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
Grammar-based distance in progressive multiple sequence alignment.
PMID 18616828 · PMC2478692 · BMC bioinformatics · 2008 · 7 claims · 3 setups
A grammar-based (LZ complexity) distance metric can be used to determine the order in which sequences are progressively pairwise aligned
-
Full-text index only
Oligomeric protein structure networks: insights into protein-protein interactions.
PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups
Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization
-
Full-text index only
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.
PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups
An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale
-
Has reproduction · 84
Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.
PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups
SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA
-
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.
-
Full-text index only
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.
PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups
Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested
-
Full-text index only
Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.
PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups
A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.
-
Full-text index only
Genomic signatures of human versus avian influenza A viruses.
PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups
52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses
-
Full-text index only
Species-specific protein sequence and fold optimizations.
PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups
Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes
-
Full-text index only
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.
PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups
Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin
-
Full-text index only
Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.
PMID 16261191 · PMC1246807 · PLoS computational biology · 2005 · 7 claims · 7 setups
A comprehensive stoichiometric model of the MAP was built comprising 197 metabolites, 219 reactions, and 28 proteins
-
Full-text index only
Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.
PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups
Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene
-
Full-text index only
Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.
PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups
Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group
-
Full-text index only
Causes of early-onset type 1 diabetes: toward data-driven environmental approaches.
PMID 19075294 · PMC2605242 · The Journal of experimental medicine · 2008 · 8 claims · 1 setups
Serum metabolite profiling reveals metabolic changes that precede islet autoantibody appearance and predict which children will develop T1D
-
Full-text index only
The lords of the genomes.
PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups
Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them
-
Full-text index only
Microbial metagenomics.
PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups
Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides
-
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
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.
PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups
Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.
-
Full-text index only
Genetic variation of St. Louis encephalitis virus.
PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups
Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)
-
Full-text index only
Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.
PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups
Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.