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 21

System / cell line: paired ✕ Assay: screening ✕ Clear

Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer.

PMID 16620376 · PMC1459869 · BMC cancer · 2006 · 8 claims · 3 setups

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Somatic mtDNA mutations are frequent in esophageal cancer, found in 55% (11/20) of tumors analyzed

paired fragments ttge direct real-time
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

paired lung tissue-pair pooled hiv-1 maximum statistical
Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups

Has reproduction · 69

Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII

gbs whole-genome multilocus capsular
Multiple polymorphisms, but no mutations, in the WAF1/CIP1 gene in human brain tumours.

PMID 7577473 · PMC2033923 · British journal of cancer · 1995 · 8 claims · 5 setups

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No somatic mutations of WAF1/CIP1 were found in 158 primary human brain tumours

reamplified same brain healthy sscp direct microsatellite
Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families.

PMID 9099970 · PMC2222784 · British journal of cancer · 1997 · 6 claims · 6 setups

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No germline TP53 mutations (exons 5-8) were found in 128 breast cancer patients from 109 families with familial cancer.

genomic tumour paired constant restriction sequencing
Genome-wide signatures of convergent evolution in echolocating mammals.

PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

Has reproduction

Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

four raw orthologous mammalian whole-genome novo homology-based
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

Has reproduction · 79

Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

pooled individual liver serum viral pcr strand-specific
Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

PMID 15138484 · PMC2409464 · British journal of cancer · 2004 · 8 claims · 4 setups

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High-grade breast tumours show a high frequency of LOH and/or abnormal expression of ATM, BRCA1 and TP53

early-onset same peripheral breast allelotyping immunohistochemistry direct
A novel GCAP1(N104K) mutation in EF-hand 3 (EF3) linked to autosomal dominant cone dystrophy.

PMID 18706439 · PMC2584361 · Vision research · 2008 · 8 claims · 7 setups

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A novel N104K mutation in GCAP1's third EF-hand (EF3) motif was identified in two affected members of a family with autosomal dominant cone dystrophy, the first naturally occurring mutation in the EF3 Ca2+-binding loop.

genomic patients high recombinant pcr full-field paired-flash
Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

PMID 10027310 · PMC2362430 · British journal of cancer · 1999 · 8 claims · 6 setups

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CDX2 expression is decreased in colorectal carcinomas in prior studies

genomic sporadic hnpcc carcinoma standard pcr-sscp cloning
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups

Has reproduction · 82

Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

klebsiella isolate a55848 assembled short-read phenotypic genome-based
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

Has reproduction · 43

TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

mdr-tb paired-end raw bam whole-genome kraken raw
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

Full-text index only

A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

ovarian case matched same pcr-sscp subcloning loh
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

Has reproduction · 87

TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

testseta bprna-new ts-inter individual jaccard pca ensemble
Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

Full-text index only

Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

sporadic msi-positive tumour unstable microsatellite denaturing sequencing
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
Whither genomics?

PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

Full-text index only

Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

mammalian budding yeast general expression genome-wide synthetic
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

Full-text index only

Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer.

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

Multiple polymorphisms, but no mutations, in the WAF1/CIP1 gene in human brain tumours.

Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families.

Genome-wide signatures of convergent evolution in echolocating mammals.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

A novel GCAP1(N104K) mutation in EF-hand 3 (EF3) linked to autosomal dominant cone dystrophy.

Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

Whither genomics?

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.