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).

• Genomic data sampling and its effect on classification performance assessment.

  PMID 12553886 · PMC149349 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Cross-validation, leave-one-out, and bootstrap are designed to reduce bias and variance in accuracy estimation from small samples.

  leukemia srbct splice-junction supervised

• Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

  PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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  The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

  benchmarking same pirsf pdb supervised wrapper sequence

• Retentive Network promotes efficient RNA language modeling of long sequences.

  PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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  RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

  million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• 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

• SePaCS--a web-based application for classification of seroreactivity profiles.

  PMID 17478503 · PMC1933220 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  SePaCS is a freely available web-based tool that trains and applies multiple classification methods (4 Naive Bayes variants, SVM with RBF kernel, LDA, DLDA) to seroreactivity profiles and outputs results as a summary table plus a detailed PDF report

  blood computational seroreactivity supervised mutual

• Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

  PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

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  An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

  serum computational kda spin-column seldi-tof supervised peptide

• Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX.

  PMID 41723123 · PMC13035843 · Nature communications · 2026 · 8 claims · 6 setups

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  CAMEX outperforms state-of-the-art integration methods on cross-species scRNA-seq benchmarking datasets ranging from one to eleven species

  liver ovary pancreas testis scrna-seq type

• 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

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

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

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  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

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.

  PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups

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  SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA

  serum clustered pooled trypsin-digested seldi-tof cart immunoprecipitation

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch