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).
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Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups
A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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Genome wide identification of recessive cancer genes by combinatorial mutation analysis.
PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups
A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)
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Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.
PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups
The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes
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In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.
PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups
This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle
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DiRE: identifying distant regulatory elements of co-expressed genes.
PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups
DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures
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Has reproduction · 95
Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.
PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups
Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input
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Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.
PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups
Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes
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Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.
PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups
The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.
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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
Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait
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Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.
PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups
A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size
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Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions
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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
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
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Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups
A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures
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Has reproduction · 69
Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.
PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 5 claims · 8 setups
Meta-analysis of GWAS across six dairy cattle breeds identifies 58 lead markers associated with clinical mastitis and somatic cell score
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Has reproduction · 100
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
French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.
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New perspectives on an old disease: proteomics in cancer research.
PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups
The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.
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Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.
PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups
A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.
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A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.
PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups
A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability
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Improvements to cardiovascular gene ontology.
PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups
Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.