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: computational ✕ Assay: upstream ✕ Clear

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

PMID 18353860 · PMC2377421 · Nucleic acids research · 2008 · 7 claims · 1 setups

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A large number of upstream PQSSs incorporate the SP1-binding element, establishing a clear link between PQSS occurrence and SP1 elements

genome genome-wide
The stem cell population of the human colon crypt: analysis via methylation patterns.

PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

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A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

colon computational simulated bisulfite coalescent posterior
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

cerevisiae elegans randomized computational randomized microarray
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Automatic annotation of eukaryotic genes, pseudogenes and promoters.

PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

encode regions genes chromosome computational pseudogene promoter
E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

Has reproduction · 62

E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

preimplantation genome erna bulk computational motif
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 6 claims · 7 setups

Has reproduction · 62

Combining four de novo models (PWM, diPWM, BaMM, InMoDe) significantly increases the fraction of recognized peaks versus PWM alone (by 26.3%).

hg38 foxa2 pwm whole-genome chip-seq pwm dipwm
Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

Has reproduction · 57

A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

genome pbmc lung il4-stimulated motif chip-seq bulk
QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

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QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

chimpanzee prokaryotic promoters genome-wide cross-species
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

drosophila genome melanogaster real-time comparative gfp
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

orthologous literature sequence pairwise
VISTA Enhancer Browser--a database of tissue-specific human enhancers.

PMID 17130149 · PMC1716724 · Nucleic acids research · 2007 · 8 claims · 2 setups

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Comparative genome analysis can identify candidate human enhancer elements whose tissue-specific in vivo activity can then be experimentally validated in transgenic mice.

genomic genome transgenic comparative
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
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

cd4+ jurkat hela computational chip-seq novo motif
DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

PMID 41055236 · PMC12505516 · RNA biology · 2025 · 7 claims · 5 setups

Has reproduction · 100

DeepRNA-Reg, a recurrent neural network-based algorithm, predicts differentially enriched sites in paired HITS-CLIP datasets and outperforms dCLIP 1.7.

dgcr8 mir-23 deeprna-reg ago2 gene flow
A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups

Has reproduction · 71

Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).

hand-sorted drosophila chip-seq immunostaining dapi
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

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A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

p53 tumor tumors computational retroviral linker-mediated flow
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood

Experiments

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

The stem cell population of the human colon crypt: analysis via methylation patterns.

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

Inferring combinatorial regulation of transcription in silico.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Genome informatics: taming the avalanche of genomic data.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.