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 14

System / cell line: same ✕ Assay: vector ✕ Clear

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

missense same synthetic tp53 random support principal
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

colorectal cdna matched thyroid rt-pcr restriction genomic
Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

globally same computational publicly y-str snp supervised
Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

PMID 36882868 · PMC9991879 · BMC medicine · 2023 · 8 claims · 6 setups

Has reproduction · 89

Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes

population-level age-structured same ethiopia dynamic epidemiological daly
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
Analysis of polymorphic TGFB1 codons 10, 25, and 263 in a German patient group with non-syndromic cleft lip, alveolus, and palate compared with healthy adults.

PMID 15212689 · PMC441379 · BMC medical genetics · 2004 · 8 claims · 3 setups

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Arg25Pro heterozygous genotype is significantly less frequent in CLP patients (3.3%) than in healthy controls (16.7%)

peripheral genomic platelet-poor real-time sanger enzyme-linked
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

Has reproduction · 92

Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

six same polished each nanopore illumina novo
The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

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UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

panel 293-t malignant same rt-pcr northern fluorescence
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

PMID 18784923 · PMC2755762 · Annals of hematology · 2009 · 6 claims · 4 setups

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A non-radioactive, enzyme-coupled luminometric assay can quantify Ras activation as %GTP/(GTP+GDP) with high sensitivity (detects 1 fmol GTP)

bone n=23 3t3 ras genomic

Experiments

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

Analysis of polymorphic TGFB1 codons 10, 25, and 263 in a German patient group with non-syndromic cleft lip, alveolus, and palate compared with healthy adults.

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

Does distance matter? Variations in alternative 3' splicing regulation.

Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.