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).

Publications 1.3k Datasets 392.5k Experiments 10

System / cell line: comparative ✕ Assay: information ✕ Clear

Comprehensive splice-site analysis using comparative genomics.

PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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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.

refseq u2-type genes comparative information phylogenetic
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

genome tissues novo pairwise rt-pcr
Negotiating the boundary between medicine and consumer culture: online marketing of nutrigenetic tests.

PMID 20022680 · PMC2824846 · Social science & medicine (1982) · 2010 · 8 claims · 3 setups

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Nutrigenetic testing companies create a new social/marketing space for their products positioned between medicine and consumer culture, rather than being simply delegitimized by boundary work.

webpages same fda qualitative framing document
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

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CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

genome sequence drosophila novo gene coding
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

genome random cd4+ six average mutual chip-seq
Randomised trial of a decision aid and its timing for women being tested for a BRCA1/2 mutation.

PMID 14735173 · PMC2410151 · British journal of cancer · 2004 · 6 claims · 3 setups

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The DA had no impact on well-being (anxiety, depression, cancer-related distress, general health)

women brca1 same randomised comparative validated
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

6x6 ortholog 3'utr comparative chi-squared
CanPredict: a computational tool for predicting cancer-associated missense mutations.

PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

missense observed sjoblom refseq cross-validation recurrence comparative
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based

Experiments

Comprehensive splice-site analysis using comparative genomics.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Negotiating the boundary between medicine and consumer culture: online marketing of nutrigenetic tests.

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

Randomised trial of a decision aid and its timing for women being tested for a BRCA1/2 mutation.

Evolutionary origins of human apoptosis and genome-stability gene networks.

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

CanPredict: a computational tool for predicting cancer-associated missense mutations.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.