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).

• Epistemic uncertainty challenges aging clock reliability in predicting rejuvenation effects.

  PMID 39072888 · PMC11561706 · Aging cell · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  DNA methylation profiles observed across cellular reprogramming are poorly represented in the training data of existing aging clocks, introducing high out-of-distribution/epistemic uncertainty in their age estimates

  males skin liver linear dnam epigenetic

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  AE networks trained on the 266 shared DEGs reveal a comorbidity (positive correlation) relationship between Alzheimer's disease and lung cancer, rather than the inverse relationship suggested by prior epidemiological studies.

  integrated expression overlapped moderated autoencoder pathway

• Endurance exercise as a countermeasure for aging.

  PMID 18716044 · PMC2570389 · Diabetes · 2008 · 8 claims · 8 setups

  Full-text index only

  Reduced insulin sensitivity with age is likely related to adiposity and physical inactivity rather than being an inevitable consequence of aging.

  vastus mitochondria mitochondrial extracted euglycemic-hyperinsulinemic mitochondrial citrate

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple

• 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

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• In silico segmentations of lentivirus envelope sequences.

  PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

  Full-text index only

  C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

  eiav hiv hmm-based hmm artificial

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

  PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 8 claims · 4 setups

  Has reproduction · 62

  MultiDeNA pipeline combines PWM, diPWM, BaMM and InMoDe models to train, evaluate, threshold, and classify ChIP-seq peaks for TFBS structural heterogeneity

  foxa2 genomic frequency chip-seq novo threshold

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class Random Forest models built from meta-analyzed blood gene expression data can predict infection state (bacterial/viral/none) with high accuracy, correctly classifying 93% of bacterial and 89% of viral samples in the best model.

  blood merged affymetrix-trained microarray random gene

• SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

  PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 6 claims · 5 setups

  Has reproduction · 77

  SurvConvMixer, using pathway-level gene expression images and ConvMixer, achieves strong internal validation AUC for overall survival prediction, especially on larger datasets like LUAD

  luad lusc skcm trained deep benchmark model

• Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

  PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

  Full-text index only

  The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

  peptides peptide sax-spe ip-rp-hplc cross-run

• Decision tree-driven tandem mass spectrometry for shotgun proteomics.

  PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

  Full-text index only

  A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

  saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential

• MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

  PMID 24599324 · PMC3944147 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 29

  MOSAIK is the only aligner that consistently aligns reads from all major sequencing platforms (Illumina, AB SOLiD, Roche 454, Ion Torrent, Pacific Biosciences SMRT) using the same algorithmic approach.

  simulated million coli illumina short-read mapping neural-network

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

  archiveii bprna large-scale secondary cross-family self-supervised

• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

  PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

  Full-text index only

  AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

  genome human-mouse genes initio comparative extrinsic