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 468

System / cell line: genes ✕ Assay: sequence ✕ Clear

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Vibrio cholerae pathogenic clones.

PMID 16318732 · PMC3367346 · Emerging infectious diseases · 2005 · 8 claims · 1 setups

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The US Gulf clone, the Australian clone, and 3 prepandemic El Tor strains are related to the seventh pandemic clone.

vibrio multilocus
Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

coli se11 rapd whole-genome gene
Sequence and structure signatures of cancer mutation hotspots in protein kinases.

PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

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Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

kinase common egfr autoinhibited database-driven structure-informed evolutionary
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

bovine cow coding blast-based ensembl gene
KEGG for linking genomes to life and the environment.

PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

protein-coding newly microarray kegg sequence computational glycan
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Integrative functional genomics.

PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

yeast tissue-cultured mammalian genomic comparative targeted chip-chip
Unlocking the microbial studies through computational approaches: how far have we reached?

PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

Has reproduction

Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

clinical bacteriophage vaginal hbv ngs random whole-genome
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence
Target SNP selection in complex disease association studies.

PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

genes pooled primer computational maldi-tof blast
The functional importance of disease-associated mutation.

PMID 12220483 · PMC128831 · BMC bioinformatics · 2002 · 6 claims · 1 setups

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Disease-associated mutations occur in conserved regions of genes and can be used to identify likely disease-causing mutations

disease-associated sequence
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled
Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

family additional unrelated mutant direct linkage targeted
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

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Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Cis sequence effects on gene expression.

PMID 17727713 · PMC2077339 · BMC genomics · 2007 · 6 claims · 4 setups

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Approximately one in four genes (8 of 30, 26.7%) exhibit statistically significant cis sequence effects on gene expression in this study, consistent with a literature-wide weighted average of 26.2%

lymphoblastoid genomic oligonucleotide gene candidate snp
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based

Experiments

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Speeding disease gene discovery by sequence based candidate prioritization.

Vibrio cholerae pathogenic clones.

Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

Sequence and structure signatures of cancer mutation hotspots in protein kinases.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

KEGG for linking genomes to life and the environment.

The gentle art of gene arrangement: the meaning of gene clusters.

Integrative functional genomics.

Unlocking the microbial studies through computational approaches: how far have we reached?

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

The DNA sequence and analysis of human chromosome 13.

Target SNP selection in complex disease association studies.

The functional importance of disease-associated mutation.

Comparative genomics comes of age.

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

Cis sequence effects on gene expression.

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.