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).

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.

  PMID 41486154 · PMC12828970 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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  Frag'n'Flow is a Nextflow-based pipeline that encapsulates FragPipe, automating manifest/workflow generation, tool dependency management, and downstream analysis for HPC/cloud/cluster environments.

  laboratory institutional breast pluripotent ram cpu storage

• Application of qualifying variants for genomic analysis.

  PMID 41570118 · PMC12926777 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

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  QVs should be treated as dynamic, multifaceted elements permeating the entire analysis workflow, not as a single static filtering step

  in-house hapmap3 genome framework exome gwas wgs

• MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

  PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism

  arabidopsis grapevine pangenome invertebrate genome novo gene

• PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

  PMID 41919010 · PMC13034549 · Bioinformatics advances · 2026 · 8 claims · 7 setups

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  PeakPrime is a reproducible Nextflow pipeline that calls 3′ RNA-seq coverage peaks (MACS2), selects exonic windows, designs strand-appropriate primers (Primer3), and screens specificity (Bowtie2)

  imr-32 universal candidate 10m-read rna-seq targeted quantitative

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

  PMID 42164079 · PMC13183670 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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  BLIT provides a unified R6-based framework for seamless integration of command-line bioinformatics tools within R, replacing fragile string-based system() calls.

  core circrna clinical europe unit pipeline production

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays.

  PMID 41551929 · PMC12805889 · NAR genomics and bioinformatics · 2026 · 8 claims · 5 setups

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  nf-core/crisprseq is the first generic pipeline enabling analysis of the broad spectrum of CRISPR designs, from targeted gene edits (KO, KI, BE, PE) to large-scale functional screens

  spike-in prjeb53901 a375 prjna326019 targeted crispr computing

• Virus variant quantification with Orthanq.

  PMID 41639627 · PMC12930645 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, including in samples with mixed infections

  simulated real mixture sequencing sequencing-based pangenome variant

• 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

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• scSAMAC: saliency-adjusted masking induced attention contrastive learning for single-cell clustering.

  PMID 40131310 · PMC11934584 · Briefings in bioinformatics · 2025 · 8 claims · 1 setups

  Has reproduction · 85

  scSAMAC integrates contrastive learning and negative binomial (NB) losses into a VAE, extracting features via contrastive unit similarity while preserving intrinsic data characteristics to enhance robustness and generalization in clustering.

  scrna-seq scrna-seq

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• MobiCT: a UMI-based circulating tumor DNA analysis pipeline.

  PMID 41503160 · PMC12770973 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

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  MobiCT is a Nextflow/nf-core UMI-based ctDNA pipeline (deduplication, alignment, variant calling with VarDict, annotation with VEP) achieving sensitivity, precision, and F1-score around 90% after comprehensive filtering.

  cfdna same tumor horizon targeted droplet ngs