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).

• nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.

  PMID 41563008 · PMC12950615 · GigaScience · 2026 · 8 claims · 3 setups

  Full-text index only

  nf-core/proteinfamilies is a scalable, parametrizable, open-source Nextflow pipeline that generates new protein families or assigns sequences to existing families using profile HMMs and MSAs

  uniprot-swissprot input family diamond computational

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• 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

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag

• Macrel: antimicrobial peptide screening in genomes and metagenomes.

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

  Has reproduction · 83

  Macrel introduces a novel set of 22 peptide features (6 local, 16 global), including a new Free Energy Transition (FET) feature group, for AMP and hemolytic activity classification

  curated hemopi-1 xiao peptide random benchmark homology-aware

• Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

  PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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  Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

  medline annotated interactions consolidated conditional co-citation bayesian

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation

• epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.

  PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups

  Has reproduction · 52

  epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome

  arabidopsis great epigbs2 demultiplexed epigbs2 pcr demultiplexing

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed