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 20

System / cell line: shared ✕ Assay: domain ✕ Clear

Identifying repeat domains in large genomes.

PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

repbase elegans concatenated repeat comparative dot
GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

PMID 15790402 · PMC1274265 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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GeneKeyDB is a lightweight, gene-centric relational database that supports data mining and integration with computational analysis tools.

genekeydb database gene automated
Sequence similarity network reveals common ancestry of multidomain proteins.

PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

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Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

curated complete well-studied sequence alignment domain
POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
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
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
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
The global landscape of sequence diversity.

PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

fully eukaryotic complete gene blast-based est gene
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

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Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

ftld grn genomic post-mortem clinical volumetric direct
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

eukaryotic homo sequence species pairwise algorithm low-complexity
The integrated world of functional genomics.

PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

cerevisiae sequenced elegans drosophila chromatin integration comparative
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

Has reproduction · 89

Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

european cis-pqtl myocardial geo mendelian bayesian differential
WebGestalt: an integrated system for exploring gene sets in various biological contexts.

PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

genes gene est-based enrichment kegg
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

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The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

dentium core whole-genome 3d-structure comparative
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr

Experiments

Identifying repeat domains in large genomes.

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

Sequence similarity network reveals common ancestry of multidomain proteins.

POCUS: mining genomic sequence annotation to predict disease genes.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

The cohesin complex: sequence homologies, interaction networks and shared motifs.

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

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

Analysis of protein sequence and interaction data for candidate disease gene prediction.

The global landscape of sequence diversity.

Patterns of evolutionary constraints on genes in humans.

A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

The integrated world of functional genomics.

Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

WebGestalt: an integrated system for exploring gene sets in various biological contexts.

Comparative genomics search for losses of long-established genes on the human lineage.

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.