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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Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.
PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups
Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14
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The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.
PMID 14519199 · PMC328453 · Genome biology · 2003 · 8 claims · 5 setups
Sequence-profile (PSI-BLAST) searches unify archaeal Alba with eukaryotic RNase P/MRP subunits Rpp20/Pop7 and Rpp25, and with the ciliate macronuclear-development protein Mdp2, into a single Alba superfamily.
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Bioinformatic mapping of AlkB homology domains in viruses.
PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups
AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.
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The protein-phosphatome of the human malaria parasite Plasmodium falciparum.
PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups
P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.
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Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.
PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups
SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.
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RotaC: a web-based tool for the complete genome classification of group A rotaviruses.
PMID 19930627 · PMC2785824 · BMC microbiology · 2009 · 7 claims · 4 setups
RotaC is a freely available web-based tool for complete genome classification of group A rotaviruses across all 11 gene segments.
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SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups
SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models
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SARS-CoV genome polymorphism: a bioinformatics study.
PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups
SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.
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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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Has reproduction · 100
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).
PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups
Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.
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Predicting phenotype and emerging strains among Chlamydia trachomatis infections.
PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups
A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.
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Comparative genomics search for losses of long-established genes on the human lineage.
PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups
A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.
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Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.
PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups
The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.
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Has reproduction · 100
Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.
PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 7 claims · 7 setups
The S. Adjame outbreak produced a heterogeneous phylogeny with multiple temporally/geographically linked sub-clusters, atypical of a point-source Salmonella outbreak and consistent with contamination from an endemic mixed-strain source (imported South Asian herbs/spices).
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Has reproduction · 82
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.
PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups
Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis
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Has reproduction · 87
Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex.
PMID 35342602 · PMC8928884 · Ecology and evolution · 2022 · 7 claims · 5 setups
At least five distinct species exist within the E. ruidum species complex
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Has reproduction · 94
Genome-wide insights into population structure and host specificity of Campylobacter jejuni.
PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups
Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path
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Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.
PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups
A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.
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Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.
PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups
A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations