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).

Publications 1.3k Datasets 392.5k Experiments 363

Assay: molecular ✕ Clear

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

recombinant selenomethionine-substituted ge-gi models surface x-ray computational
A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

PMID 17997604 · PMC2065879 · PLoS pathogens · 2007 · 8 claims · 5 setups

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Two enJSRV proviruses (enJS56A1 and enJSRV-20) independently acquired a defective, transdominant Gag (R21W substitution) that blocks late replication steps of exogenous JSRV/ENTV

sheep nih3t3 domestic enjsrv bac retroviral locus-specific
Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

genome synthetic c-kit87 c-kit genome-wide circular molecular
Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

microdissected formalin-fixed archival clinical pcr fluorescence laser
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
Reconstruction of human protein interolog network using evolutionary conserved network.

PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

ppi sequences interaction predicted interolog orthology quasi-clique
Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

breast early-stage diffuse dlbcl gene
Melanesian mtDNA complexity.

PMID 17327912 · PMC1803017 · PloS one · 2007 · 8 claims · 5 setups

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Among-group mtDNA variation in Northern Island Melanesia is structured by island, island size, and language affiliation.

populations near mtdna mtdna analysis coalescence
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

PMID 19102774 · PMC2630979 · BMC medical genetics · 2008 · 8 claims · 6 setups

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Variation in SYN III distal CpG island methylation is not related to schizophrenia in the population sample or in a monozygotic twin pair discordant for schizophrenia

brain blood non-human semi-quantitative sodium bisulfite
ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI

clinical gonorrhoeae coli mic spontaneous pcr
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

coli sds-page glutathione pepck-gst sds-page maldi-tof native
Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

PMID 19028587 · PMC2686088 · Journal of structural biology · 2009 · 8 claims · 8 setups

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Nucleotide-bound (ADP and ANP/AMP-PNP) Mer kinase domain adopts an autoinhibited DFG-Asp-in/αC-Glu-out conformation with an activation-loop residue inserted into the active site

recombinant phosphorylated mer x-ray positional differential
Increased constraints on MC4R during primate and human evolution.

PMID 19011902 · PMC9947067 · Human genetics · 2009 · 6 claims · 7 setups

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There is a significant paucity of genetic diversity at MC4R in humans but not in chimpanzees.

hgdp-ceph germans central additional dhplc direct coding
Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

egfr tp53 laci lung literature comparative statistical
Organization of physical interactomes as uncovered by network schemas.

PMID 18949022 · PMC2561054 · PLoS computational biology · 2008 · 7 claims · 5 setups

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A computational procedure can systematically identify 'emergent' network schemas that are both recurrent and over-represented relative to randomized networks preserving lower-order subschema distributions

cerevisiae sapiens uncharacterized network cross-species functional
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular
Metabolic syndrome: from epidemiology to systems biology.

PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

populations rats adipose four genome-wide linkage gene

Experiments

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

Reconstruction of human protein interolog network using evolutionary conserved network.

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

Melanesian mtDNA complexity.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

Increased constraints on MC4R during primate and human evolution.

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

Organization of physical interactomes as uncovered by network schemas.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

Metabolic syndrome: from epidemiology to systems biology.