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).
-
Full-text index only
Computational identification of transcriptional regulatory elements in DNA sequence.
PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups
Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy
-
Full-text index only
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.
PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups
TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.
-
Full-text index only
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.
PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups
A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle
-
Full-text index only
Comprehensive splice-site analysis using comparative genomics.
PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups
Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.