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).

• MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

  PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

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  MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

  validated gut representative predicted acp shotgun genome

• Charting spatial ligand-target activity using Renoir.

  PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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  Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

  intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell

• Benchmarking of methods to analyse data derived from GBS-MeDIP.

  PMID 41555215 · PMC12829230 · BMC bioinformatics · 2026 · 7 claims · 4 setups

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  featureCounts is the most reliable tool for count matrix generation from GBS-MeDIP data, outperforming MEDIPS

  gbs-medip randomized simulated count distribution null

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

  PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world

• RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

  PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

  Has reproduction · 79

  RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

  wgs single whole-genome nested capillary

• OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

  PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

  simulated classical degs naive simulated bulk real

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.

  PMID 42046229 · PMC13171174 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Duplex-Indel is a Snakemake pipeline for somatic Indel calling from Tn5 transposase-based duplex sequencing data that requires consensus support from both DNA strands to minimize technical artifacts.

  colo829-t colo829-bl colo829-blt duplex tn5 bulk cosine

• scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

  PMID 41915012 · PMC13142155 · GigaScience · 2026 · 8 claims · 7 setups

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  Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

  10x brain ucsc datasets scrna-seq integration snrna-seq

• Semi-parametric empirical bayes method for multiplet detection in snATAC-seq with probabilistic multi-omic integration.

  PMID 42054434 · PMC13148828 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  SEBULA models the singlet background directly from observed HCLC (high-coverage locus count) statistics using fragment-level snATAC-seq information, avoiding reliance on synthetic/artificial doublets.

  dogma-seq dogma-seq-derived seven snatac-seq q-q density

• Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

  PMID 41503159 · PMC12770975 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

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  Eight prominent imputation methods (MAGIC, SAVER, scVI, DCA, scBiG, kNN-smoothing, scImpute, ALRA) were systematically evaluated for their ability to recover the true non-zero expression fraction using simulated and real-world scRNA-seq data

  basal tracheal airway k562 simulated scrna-seq imputation