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
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.
PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups
Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity
-
Full-text index only
A chromosomally integrated bacteriophage in invasive meningococci.
PMID 15967821 · PMC2212043 · The Journal of experimental medicine · 2005 · 8 claims · 7 setups
An 8-kb genetic island (NMA1792-NMA1799) is specifically associated with hyperinvasive meningococcal clonal complexes
-
Full-text index only
Integrative functional genomics.
PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups
Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes
-
Full-text index only
Science star over Asia.
PMID 16149850 · PMC1201306 · PLoS biology · 2005 · 8 claims · 7 setups
Ariff Bongso and associates at Singapore's National University Hospital were the first to derive human embryonic stem cells, from a five-day-old discarded human embryo in 1994, and showed the cells were pluripotent with therapeutic transplant potential.
-
Full-text index only
A comparison of programmed cell death between species.
PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups
The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.
-
Full-text index only
Biodefense versus bioterrorism.
PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups
Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask
-
Full-text index only
Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109.
PMID 20035377 · PMC2929293 · Breast cancer research and treatment · 2010 · 8 claims · 8 setups
Serine protease inhibitors (aprotinin, SBTI) cause morphological reversion of malignant T4-2 breast cancer cells in 3D culture, restoring acinar structure and basal polarity
-
Has reproduction · 84
Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.
PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups
Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).
-
Full-text index only
Genomic sequencing of the severe acute respiratory syndrome-coronavirus.
PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups
PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.
-
Full-text index only
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.
PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups
High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.
-
Full-text index only
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups
Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation
-
Has reproduction · 97
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.
PMID 34471117 · PMC8410849 · Nature communications · 2021 · 7 claims · 5 setups
Chromosome 3D structure in S. ambofaciens correlates with genetic compartmentalization during exponential phase, with the central region segmented into domains and quiescent terminal compartments
-
Has reproduction
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.
PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups
Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph
-
Full-text index only
A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.
PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups
Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines
-
Full-text index only
Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.
PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups
Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence
-
Has reproduction · 58
Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.
PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups
Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)
-
Has reproduction · 54
Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.
PMID 36560952 · PMC9763275 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress
-
Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
-
Full-text index only
G, N, and P gene-based analysis of Chandipura viruses, India.
PMID 15705335 · PMC3294343 · Emerging infectious diseases · 2005 · 8 claims · 4 setups
The 2003 epidemic CHPV isolates are closely related to, and not very divergent from, the 1965 isolate, indicating the outbreak was not associated with extensive mutations in the G, N, and P genes.
-
Full-text index only
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.
PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups
A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)