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 1.3k

System / cell line: across ✕ Clear

Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

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Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

perfused lung microarray principal wilcoxon
The spectrum of NF1 mutations in Korean patients with neurofibromatosis type 1.

PMID 16479075 · PMC2733956 · Journal of Korean medical science · 2006 · 7 claims · 5 setups

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NF1 mutations in Korean patients show a wide spectrum distributed across exon 3 to intron 47 with no mutational hot spots

blood-derived lymphocytes blood unrelated genomic rt-pcr microsatellite
Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
How accurately is ncRNA aligned within whole-genome multiple alignments?

PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

genome vertebrate nonhuman genomic sequence whole-genome covariance
Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

PMID 17900363 · PMC2098775 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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M. ulcerans has evolved into five InDel haplotypes that separate into two distinct phylogenetic lineages: a 'classical' lineage (Africa, Australia, South East Asia) and an 'ancestral' lineage (Asia, South America, Mexico)

ulcerans marinum plasmid-based pcr genome
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

genome protein-protein genes artificial kappa clustering gene
Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

PMID 17653048 · PMC2776539 · Molecular vision · 2007 · 8 claims · 4 setups

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No RP patient among 68 Japanese subjects carried a RHO mutation causing an amino acid substitution

blood-derived genomic chromosomes rho whole-locus pcr haplotype
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

PMID 17553837 · PMC1933173 · Nucleic acids research · 2007 · 8 claims · 8 setups

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MultiPhyl is the first high-throughput distributed phylogenetics platform capable of using idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer

50sc 101sc 150sc 150arb tree-search
Simple models of genomic variation in human SNP density.

PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

genome observed simulated genome hierarchical coalescent
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

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Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Cataloging coding sequence variations in human genome databases.

PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

coding hapmap concurrent nssnps database hapmap amino
Improving the specificity of exon prediction using comparative genomics.

PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

human-mouse human-dog genome simulated comparative single-genome simulated
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

PMID 18680585 · PMC2529308 · BMC evolutionary biology · 2008 · 8 claims · 7 setups

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R7a1, a recently derived sub-branch of haplogroup R7, is particularly frequent among Munda-speaking tribal groups

mtdnas haplogroup genetic geographic complete hvs-i reduced-median
A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

PMID 18615428 · PMC2855839 · Proteomics · 2008 · 6 claims · 4 setups

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Noise in SELDI-TOF/MALDI-TOF mass spectrometry data is heteroscedastic across the m/z range, with larger variance at lower m/z values, contrary to the homogeneous noise assumption of existing wavelet denoising methods.

serum raw denoised simulated seldi-tof wavelet-based peak
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation

Experiments

Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

The spectrum of NF1 mutations in Korean patients with neurofibromatosis type 1.

Direct maximum parsimony phylogeny reconstruction from genotype data.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

How accurately is ncRNA aligned within whole-genome multiple alignments?

Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

Population genomics of human gene expression.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Simple models of genomic variation in human SNP density.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Cataloging coding sequence variations in human genome databases.

Improving the specificity of exon prediction using comparative genomics.

An integrated genomic analysis of human glioblastoma multiforme.

Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.