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 677

System / cell line: test ✕ Clear

miRGator: an integrated system for functional annotation of microRNAs.

PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

genome predicted tissues organs computational functional mirna
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
Inconsistencies in Neanderthal genomic DNA sequences.

PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap
Finding disease candidate genes by liquid association.

PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
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
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
A newly identified insertion mutation in the thyroid hormone receptor-beta gene in a Korean family with generalized thyroid hormone resistance.

PMID 17596672 · PMC2693656 · Journal of Korean medical science · 2007 · 7 claims · 8 setups

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Two members of a Korean family (mother and son) with generalized RTH harbor a novel insertion mutation, 1358_1359insC, in exon 10 of the THRB gene, causing a frameshift (Leu454PhefsX11)

peripheral serum thyroid pcr radioimmunoassay thyroid
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
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
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

Has reproduction · 30

MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

simplified genome-scale cerevisiae coli minspan spearman comparative
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

cell-cycle-synchronized hela computational differentially tiling cdna statistical
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis.

PMID 17311103 · PMC1794595 · PloS one · 2007 · 5 claims · 4 setups

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B-RAF and N-RAS mutation status is well preserved (strongly concordant) between tumor tissue biopsies and corresponding short-term in vitro propagated cell lines.

tumor biopsy-derived metastatic pcr direct survival
A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

PMID 17308433 · PMC3479083 · Hormone research · 2007 · 7 claims · 6 setups

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A novel C794G transversion causing missense mutation T265R in DAX1 (NR0B1) is responsible for X-linked adrenal hypoplasia congenita in this kindred

genomic tsa201 unspecified proband sequence modified full-length
Long-term trends in evolution of indels in protein sequences.

PMID 17298668 · PMC1805498 · BMC evolutionary biology · 2007 · 8 claims · 5 setups

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More than one third of protein domains show a statistically significant tendency to increase or decrease in size over evolutionary distance.

curated individual cdd linear pearson binomial
Exploiting noise in array CGH data to improve detection of DNA copy number change.

PMID 17272296 · PMC1994778 · Nucleic acids research · 2007 · 7 claims · 4 setups

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When aberrations are present, noise in BAC, 19k oligo, and 385k oligo array-CGH data is highly non-Gaussian and shows long-range spatial correlations.

atm-deficient normal simulated array simulated
Severe loss-of-function mutations in the adrenocorticotropin receptor (ACTHR, MC2R) can be found in patients diagnosed with salt-losing adrenal hypoplasia.

PMID 17223989 · PMC1859977 · Clinical endocrinology · 2007 · 7 claims · 5 setups

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MC2R mutations can be found in children diagnosed with salt-losing forms of adrenal hypoplasia

genomic plasma children direct plasma standard

Experiments

miRGator: an integrated system for functional annotation of microRNAs.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Inconsistencies in Neanderthal genomic DNA sequences.

Finding disease candidate genes by liquid association.

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

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

TEMP: a computational method for analyzing transposable element polymorphism in populations.

A newly identified insertion mutation in the thyroid hormone receptor-beta gene in a Korean family with generalized thyroid hormone resistance.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

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

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis.

A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

Long-term trends in evolution of indels in protein sequences.

Exploiting noise in array CGH data to improve detection of DNA copy number change.

Severe loss-of-function mutations in the adrenocorticotropin receptor (ACTHR, MC2R) can be found in patients diagnosed with salt-losing adrenal hypoplasia.