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 242

Assay: response ✕ Clear

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

Has reproduction · 78

METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

microbiome pooled hmp metarep genome assembly-based enzymatic
Autoantibody profiling for the study and treatment of autoimmune disease.

PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

serum antigen-antibody antigens fetal spotted elisa microarray
Genomic and proteomic profiling of responses to toxic metals in human lung cells.

PMID 12760830 · PMC1241504 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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Toxic metals (Cd, Cr, Ni, As) each induce a largely distinct, metal-specific pattern of gene expression changes in BEAS-2B human bronchial epithelial cells

beas-2b cdna western kinetworks
Molecular epidemiology of DFNB1 deafness in France.

PMID 15070423 · PMC385234 · BMC medical genetics · 2004 · 8 claims · 7 setups

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35delG remains the most common pathogenic GJB2 mutation in the studied French (Languedoc Roussillon) population despite being less frequent than in other Mediterranean populations

gjb2 dried genomic deaf dhplc pcr-mediated pcr-dhplc
A Korean family of hypokalemic periodic paralysis with mutation in a voltage-gated calcium channel (R1239G).

PMID 15716625 · PMC2808567 · Journal of Korean medical science · 2005 · 8 claims · 6 setups

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A 13-year-old boy and five affected relatives across three generations with hypokalemic periodic paralysis carry the R1239G mutation in CACNA1S

proband cousins mutation serum electrocardiography
Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

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A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

t-47d agarose chromatin cloning
Variants in the vitamin D receptor gene and asthma.

PMID 15651992 · PMC546000 · BMC genetics · 2005 · 8 claims · 6 setups

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VDR gene variants are candidate risk factors for asthma/allergy because vitamin D effects are mediated through the VDR and VDR maps to the 12q asthma linkage region

individuals children parents transmission bronchial pulmonary
Antibody binding loop insertions as diversity elements.

PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface
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
Functional genomics of early cortex patterning.

PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

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The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray
'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

PMID 18000506 · PMC2360265 · British journal of cancer · 2007 · 8 claims · 4 setups

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'Classical' EGFR mutations (exon 18 G719X, exon 19 DEL19, exon 21 L858R) are associated with better clinical outcome (disease control) with gefitinib

microdissected genomic ffpe advanced direct nested immunohistochemistry
Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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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

tigr xanthomonas xcc ann wu-blast whole-genome
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
Mutations in NYX of individuals with high myopia, but without night blindness.

PMID 17392683 · PMC2642916 · Molecular vision · 2007 · 7 claims · 5 setups

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Two novel NYX missense mutations (Cys48Trp and Arg191Gln) were found in unrelated males with high myopia but no night blindness.

unrelated individuals high model direct sequencing electroretinogram
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

genome affymetrix probe database microarray interactive
Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis.

PMID 19093009 · PMC2603250 · Molecular vision · 2008 · 8 claims · 6 setups

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OCT detects foveal and lamellar macular retinoschisis more frequently than funduscopy alone

xlrs genomic optical full-field multifocal
Searching for genes underlying behavior: lessons from circadian rhythms.

PMID 18988844 · PMC3744585 · Science (New York, N.Y.) · 2008 · 8 claims · 5 setups

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Forward genetic mutagenesis screens successfully identified the molecular components of the circadian clock across Drosophila, Neurospora, cyanobacteria, Arabidopsis, and mouse.

c57bl genomic automated contextual psychostimulant-induced
Truncation of retinoschisin protein associated with a novel splice site mutation in the RS1 gene.

PMID 18728755 · PMC2519029 · Molecular vision · 2008 · 8 claims · 5 setups

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Male patients exhibit typical bilateral foveal retinoschisis in two retinal layers detected by OCT

retina genomic rs1 optical full-field multifocal
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
Nicotinic acetylcholine receptor subunit variants are associated with blood pressure; findings in the Old Order Amish and replication in the Framingham Heart Study.

PMID 18625075 · PMC2478679 · BMC medical genetics · 2008 · 7 claims · 5 setups

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A synonymous coding SNP (rs2099489) in CHRNG is associated with higher systolic blood pressure in both the Old Order Amish (AFDS) and the Framingham Heart Study

amish non-first-degree-relative afds framingham variance direct snp

Experiments

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

Autoantibody profiling for the study and treatment of autoimmune disease.

Genomic and proteomic profiling of responses to toxic metals in human lung cells.

Molecular epidemiology of DFNB1 deafness in France.

A Korean family of hypokalemic periodic paralysis with mutation in a voltage-gated calcium channel (R1239G).

Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

Variants in the vitamin D receptor gene and asthma.

Antibody binding loop insertions as diversity elements.

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

Functional genomics of early cortex patterning.

'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

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

Mutations in NYX of individuals with high myopia, but without night blindness.

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis.

Searching for genes underlying behavior: lessons from circadian rhythms.

Truncation of retinoschisin protein associated with a novel splice site mutation in the RS1 gene.

Rise of the machines.

Nicotinic acetylcholine receptor subunit variants are associated with blood pressure; findings in the Old Order Amish and replication in the Framingham Heart Study.