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 48

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

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
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
Ontological Discovery Environment: a system for integrating gene-phenotype associations.

PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

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ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

strains integrated bipartite phish gene differential pairwise
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

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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

pubmed genes same randomly geneseeker evoc disease
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
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

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
DiRE: identifying distant regulatory elements of co-expressed genes.

PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

liver myod transgenic microarray tfbs enhancer
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

PMID 16686952 · PMC1471797 · BMC genetics · 2006 · 7 claims · 1 setups

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CapsID identifies snip-SNPs (SNPs that alter restriction endonuclease recognition sites) within reference sequence alignments and designs PCR primers around them

sequence restriction
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

tissues inter-subspecies placenta genomic microarray rt-pcr sequencing
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
Reconstructing the evolution of the mitochondrial ribosomal proteome.

PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.

proteomes eukaryotic aligned alignments iterative hmm-based neighbor-joining
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups

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An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.

pepseeker local known swissprot tandem peptide pmf
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

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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.

lsl-krasg12d soft combined mfh microarray gene oncogenic
Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

Has reproduction · 92

Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

post-mortem adra immunohistochemistry protein-protein pathway

Experiments

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

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.

Ontological Discovery Environment: a system for integrating gene-phenotype associations.

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

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

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

DiRE: identifying distant regulatory elements of co-expressed genes.

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

Reconstructing the evolution of the mitochondrial ribosomal proteome.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.