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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What makes species unique? The contribution of proteins with obscure features.
PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups
POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome
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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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In Silico screening for functional candidates amongst hypothetical proteins.
PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups
An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins
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Has reproduction · 24
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.
PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups
MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics
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POCUS: mining genomic sequence annotation to predict disease genes.
PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups
Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance
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Has reproduction · 90
Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.
PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups
MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells
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Has reproduction · 84
An accurate method for identifying recent recombinants from unaligned sequences.
PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups
A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.
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Proteomic-based identification of maternal proteins in mature mouse oocytes.
PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups
625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date
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Has reproduction · 71
Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.
PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups
A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).
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Has reproduction · 89
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.
PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups
Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM
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Investigating hookworm genomes by comparative analysis of two Ancylostoma species.
PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups
Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum
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MODBASE, a database of annotated comparative protein structure models and associated resources.
PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups
MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.
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Prioritization of candidate cancer genes--an aid to oncogenomic studies.
PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups
Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes
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Has reproduction · 62
scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.
PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups
scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer
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Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups
Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.