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 176

System / cell line: candidate ✕ Assay: genome ✕ Clear

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups

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A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches

genome boreoeutherian ferungulate marker-presence whole-genome ancestral combinatorial
Designing candidate gene and genome-wide case-control association studies.

PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

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Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

population monozygotic international genome-wide candidate twin
SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes.

PMID 17169995 · PMC1802603 · Nucleic acids research · 2007 · 8 claims · 5 setups

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SECIS elements located within coding regions of selenoprotein mRNAs support functional Sec insertion in mammalian cells

viral hek293 hepatoma tblastn computational western
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

genome cytomegalovirus six probabilistic 5-fold directional
Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

PMID 18621558 · PMC2697027 · European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery · 2008 · 8 claims · 3 setups

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AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals

aaa cases candidate genome-wide
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

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An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

genome training svm support leave-one-out sensitivity
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
Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 7 claims · 5 setups

Has reproduction · 71

311 SNPs and 73 candidate genes (e.g., IGF2BP1, BMP3, ACSL5) are significantly associated with carcass traits in Sanhuang chickens

sanhuang chickens chicken breast whole-genome phenotypic genomic
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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P. falciparum encodes substantially more membrane transport proteins than originally annotated

falciparum genome-wide bioinformatic quantification
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
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race
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
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
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
TFBScluster web server for the identification of mammalian composite regulatory elements.

PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

imr90 tissues dog transgenic microarray-based gene
Finding disease candidate genes by liquid association.

PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation
Update of the G2D tool for prioritization of gene candidates to inherited diseases.

PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

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G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

genome genomic etrb computational literature go-similarity
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

Has reproduction · 100

French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

boars lwd lws pig whole-genome genetic genome-wide

Experiments

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Designing candidate gene and genome-wide case-control association studies.

SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes.

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

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

Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

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

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

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

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

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

TFBScluster web server for the identification of mammalian composite regulatory elements.

Finding disease candidate genes by liquid association.

Update of the G2D tool for prioritization of gene candidates to inherited diseases.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.