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 110

System / cell line: acid ✕ Assay: genomic ✕ 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
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
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups

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Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin

rabbit gtm66 myoc myocilin cdna sds-page transfection
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups

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Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.

genomic myoc poag pcr amino clinical
Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

Has reproduction · 91

SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

deep co-assembled surf_17 surf_5 whole-genome novo 16s
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
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
Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

pbmc his-tagged cem mammalian pcr electrophoretic western
Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

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A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

genomic stra6 direct variant
Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

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Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

healthy genomic genotype trial randomized snp haplotype
Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

PMID 18820594 · PMC2905378 · Pharmacogenetics and genomics · 2008 · 7 claims · 8 setups

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The tRNA-Thr G15927A mutation has a potential modifier role that increases penetrance and expressivity of A1555G-associated deafness.

blood genomic lymphoblastoid same pcr-rflp mitochondrial northern
The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

PMID 18718264 · PMC3835188 · The Journal of pediatrics · 2008 · 6 claims · 5 setups

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The patient carries two identical homozygous mutations (GC>AA at positions 197/198) in exon 1 of PCFT, causing a premature stop codon (C66X)

parental rfc hela blood genomic [3h]5-methyltetrahydrofolate northern
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

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The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

genomic somali sri ethnically dhplc snp sanger
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Microbial metagenomics.

PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

gastrointestinal acid ocean group metagenomic shotgun comparative

Experiments

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

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

Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

Species-specific protein sequence and fold optimizations.

Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

Evidence for a novel gene associated with human influenza A viruses.

Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

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

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Microbial metagenomics.