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 many uses of a genome sequence.
PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups
Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction
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Rats go genomic.
PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups
A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs
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Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.
PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups
Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.
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Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.
PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups
Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase
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Has reproduction · 68
Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.
PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups
LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array
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In silico meets in vivo.
PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups
About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.
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Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.
PMID 15479470 · PMC526369 · BMC genomics · 2004 · 8 claims · 4 setups
65 ePK sequences were identified in the P. falciparum genome and classified via phylogenetic analysis relative to the seven established ePK groups
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Obesity genes: so close and yet so far..
PMID 19046411 · PMC2776388 · Journal of biology · 2008 · 8 claims · 7 setups
GWA studies have confirmed only a few obesity-associated loci (INSIG2, FTO, MC4R) so far, each with modest individual effects on BMI
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Genetical genomic determinants of alcohol consumption in rats and humans.
PMID 19874574 · PMC2777866 · BMC biology · 2009 · 8 claims · 6 setups
A genetical genomics approach combining brain gene expression, bQTL, and eQTL analysis in HXB/BXH RI rats identifies candidate genes for alcohol consumption
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Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups
Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM
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Has reproduction · 68
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.
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Cohesin regulates alternative splicing.
PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups
Cohesin regulates alternative splicing independently of its effects on transcription.
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Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.
PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups
The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.
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Has reproduction · 67
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups
A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.