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 20

System / cell line: single ✕ Assay: substitution ✕ Clear

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

PMID 33397809 · PMC7826347 · Proceedings of the National Academy of Sciences of the United States of America · 2021 · 8 claims · 7 setups

Has reproduction · 48

An AD-specific frameshift single-nucleotide insertion in exon 27 of PLCγ1 substitutes isoleucine 970 to asparagine in the 5xFAD AD mouse model.

cortex 5xfad forebrain plcγ1 rna-seq rna-seq-based western
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 6 setups

Has reproduction · 79

CLSM6A, a CNN-based model set, predicts single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

clsm6a learned last-layer computational model-based propagation-based
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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OPTC is a candidate gene involved in POAG pathogenesis

genomic pcr optc retinal pcr-sscp dhplc sequencing
Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

Has reproduction · 66

A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

zygotes aorta genomic aortae crispr prime quantitative
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
SNAP: predict effect of non-synonymous polymorphisms on function.

PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

combined escherichia bacteriophage hiv-1 neural benchmark comparative
The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

PMID 19908860 · PMC2787777 · Journal of the American Chemical Society · 2009 · 8 claims · 6 setups

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The full-length bcl-2 C-rich promoter sequence (Py39WT) forms one major intramolecular i-motif structure with a transitional pH of 6.6

py39wt fam 32p-labeled circular melting fret
Infrequent involvement of p53 gene mutations in the tumourigenesis of Japanese prostate cancer.

PMID 7691145 · PMC1968625 · British journal of cancer · 1993 · 6 claims · 3 setups

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p53 gene mutations are infrequent in the tumorigenesis of primary Japanese prostate cancer

prostate pcr-sscp sequencing
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

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Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389
APC mutation analysis by chemical cleavage of mismatch and a protein truncation assay in familial adenomatous polyposis.

PMID 7524601 · PMC2033526 · British journal of cancer · 1994 · 7 claims · 8 setups

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Chemical cleavage of mismatch (HOT) analysis combined with sequencing identified inactivating constitutional APC mutations in 9 of 10 (90%) linkage-confirmed FAP patients, far exceeding the ~30% detection rate reported in the literature.

blood pcr pcr-amplified cdna chemical sequencing single-strand
Physiology engages with functional genomics - at last.

PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

wild-type caenorhabditis kidney pcr qtl enu copas
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

env u373 mt4-r5 u373-r5 phylogenetic infectivity flow
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

PMID 15905472 · PMC1131937 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Introducing streptavidin-coated magnetic microparticles (MMPs) into a sandwich-type CP-based DNA sensor significantly improves selectivity against non-cognate DNA compared with previously reported CP-amplified sensors.

cell-free synthetic brca1-related artificial fluorescence magnetically salt-stringency
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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Expression context is largely conserved between orthologs across four eukaryote species.

elegans pairwise orthologs cerevisiae microarray ortholog functional
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state

Experiments

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

Heterotachy in mammalian promoter evolution.

SNAP: predict effect of non-synonymous polymorphisms on function.

The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

Infrequent involvement of p53 gene mutations in the tumourigenesis of Japanese prostate cancer.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

APC mutation analysis by chemical cleavage of mismatch and a protein truncation assay in familial adenomatous polyposis.

Physiology engages with functional genomics - at last.

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

Bias of selection on human copy-number variants.

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.