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 20

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

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
A computational screen for type I polyketide synthases in metagenomics shotgun data.

PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds
Genomic view of the evolution of the complement system.

PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

chicken complement sponge shark comparative phylogenetic reverse
Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

family p2ry5 affected snp microsatellite sanger
Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

cmt2c affected spinal drg genetic sanger quantitative
Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

PMID 11532213 · PMC55326 · Genome biology · 2001 · 7 claims · 5 setups

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The human genome contains fewer than 50 functional nuclear receptors, far fewer than C. elegans and about twice as many as Drosophila

genome elegans genomic panel tblastn hmmer pcr
Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

PMID 18997096 · PMC4836613 · Investigative ophthalmology & visual science · 2009 · 7 claims · 8 setups

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High T8993C mutant load (>77%) is associated with severe neurologic and/or retinal abnormalities, while low mutant load (42-54%) causes no detectable abnormalities.

retina blood visual adaptive real-time genetic
A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

PMID 19649163 · PMC2718742 · Molecular vision · 2009 · 7 claims · 7 setups

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A novel heterozygous UBIAD1 mutation, G98S, was identified in two affected members (proband and her father) of a Chinese SCCD family.

genomic cornea corneas blood direct pcr laser
A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

PMID 19693293 · PMC2728569 · Molecular vision · 2009 · 7 claims · 5 setups

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A novel in-frame 51 bp deletion (c.526_576del51) in TACSTD2, causing loss of 17 amino acids (codons 176-192), was identified as homozygous in two affected brothers with GDLD.

genomic excised left pcr pcr-restriction histopathology
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

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Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

Has reproduction · 84

Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

blood-derived four patients col2a1 targeted clinical transthoracic
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

PMID 14519199 · PMC328453 · Genome biology · 2003 · 8 claims · 5 setups

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Sequence-profile (PSI-BLAST) searches unify archaeal Alba with eukaryotic RNase P/MRP subunits Rpp20/Pop7 and Rpp25, and with the ciliate macronuclear-development protein Mdp2, into a single Alba superfamily.

archaeal eukaryotic alba sulfolobus psi-blast sequence phylogenetic
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

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Mutations in USH2A are responsible for most cases of USH2

genomic family probands ush2a direct restriction single
Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

lee-encoded escc sepq escd psi-blast blastp domain
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

Has reproduction · 94

The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

casei orthogroups unclassified selected whole-genome comparative pairwise
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood
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

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Computational comparison of two mouse draft genomes and the human golden path.

A computational screen for type I polyketide synthases in metagenomics shotgun data.

Genomic view of the evolution of the complement system.

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

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.