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 26

System / cell line: multi-species ✕ Assay: alignment ✕ Clear

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
Dcode.org anthology of comparative genomic tools.

PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

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The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

dlx1 hoxa prothrombin gene comparative multi-species phylogenetic
Developments in CORG: a gene-centric comparative genomics resource.

PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

upstream gene overlapping c-fos pairwise sequence comparative
Of rats and men.

PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

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The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

rattus cftr fugu transgenic whole-genome comparative genome
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
Ensembl's 10th year.

PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

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Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

anole western genome cd4+ whole-genome gene cross-database
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
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

chromosome genomic comparative phylohmmcons conserved
The UCSC Genome Browser Database: update 2006.

PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

dog vertebrate encode genome comparative automated cross-species
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

sequences poly cdna trace pssm-based
SNP-VISTA: an interactive SNP visualization tool.

PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets

abo homologous acid snp multi-species blast-based
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
Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

PMID 19727905 · PMC2946578 · Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2010 · 7 claims · 6 setups

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Multiple SNPs and haplotypes in FLNB are significantly associated with BMD at lumbar spine, femoral neck, and total hip

southern same subjects genotype tag taqman dual-energy
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

genome vertebrate multi-species whole-genome conservation non-synonymous
Analysis of chimpanzee history based on genome sequence alignments.

PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups

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Bonobos and common chimpanzees separated approximately 1.29 million years ago

bonobo bonobos chimpanzee simulated shotgun sequenom principal
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

drosophila caenorhabditis xenopus five pairwise evoprint comparison
Ensembl 2008.

PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

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The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

embryonic amniota multi-species individuals automated chip-chip comparative

Experiments

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

Dcode.org anthology of comparative genomic tools.

Developments in CORG: a gene-centric comparative genomics resource.

Of rats and men.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

Ensembl's 10th year.

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

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

The UCSC Genome Browser Database: update 2006.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

SNP-VISTA: an interactive SNP visualization tool.

The DNA sequence and analysis of human chromosome 13.

Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Analysis of chimpanzee history based on genome sequence alignments.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Ensembl 2008.