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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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
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In silico segmentations of lentivirus envelope sequences.
PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups
C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.
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QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.
PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups
QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)
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AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.
PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups
AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP