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 19

System / cell line: test ✕ Assay: motif ✕ Clear

Optimized mixed Markov models for motif identification.

PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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OMiMa can incorporate more than NNSplice's pairwise dependencies

simulated regulatory splice biological motif pairwise
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Automatic discovery of cross-family sequence features associated with protein function.

PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

non-redundant same evolved eukaryotic self-supervised experiment self-organizing
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

6x6 ortholog 3'utr comparative chi-squared
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

3'-utr mirbase hapmap comparative snp mirna
CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Identifying cis-regulatory sequences by word profile similarity.

PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

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WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

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EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

rice preliminary primer sequence quality
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

upstream co-expression pre-b microarray-based motif gene
Integrative analysis of RUNX1 downstream pathways and target genes.

PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

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Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

lymphoblastic hela runx1 aml cdna microarray affymetrix
PCR-free method detects high frequency of genomic instability in prostate cancer.

PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

blood normal prostate matched pcr-free degenerate-pcr blastn
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

Optimized mixed Markov models for motif identification.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Automatic discovery of cross-family sequence features associated with protein function.

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

CRSD: a comprehensive web server for composite regulatory signature discovery.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Identifying cis-regulatory sequences by word profile similarity.

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

Integrative analysis of RUNX1 downstream pathways and target genes.

PCR-free method detects high frequency of genomic instability in prostate cancer.

Computational comparison of two mouse draft genomes and the human golden path.

Genome informatics: taming the avalanche of genomic data.

TEMP: a computational method for analyzing transposable element polymorphism in populations.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.