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 2k

Assay: sequencing ✕ Clear

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
Mutations in PIK3CA are infrequent in neuroblastoma.

PMID 16822308 · PMC1533846 · BMC cancer · 2006 · 8 claims · 6 setups

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PIK3CA activating mutations are infrequent in human neuroblastoma (2.9%, 2/69 tumors)

neuroblastoma neuroblastoma-derived patients th-mycn targeted sanger rt-pcr
Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

hiv-1 four simulated population-based maximum bayesian
Viruses take center stage in cellular evolution.

PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups

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A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)

acanthamoeba coccolithovirus nucleocytoplasmic dsdna whole-genome phylogenetic comparative
In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups

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The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India

mtdna mitochondrial partial hvs1
JAK2 V617F: a single mutation in the myeloproliferative group of disorders.

PMID 16755940 · PMC1891745 · The Ulster medical journal · 2006 · 8 claims · 8 setups

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A single acquired JAK2 mutation (V617F, G1849T in exon 14) is found across polycythaemia vera, essential thrombocythaemia and idiopathic myelofibrosis

blood haematopoietic granulocytes mpd pcr-direct sirna microsatellite
The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

chimpanzee chimp population non-human genome snp high-density
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 68

LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

schizosaccharomyces pombe rna-seq lasso lariat-specific
Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

armd dutch fibulin pef6-ssflag mutation computational site-directed
Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

formalin-fixed ffpe paired study direct pcr restriction
Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

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No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

t1d european warren resequencing database tag
Comparative genomics of emerging human ehrlichiosis agents.

PMID 16482227 · PMC1366493 · PLoS genetics · 2006 · 8 claims · 5 setups

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Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins (OMP-1/P44/Msp2 family) facilitating antigenic variation

phagocytophilum representative concatenated rickettsiales whole-genome comparative phylogenetic
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
WNT10B mutations in human obesity.

PMID 16477437 · PMC4304000 · Diabetologia · 2006 · 8 claims · 8 setups

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The WNT10B C256Y missense mutation abrogates the protein's ability to activate canonical WNT signalling and block adipogenesis

genomic 3t3-l1 subject proband dhplc top-flash western
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
Comparative genomics of multidrug resistance in Acinetobacter baumannii.

PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

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A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

baumannii resistance clinical whole-genome comparative sequence
Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

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Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

peripheral patients mody young-onset pcr microsatellite variant

Experiments

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

Mutations in PIK3CA are infrequent in neuroblastoma.

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

Viruses take center stage in cellular evolution.

In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

JAK2 V617F: a single mutation in the myeloproliferative group of disorders.

The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

Genetic diversity among five T4-like bacteriophages.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

Comparative genomics of emerging human ehrlichiosis agents.

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

WNT10B mutations in human obesity.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

Comparative genomics of multidrug resistance in Acinetobacter baumannii.

Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.