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 38

System / cell line: identified ✕ Assay: alignment ✕ Clear

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

genomic genome extracted pairwise online genome-wide
Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

genomic electronic pcr pcr-restriction
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

genome insect yy1-related zinc blast sequence synonymous
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
Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

metazoan identified amphimedon nematostella genome sequence gene
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

Has reproduction · 100

NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

garlic pepper pear grapevine rna-seq mrna-seq transcriptome
Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

PMID 37243151 · PMC10224212 · Viruses · 2023 · 8 claims · 7 setups

Has reproduction · 100

An exhaustive-search workflow can recover intra-host co-existing SARS-CoV-2 strains from the reference-genome read set (SRR11092062) that de Bruijn-graph assemblers discard.

sars-cov-2 spike predicted california short-read read sequence
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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202 novel box H/ACA RNA-related sequences were identified in the human genome

genome chimpanzee aca flanking megablast comparative sequence
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

drosophila caenorhabditis xenopus five pairwise evoprint comparison
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

tcp0 tcp2β blast-p phylogenetic structure
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

standard thp-1 replicate lc-ms manual cross-instrument
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

Has reproduction · 54

Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

pad phylogenetic est est-based
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

PigGIS: Pig Genomic Informatics System.

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

A mouse plasma peptide atlas as a resource for disease proteomics.

A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.