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 15

System / cell line: codon ✕ Assay: statistical ✕ Clear

Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

PMID 16969349 · PMC2360724 · British journal of cancer · 2006 · 8 claims · 8 setups

Full-text index only

K-Ras codon 12 mutations are significantly associated with metastatic (M+) CRC

crc 202-patient pcr-rflp sscp immunohistochemistry
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

Full-text index only

The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Recurrent KRAS codon 146 mutations in human colorectal cancer.

PMID 16969076 · PMC2714972 · Cancer biology & therapy · 2006 · 8 claims · 8 setups

Full-text index only

KRAS A146 missense mutations are a recurrent, previously unrecognized class of somatic mutation in colorectal cancer

colorectal sporadic familial cancer pcr direct chi-squared
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

Full-text index only

The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

longitudinal backbone env intra-patient relaxed-clock correlation site-to-site
A role for the p53 pathway in the pathology of meningiomas with NF2 loss.

PMID 18974932 · PMC2692701 · Journal of neuro-oncology · 2009 · 7 claims · 4 setups

Full-text index only

The Pro72 allele of p53 codon 72 was not selected for in the meningioma cohort, and its distribution did not differ from control populations, indicating no role in meningioma initiation.

sporadic meningioma loss pcr-rflp histopathological
PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

Full-text index only

All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

vcjd scjd scottish controls pcr-rflp full chi-squared
WAF1/CIP1 structural abnormalities do not contribute to cell cycle deregulation in ovarian cancer.

PMID 8645586 · PMC2074480 · British journal of cancer · 1996 · 7 claims · 5 setups

Full-text index only

No WAF1/CIP1 coding mutations were found in any of 36 ovarian carcinomas sequenced, including tumors with LOH on 6p and those lacking p53 mutations

ovarian blood tumor pcr sequencing loss
Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

Full-text index only

IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

igvh germline non-igv immunogenetics flow cdna bioinformatic
Increased frequency of the k-ras G12C mutation in MYH polyposis colorectal adenomas.

PMID 15083190 · PMC2410274 · British journal of cancer · 2004 · 8 claims · 2 setups

Full-text index only

Somatic k-ras mutations occur in 9 of 54 (16.7%) MYH polyposis colorectal tumours, with frequency increasing with degree of dysplasia.

microdissected previously pcr literature-derived
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

Full-text index only

A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

expressed representative random genes computational orf statistical
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

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

Full-text index only

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
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

Full-text index only

Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

PMID 19918099 · PMC4155129 · Antiviral therapy · 2009 · 8 claims · 6 setups

Full-text index only

Primary integrase inhibitor resistance mutations (T66I, E92Q, G140S, Y143C/H/R, Q148H/R/K, N155S/H) were absent in 342 drug-naive individuals, indicating these sites are highly constrained.

plasma genomic viral aligned bulk sequence-based quantitative
Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

Full-text index only

Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

human-mouse high aarm orthologous content pairwise
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

Full-text index only

Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative

Experiments

Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

Empirical codon substitution matrix.

Recurrent KRAS codon 146 mutations in human colorectal cancer.

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

A role for the p53 pathway in the pathology of meningiomas with NF2 loss.

PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

WAF1/CIP1 structural abnormalities do not contribute to cell cycle deregulation in ovarian cancer.

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

Increased frequency of the k-ras G12C mutation in MYH polyposis colorectal adenomas.

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

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

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.