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
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.
PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups
E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.
-
Full-text index only
Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.
PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups
MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo
-
Full-text index only
Genome reannotation of Escherichia coli CFT073 with new insights into virulence.
PMID 19930606 · PMC2785843 · BMC genomics · 2009 · 8 claims · 7 setups
Reannotation excluded 608 CDSs from the original RefSeq annotation, mostly unfunctional 'hypothetical'/'putative' genes
-
Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
-
Full-text index only
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.
PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups
MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.
-
Has reproduction · 95
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.
PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 8 claims · 7 setups
254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.
-
Full-text index only
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.
PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups
The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history
-
Full-text index only
Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.
PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups
There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.
-
Full-text index only
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.
PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups
An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.
-
Full-text index only
Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.
PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups
The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology
-
Full-text index only
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.
PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups
Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.
-
Has reproduction · 98
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.
PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups
Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)
-
Full-text index only
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).
PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups
The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species
-
Full-text index only
Recombinant vaccine-derived poliovirus in Madagascar.
PMID 12899139 · PMC3023450 · Emerging infectious diseases · 2003 · 7 claims · 4 setups
Five acute flaccid paralysis cases in southern Madagascar were associated with vaccine-derived poliovirus (VDPV) type 2 isolates
-
Full-text index only
Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.