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 role of positive selection in determining the molecular cause of species differences in disease.
PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups
Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals
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Benchmarking ortholog identification methods using functional genomics data.
PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups
InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.
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How accurately is ncRNA aligned within whole-genome multiple alignments?
PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups
MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.
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MEROPS: the peptidase database.
PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups
MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.
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Web-based resources for comparative genomics.
PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups
Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics
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GPCR genes are preferentially retained after whole genome duplication.
PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups
WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)
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Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.
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Sequence similarity network reveals common ancestry of multidomain proteins.
PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups
Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.
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Has reproduction · 90
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.
PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups
Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified
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Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.
PMID 18700039 · PMC2529317 · BMC genomics · 2008 · 8 claims · 6 setups
Complete genome of P. zucineum HLK1T consists of a 3,996,255 bp circular chromosome and a 382,976 bp circular plasmid encoding 3,861 proteins, 42 tRNAs, and one 16S-23S-5S rRNA operon
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Molecular characterization of retinitis pigmentosa in Saudi Arabia.
PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups
The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.
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Has reproduction · 84
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.
PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups
The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus
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Reconstructing the evolution of the mitochondrial ribosomal proteome.
PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups
The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.
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Comparative genomics of vertebrate Fox cluster loci.
PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups
Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci
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Has reproduction · 80
A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.
PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups
A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.