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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Discovering cancer genes by integrating network and functional properties.
PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups
Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes
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WebGestalt: an integrated system for exploring gene sets in various biological contexts.
PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups
WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.
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Has reproduction · 76
Bayesian prediction of microbial oxygen requirement.
PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups
A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.
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Pseudofam: the pseudogene families database.
PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups
Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments
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Analysis of protein sequence and interaction data for candidate disease gene prediction.
PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups
Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold
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Has reproduction · 91
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.
PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups
De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads
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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.
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Has reproduction · 92
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.
PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups
A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)
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Has reproduction · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 30
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.
PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 8 claims · 7 setups
Combined PacBio SMRT and Illumina RNA sequencing generated a full-length reference transcriptome for tall fescue in the absence of a genome sequence.