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 14

System / cell line: novel ✕ Assay: domain ✕ Clear

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

pooled genome est novel tandem whole-genome est
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

hamster testis predicted cdna northern comparative
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

Has reproduction · 100

H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

longissimus muscle snps pig h3k27ac strand-specific starr-seq
SARS--beginning to understand a new virus.

PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups

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A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS

frhk-4 macaques sars-cov coronavirus virus infection whole-genome
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic
International research networks in viral structural proteomics: again, lessons from SARS.

PMID 18054092 · PMC2793675 · Antiviral research · 2008 · 8 claims · 8 setups

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International research networks (SPINE, VIZIER, FSPS, SEPSDA, SARS-DTV) coordinated a global effort to structurally characterize the SARS-CoV proteome

sars-cov x-ray nmr genome
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

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Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

ftld grn genomic post-mortem clinical volumetric direct
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct

Experiments

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Genetic diversity among five T4-like bacteriophages.

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

SARS--beginning to understand a new virus.

The EH1 motif in metazoan transcription factors.

International research networks in viral structural proteomics: again, lessons from SARS.

Tubulin proteomics: towards breaking the code.

A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.