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 37

System / cell line: specific ✕ Assay: repeat ✕ Clear

Identifying repeat domains in large genomes.

PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

repbase elegans concatenated repeat comparative dot
SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups

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SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools

genome reference genomic runtime sequence comparative
An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

Has reproduction · 90

Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.

pearl old oxford bionano illumina
Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

PMID 12589088 · PMC3054991 · Journal of Korean medical science · 2003 · 6 claims · 5 setups

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The t-PA I/D or D/D genotype is significantly associated with duodenal (vs gastric) ulcer location

genomic randomly patients endoscopic allele-specific pcr logistic
Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

csf brain normal 2d-dige label-free isotopic
Surfactant protein B gene variations enhance susceptibility to squamous cell carcinoma of the lung in German patients.

PMID 12107845 · PMC2376109 · British journal of cancer · 2002 · 8 claims · 1 setups

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The SP-B intron 4 gene variant is significantly more frequent in squamous cell lung carcinoma (SCC) patients (25.0%) than in matched controls, OR=3.2, P=0.016

peripheral allele-specific
Structure of the intergenic spacers in chicken ribosomal DNA.

PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

Has reproduction · 80

Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping
Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

serum-derived tumour serum ht29 arms sanger topo
PigGIS: Pig Genomic Informatics System.

PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

million pig matched wgs blastx repeat sequence
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
A dispermic chimera with mixed field blood group B and mosaic 46,XY/47,XYY karyotype.

PMID 17596670 · PMC2693654 · Journal of Korean medical science · 2007 · 7 claims · 7 setups

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The propositus shows mixed-field agglutination with anti-B that mimics the B3 ABO subtype but is not caused by a B3 allele.

propositus relatives serologic allele-specific haplotype-specific
Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

costa buffy genetic real-time allele-specific
Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

PMID 15528790 · PMC3888729 · Disease markers · 2004 · 8 claims · 8 setups

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Mononucleotide repeats are more sensitive, specific, and easier to use than dinucleotide repeats for detecting MSI-H tumors

msi-h colon hmsh6-mutated tumors pentaplex pcr dinucleotide
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

peripheral ceph individuals cases strp genotyping fluorescent
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 76

The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

pyronema confluens fungal whole-genome k-mer rna-seq
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

PMID 18957099 · PMC2582241 · Malaria journal · 2008 · 7 claims · 8 setups

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pfhrp2 and pfhrp3 genes show markedly higher polymorphism than the P. falciparum and P. vivax aldolase and pldh genes

falciparum vivax extracted febrile pcr nested species-specific

Experiments

Identifying repeat domains in large genomes.

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

Surfactant protein B gene variations enhance susceptibility to squamous cell carcinoma of the lung in German patients.

Structure of the intergenic spacers in chicken ribosomal DNA.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

PigGIS: Pig Genomic Informatics System.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

A dispermic chimera with mixed field blood group B and mosaic 46,XY/47,XYY karyotype.

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

'Genome design' model and multicellular complexity: golden middle.

Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

Recent segmental and gene duplications in the mouse genome.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.