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 81

System / cell line: clonal ✕ Clear

Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

PMID 12194772 · PMC2732546 · Emerging infectious diseases · 2002 · 8 claims · 5 setups

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Clonal complex, as defined by MLST, is an epidemiologically relevant unit for long- and short-term investigation of C. jejuni epidemiology.

jejuni same clonal mlst multilocus heat-stable flaa
A biomedically enriched collection of 7000 human ORF clones.

PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

genes mgc plasmid literature pcr sequence
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 8 claims · 6 setups

Has reproduction · 78

Genomics can identify malignant transformation in MGUS and SMM, defining biologically distinct subsets termed genomic MM and genomic MGUS that are indistinguishable from or distinct from MM at the genomic level.

cd138+ mgus bone whole-exome whole-genome cnv
Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 7 claims · 8 setups

Has reproduction · 68

The integrated stress response induces colorectal cancer cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

ht29-derived nod ±dox ht29 qpcr death tumor
Genomic variability within an organism exposes its cell lineage tree.

PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

robinia arabidopsis randomly genotyping multiplex computer
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

serum hvr1 svr rt-pcr shannon hamming
Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

PMID 19903857 · PMC2973841 · Cancer research · 2009 · 8 claims · 8 setups

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S1P2−/− mice develop clonal B-cell lymphomas with age, with ~half affected by 1.5-2 years

s1p2− lymphoma bone genomic necropsy histology flow
A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese.

PMID 18811933 · PMC2565682 · BMC cancer · 2008 · 7 claims · 2 setups

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The hMYH haplotype T/A variant allele is present at significantly higher frequency in CRC patients than in healthy controls

peripheral cos-7 dhplc immunofluorescence
Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups

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There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.

jejuni ssh panel suppression blastx dot-blot
CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

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TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

snap-frozen tumor u-2-os patients pcr bisulphite loss
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
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
Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

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MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

trachomatis pneumoniae chlamydiales mlst eburst upgma
Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

Has reproduction · 90

Weak selection conferred by stem cell variation created before birth can reliably yield clonal hematopoiesis later in life.

hscs simulated methylation single-cell
Base editing in human cells with monomeric DddA-TALE fusion deaminases.

PMID 35821233 · PMC9276701 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 95

mDdCBEs built from non-toxic full-length DddA_tox variants enable mitochondrial DNA base editing with efficiencies of up to 50% upon transient expression in human cells

hek293t nih3t3 targeted clonal aav2
Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

falciparum cdna c18 genomic rt-pcr southern genomic
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic

Experiments

Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

A biomedically enriched collection of 7000 human ORF clones.

Toward the use of genomics to study microevolutionary change in bacteria.

Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

Genomic variability within an organism exposes its cell lineage tree.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese.

Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

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

Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

Base editing in human cells with monomeric DddA-TALE fusion deaminases.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.