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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nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.
PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups
nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information
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Has reproduction · 83
Macrel: antimicrobial peptide screening in genomes and metagenomes.
PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups
Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes
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Has reproduction · 98
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups
maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors
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The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups
Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data