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 879

System / cell line: per ✕ Clear

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

genes autosomes dog genome comparative blat sliding-window
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

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Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

kegg 8192x8192 user-submitted species pathway zoomable sequence
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

PMID 19906696 · PMC2811030 · Nucleic acids research · 2010 · 6 claims · 4 setups

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MiGS combines MBD2 MBD-domain precipitation of methylated DNA with massively parallel sequencing to enable unbiased, high-throughput genome-wide DNA methylation profiling

hct116 migs mbd-isolated bisulfite gene
Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

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Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

hcv-1a phylogenetic sequence nucleotide
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

serum hbv full-length o-hbv nested phylogenetic quasispecies
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Structure of protein interaction networks and their implications on drug design.

PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

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Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

budding pin yeast protein-protein graph-theoretic gene
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

Has reproduction · 93

24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

jatropha geo bulk semi-quantitative quantitative
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

PMID 19850495 · PMC2818324 · Journal of the American Society for Mass Spectrometry · 2010 · 7 claims · 4 setups

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MAZIE is a post-acquisition Perl algorithm that determines precursor ion monoisotopic mass and charge (+1 to +4) from MS1 zoom scan isotopic distributions on a Thermo LTQ-XL

urine same lc-ms2 ms1 comparative
A new paradigm for MAPK: structural interactions of hERK1 with mitochondria in HeLa cells.

PMID 19847302 · PMC2760858 · PloS one · 2009 · 8 claims · 8 setups

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hERK1 translocates to the mitochondria of HeLa cells upon a proliferative stimulus

hela confocal immunofluorescence western
Enrichment of sequencing targets from the human genome by solution hybridization.

PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

genome genomic same technical capture solution-hybridization sequence
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

PMID 19828875 · PMC2816009 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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A stacked-ring ion guide (S-lens) increases ion transmission from the source into the instrument roughly 10-fold in MS/MS mode and 3-5-fold in full scan mode

intact bsa hela model top-down nanoflow ion
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

PMID 19813771 · PMC2789208 · Journal of proteome research · 2009 · 7 claims · 7 setups

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Coupling DRC (hexapeptide libraries) with 3D peptide fractionation (IEF + SCX + µLC-MS/MS) substantially increases the number of proteins identified in whole saliva

saliva offgel-fractionated identified sds-page trypsin strong
Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

hiv-1 polyclonally shannon cross-clade ctl
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm

Experiments

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Structure of protein interaction networks and their implications on drug design.

Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

A new paradigm for MAPK: structural interactions of hERK1 with mitochondria in HeLa cells.

Enrichment of sequencing targets from the human genome by solution hybridization.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.