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 45

System / cell line: analysis ✕ Assay: breakpoint ✕ Clear

Expanding CEP290 mutational spectrum in ciliopathies.

PMID 19764032 · PMC4340070 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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A large heterozygous genomic deletion spanning the CEP290 C-terminus (exons 42-54) was identified in a JSRD-COR patient previously known to carry only one CEP290 point mutation.

peripheral genomic quantitative cdna pcr
The fragile breakage versus random breakage models of chromosome evolution.

PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

small synthetic synteny random whole-genome
New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

PMID 18673538 · PMC2553414 · Retrovirology · 2008 · 7 claims · 5 setups

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04FR-KZS clusters with two previously described DRC viruses and represents CRF27_cpx, a complex recombinant involving A/E/G/H/J/K/U subtypes.

pbmcs v3-v5 full-length undetermined v3-v5 full-length phylogenetic
Chromosomal phenotypes and submicroscopic abnormalities.

PMID 15601540 · PMC3525070 · Human genomics · 2004 · 8 claims · 8 setups

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Microdeletion syndromes are flanked by region-specific low-copy repeats (LCRs), and non-allelic homologous recombination (NAHR) between these LCRs, via interchromosomal or intrachromosomal mechanisms, causes the deletions.

patients parents vegf164 zebrafish breakpoint parental inversion
The signal in the genomes.

PMID 16683016 · PMC1447653 · PLoS computational biology · 2006 · 7 claims · 3 setups

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A high breakpoint reuse rate in the output of rearrangement algorithms indicates loss of historical signal, not good evidence for genomic fragile regions

simulated genome
Recurring genomic breaks in independent lineages support genomic fragility.

PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

hg17 genome computationally comparative marker segmental
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
A statistical approach for array CGH data analysis.

PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data

fibroblast simulated bt474 dissected array numerical
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

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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
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

PMID 19888473 · PMC2768585 · PLoS computational biology · 2009 · 8 claims · 5 setups

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Translocation-related human proteins are significantly enriched in intrinsic structural disorder compared to all human proteins

translocation-related translocation cyclin-dependent intrinsic pfam randomized
Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers.

PMID 10027311 · PMC2362423 · British journal of cancer · 1999 · 6 claims · 5 setups

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Abnormal (aberrant) TSG101 transcripts are common in both cancerous and non-cancerous cervical/endometrial tissue as well as in normal peripheral mononuclear cells

cervical peripheral rt-pcr southern long
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

hcv 5'ncr serum maximum sequence recombination
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original
Identifying the important HIV-1 recombination breakpoints.

PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

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Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

inter-subtype parental copy-choice probabilistic comparative
Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

PMID 14735197 · PMC2409581 · British journal of cancer · 2004 · 8 claims · 8 setups

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Kindred MON1080 carries germline truncating mutations in both MSH2 and BRCA2, with two family members being double heterozygotes

colonic astrocytoma breast microdissected immunohistochemistry microsatellite truncation
Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

hiv-1 four simulated population-based maximum bayesian
Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination.

PMID 18824584 · PMC2571921 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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Homozygous deleterious PMS2 mutations are associated with a B cell-intrinsic CSR deficiency in three patients

pbls fibroblasts cd19+ rt-pcr genomic western
Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups

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Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2

genomic peripheral setx sanger dosage long-range
Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

metaphase genomic ebv-transformed serum fluorescence multiplex sanger

Experiments

Expanding CEP290 mutational spectrum in ciliopathies.

The fragile breakage versus random breakage models of chromosome evolution.

New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

Chromosomal phenotypes and submicroscopic abnormalities.

The signal in the genomes.

Recurring genomic breaks in independent lineages support genomic fragility.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

A statistical approach for array CGH data analysis.

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.

Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers.

Probing the cancer genome.

Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

Identifying the important HIV-1 recombination breakpoints.

Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination.

Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.