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).

• 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

• A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

  PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

  urinary tcga paired urine sequencing lncrna qrt-pcr

• 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

• 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

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

  PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

  globally same computational publicly y-str snp supervised

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

  Full-text index only

  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• 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

• 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

• Constructing support vector machine ensembles for cancer classification based on proteomic profiling.

  PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups

  Full-text index only

  CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.

  serum computational seldi-tof svm-rfe-based 10-fold

• 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

• 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

• Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

  PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

  neuroblastoma shep-tet21 stem-loop array tlda

• Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups

  Has reproduction · 62

  A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.

  breast degs geo tcga gene protein-protein machine

• 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

• 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

• Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.

  PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 68

  RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)

  endometrial in-house bulk rif-degs meta-analysis sequencing immune