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
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.
PMID 18828897 · PMC2760871 · Genome biology · 2008 · 8 claims · 8 setups
The overlap between phosphoproteomes of six eukaryotes (human, mouse, fly, yeast, plant, zebrafish) is significantly greater than expected by chance.
-
Full-text index only
Structural evolution of the protein kinase-like superfamily.
PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups
All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.
-
Full-text index only
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups
MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.
-
Full-text index only
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.
PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups
Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.
-
Full-text index only
Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
-
Full-text index only
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.
PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups
Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta
-
Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
-
Full-text index only
Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.
PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups
Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.
-
Has reproduction · 98
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.
PMID 33295865 · PMC8116671 · Microbial genomics · 2020 · 8 claims · 4 setups
wCtub and wDcau (863 988 bp and 863 427 bp) are the smallest Wolbachia genomes sequenced to date and are the first genomes representing supergroup J.
-
Has reproduction · 95
In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.
PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups
icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses
-
Has reproduction · 93
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups
24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).
-
Full-text index only
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.
PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups
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
-
Full-text index only
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.
PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups
The human genome encodes at least 71 kelch-repeat proteins
-
Full-text index only
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.
PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups
The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.
-
Full-text index only
Empirical codon substitution matrix.
PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups
The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.