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 28

System / cell line: putative ✕ Assay: comparative ✕ Clear

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
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
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
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
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
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

Has reproduction · 90

Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

tsitsikamma tethybacterales putative bin genome 16s multi-locus
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
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
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
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
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
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

rt4d6 gst-sox10 microarray comparative real
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
Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

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This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

acropora millepora coral snp genetic segregation
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

tuberculosis putative orthologous genomewide blastp clustal nei-gojobori
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
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat

Experiments

Improving the specificity of exon prediction using comparative genomics.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

A genomics-based approach to biodefence preparedness.

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

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

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

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

A genome annotation-driven approach to cloning the human ORFeome.

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

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

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

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

Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

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

Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

The DNA sequence and analysis of human chromosome 13.

GENCODE: producing a reference annotation for ENCODE.

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.