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 200

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

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
TreeFam: a curated database of phylogenetic trees of animal gene families.

PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

sequences animal treefam-b lamin phylogenetic homology sequence
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

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GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

ac133+ excised e14 tissues 2-de lc-ms rt-pcr
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
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups

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Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.

mammalian aligned constrained sequence evolutionary comparative
NCBI Reference Sequences: current status, policy and new initiatives.

PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

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RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

microbial bacterial prokaryotic refseq spliced structural functional
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
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
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
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
Using multiple alignments to improve seeded local alignment algorithms.

PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

alignment query leave-one-species-out seeded
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.

PMID 15606920 · PMC544558 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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SVD-based analysis of tetrapeptide frequency vectors can compare whole eukaryotic proteomes without pre-defining orthologs or aligning homologous sites

predicted nine svd-derived ras svd species bootstrap
A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

pax6 brain yeast sequence yeast semi-quantitative
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
WebScipio: an online tool for the determination of gene structures using protein sequences.

PMID 18801164 · PMC2644328 · BMC genomics · 2008 · 7 claims · 4 setups

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WebScipio, a web interface to Scipio, determines gene structure from a query protein sequence against an assembled eukaryotic genome with quality approaching manual annotation.

homo pongo callithrix mus spliced
Comparative genomics.

PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed
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
Linking disease-associated genes to regulatory networks via promoter organization.

PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

orthologous eukaryotic genomatix pubmed promoter model additional
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome

Experiments

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

TreeFam: a curated database of phylogenetic trees of animal gene families.

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

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

The EH1 motif in metazoan transcription factors.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

NCBI Reference Sequences: current status, policy and new initiatives.

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

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

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

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

Using multiple alignments to improve seeded local alignment algorithms.

An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.

A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

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

WebScipio: an online tool for the determination of gene structures using protein sequences.

Comparative genomics.

Dcode.org anthology of comparative genomic tools.

Linking disease-associated genes to regulatory networks via promoter organization.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.