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 30

System / cell line: stratified ✕ Assay: sequence ✕ Clear

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
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic
Target SNP selection in complex disease association studies.

PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

genes pooled primer computational maldi-tof blast
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

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Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding
Genome-wide identification of human functional DNA using a neutral indel model.

PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

chromosome human-mouse genome individual whole-genome probabilistic comparative
Patterns and rates of intron divergence between humans and chimpanzees.

PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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Intron divergence (Ki) is strongly positively correlated with intron length

orthologous genome whole-genome cpg recombination
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

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GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

homologous human-mouse same gene comparative parameter micro-exon
The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
Computing Ka and Ks with a consideration of unequal transitional substitutions.

PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

simulated pairs human-mouse human-dog computer comparative
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

Has reproduction · 86

RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

ccds glioblastoma experimental simulated simulated bulk quality
Towards alignment independent quantitative assessment of homology detection.

PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

curated homologene swiss-prot fruit signalp homologene-based fhom
Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

autosomal intronic chimpanzee genes comparative human-chimpanzee background
Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

PMID 20057908 · PMC2802296 · Molecular vision · 2009 · 8 claims · 4 setups

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Mutations in CYP1B1 are a major cause of PCG in the studied patient cohort

genomic cyp1b1 pcg pcr missense clinical
Somatic mutations of KIT in familial testicular germ cell tumours.

PMID 15150569 · PMC2410291 · British journal of cancer · 2004 · 6 claims · 3 setups

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No germline KIT mutations were found in constitutional DNA from 240 familial TGCT pedigrees

blood ffpe familial csge direct contingency
Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

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Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

patients frozen genomic clinically randomized rt-pcr temporal
p53 mutation is a poor prognostic indicator for survival in patients with hepatocellular carcinoma undergoing surgical tumour ablation.

PMID 9514057 · PMC2149958 · British journal of cancer · 1998 · 8 claims · 6 setups

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p53 mutations were found in 8 of 12 HCCs with cirrhosis due to viral hepatitis and in both patients with sarcomatoid change

resected exon p53 hcc gc-clamped sscp restriction
Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.

PMID 17047654 · PMC2360725 · British journal of cancer · 2006 · 7 claims · 5 setups

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LH-MSA enables EGFR mutation analysis using small numbers of cancer cells from cytology specimens with a remarkably high success rate

cytology excised nsclc gefitinib-treated lh-mobility pcr clinical

Experiments

Inconsistencies in Neanderthal genomic DNA sequences.

Heterogeneous genomic molecular clocks in primates.

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

Target SNP selection in complex disease association studies.

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

Genome-wide identification of human functional DNA using a neutral indel model.

Patterns and rates of intron divergence between humans and chimpanzees.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

Computing Ka and Ks with a consideration of unequal transitional substitutions.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Towards alignment independent quantitative assessment of homology detection.

Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

Somatic mutations of KIT in familial testicular germ cell tumours.

Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

p53 mutation is a poor prognostic indicator for survival in patients with hepatocellular carcinoma undergoing surgical tumour ablation.

Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.