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 93

System / cell line: putative ✕ Clear

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

Has reproduction · 73

An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.

putative enterica selected assembled endpoint genome long-read
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

genomic rmrp family non-finnish sequencing comparative microsatellite
Improving the specificity of exon prediction using comparative genomics.

PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

human-mouse human-dog genome simulated comparative single-genome simulated
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription
The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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169 gene products in the Ciona genome were identified as putative GPCRs

ciona sequence molecular est
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
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

putative nonredundant homo genes computational pssm semantic
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

yoruba selected subset whole-genome targeted pcr
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

genome predicted target computational snp evolutionary
Haplotype analysis of Lrrk2 R1441H carriers with parkinsonism.

PMID 18952485 · PMC2749264 · Parkinsonism & related disorders · 2009 · 5 claims · 3 setups

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The LRRK2 R1441H substitution has arisen on multiple independent occasions rather than from a single common founder

genomic haplotype direct full
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

genome drosophila transfac b99 profile sequence case-study
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
Finding signals that regulate alternative splicing in the post-genomic era.

PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

intron-containing genome brain-specific cell-free computational comparative selex
A genomics-based approach to biodefence preparedness.

PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

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Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

bacillus brucella neisseria gastric comparative transcriptome two-dimensional
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

skin cloned mixed-type gene nested sequencing molecular

Experiments

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

Improving the specificity of exon prediction using comparative genomics.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

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

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

Haplotype analysis of Lrrk2 R1441H carriers with parkinsonism.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

Paired-end mapping reveals extensive structural variation in the human genome.

Dissecting microregulation of a master regulatory network.

Finding signals that regulate alternative splicing in the post-genomic era.

A genomics-based approach to biodefence preparedness.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.