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 33

System / cell line: derived ✕ Assay: copy ✕ Clear

Personalized copy number and segmental duplication maps using next-generation sequencing.

PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

genomes genomic interphase na18507 whole-genome array fluorescence
Free energy of DNA duplex formation on short oligonucleotide microarrays.

PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

mapping50k_xba240 dgcr hg-u133a pdnn free correlation
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
High resolution array-CGH analysis of single cells.

PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

769p hct116 peripheral single array-cgh gel fish
Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

same caucasian cau autosomal snp copy population
SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

chromosome 16p array probe-by-probe sw-array
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

PMID 41758938 · PMC12947870 · Science advances · 2026 · 7 claims · 8 setups

Has reproduction · 84

MYOD1 L122R-mutant SRMS comprises three coexisting tumor cell states (MYOD1-enriched progenitor-like, proliferative transition, and partially differentiated with reduced MYOD1 activity) reflecting disrupted myogenic differentiation.

six myod1 independent paired single-nucleus targeted bulk
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

horizon six cho-k1 cho genome rna-seq targeted
Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
Gene duplication: the genomic trade in spare parts.

PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

great genome recently yeast genome-wide molecular comparative
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
Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

PMID 17324265 · PMC1810516 · BMC medical genetics · 2007 · 8 claims · 3 setups

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Developed a real-time TaqMan PCR method that quantifies PARK2 exon 1-12 copy number by comparing amplification signal to the β-globin internal control gene

genomic same real-time prior
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species
Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

PMID 18616530 · PMC4732719 · Clinical genetics · 2008 · 8 claims · 8 setups

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TMC1 mutations were identified in seven of the families/patients segregating hearing loss linked to DFNA36/DFNB7-11

families affected tmc1 tjp2 genetic sequencing multiplex
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups

Has reproduction · 91

A hybrid de novo assembly combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X) produced the YO draft genome Ogye_1.1 with contig and scaffold NG50 of 362.3 Kbp and 16.8 Mbp.

yeonsan tissues ogye_1.1 locus whole-genome sequencing reduced
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

hapmap bladder prostate simulated affymetrix simulation
High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

single bac amplified pi-scei array quantitative dot
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

PMID 40963120 · PMC12445032 · Genome medicine · 2025 · 7 claims · 4 setups

Has reproduction · 88

Trio genome sequencing (tGS) achieves higher prospective diagnostic yield than standard-of-care (SoC) and singleton genome sequencing (sGS) even when performed by a newly trained team.

individuals index blood short-read exome array
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

Has reproduction · 71

DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

ucec ishikawa rna-seq proteomics immunohistochemistry

Experiments

Personalized copy number and segmental duplication maps using next-generation sequencing.

Free energy of DNA duplex formation on short oligonucleotide microarrays.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

High resolution array-CGH analysis of single cells.

Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

Analysis of copy number variation using quantitative interspecies competitive PCR.

Gene duplication: the genomic trade in spare parts.

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

Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.