-text index only
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 · 75
Graph-Based Approaches Significantly Improve the Recovery of Antibiotic Resistance Genes From Complex Metagenomic Datasets.
PMID 34690959 · PMC8528159 · Frontiers in microbiology · 2021 · 8 claims · 6 setups
GraphAMR, a Nextflow pipeline that aligns AMR profile HMMs (or AA sequences) to metagenomic assembly graphs via PathRacer, then dereplicates and annotates hits, recovers more and more complete AMR genes than contig-based or read-based methods.
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Has reproduction · 50
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.
PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups
BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length