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 18

System / cell line: fish ✕ Assay: in-silico ✕ Clear

Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

Has reproduction · 67

Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

vibrio coli anguillarum transposon-insertion conjugative functional
Molecular genetics and structural genomics of the human protein kinase C gene module.

PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

metaphase genome pkc genomic fluorescence bioinformatic snp
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

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The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

chicken turkey broiler chromosome single fish
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

genomic genome pcr real-time fluorescence sequence
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

genomic same pseudo-normal artificially snp fish molecular
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation.

PMID 18947387 · PMC2579299 · Molecular cancer · 2008 · 8 claims · 8 setups

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A novel t(2;11)(q11.2;p15.1) translocation was identified as the sole cytogenetic abnormality in a childhood T-ALL case

bone genomic da926692 g-banding fish vectorette
Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

PMID 32762840 · PMC7413667 · eLife · 2020 · 8 claims · 8 setups

Has reproduction · 81

mRNA localization to mitochondria is condition-dependent: ATP3 mRNA switches from low (diffuse) association in fermentative conditions to strong mitochondrial association in respiratory conditions, while TIM50 is constitutively localized and TOM22 is diffuse.

cerevisiae computational live-cell single-molecule single-cell
Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

peripheral patient-parent genomic crebbp karyotyping bac microsatellite
In silico analysis of missense substitutions using sequence-alignment based methods.

PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

clinically sequence curated deep blosum62 sift align-gvgd
New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

PMID 19686598 · PMC2736583 · BMC medical genetics · 2009 · 8 claims · 7 setups

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DGGE screening of the non-duplicated PKD1 region detects likely pathogenic mutations in Czech ADPKD patients

genomic pcr polycystin-1 czech denaturing sanger family
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

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Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

genomic pcr additional cat linkage direct heteroduplex
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

lung known leukemia tumor paired-end computational snp
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

Experiments

Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

Molecular genetics and structural genomics of the human protein kinase C gene module.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation.

Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

In silico analysis of missense substitutions using sequence-alignment based methods.

New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

Genome assembly comparison identifies structural variants in the human genome.

PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

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