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 18

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

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

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

Full-text index only

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
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

real combined pre-mirna training random independent repeated
Macrel: antimicrobial peptide screening in genomes and metagenomes.

PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups

Has reproduction · 83

Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes

curated hemopi-1 xiao cd-hit random amp homology-aware
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

Full-text index only

Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

Full-text index only

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
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

Full-text index only

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
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

Full-text index only

MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups

Full-text index only

BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant

lymphoblastoid lcl gene microarray unsupervised t-test
Optimality driven nearest centroid classification from genomic data.

PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

Full-text index only

A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

artificial simulated previously-published simulated simulation clinical
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

Full-text index only

PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
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

Full-text index only

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

cerevisiae cycle reanalysis statistical optimal
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

kidney same identified additional microarray significance fisher's
Discovering cancer genes by integrating network and functional properties.

PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

Full-text index only

Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

genes gene colon ppi pfam term
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 4 setups

Has reproduction · 76

DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities

prostate global gene metabolomic computational
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

Full-text index only

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
G2Cdb: the Genes to Cognition database.

PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

Full-text index only

G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

brain nervous genome synaptic proteomic large-scale sequence
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

Full-text index only

A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

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

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Macrel: antimicrobial peptide screening in genomes and metagenomes.

Speeding disease gene discovery by sequence based candidate prioritization.

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

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

Ab initio identification of human microRNAs based on structure motifs.

BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

Optimality driven nearest centroid classification from genomic data.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

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

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

Discovering cancer genes by integrating network and functional properties.

Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

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

G2Cdb: the Genes to Cognition database.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.