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).

• Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

  PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 8 setups

  Has reproduction · 73

  Developed OutlierMeth, an R package that computes probe-specific thresholds and flags DNA methylation outliers from array data

  normal blood tcga gse40279 illumina logistic unsupervised

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

  PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

  sonnei same shigella assembled illumina oxford novo

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Retrotransposons mobilize via a copy-and-paste mechanism involving transcription of an RNA intermediate and reinsertion as a cDNA copy, unlike DNA transposons which cut-and-paste.

  drosophila normal genomic genome synthetic whole-genome computational

• Genetic polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Blood-based epigenetic instability linked to human aging and disease.

  PMID 41690920 · PMC13018287 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  31,744 unmethylated (and 6143 methylated) CpG loci in blood show highly consistent, stable methylation in young healthy individuals and are defined as Epigenetically Stable Loci (ESLs)

  blood normal paired aml illumina whole-genome methylation

• Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.

  PMID 41760692 · PMC13066446 · Scientific data · 2026 · 7 claims · 9 setups

  Full-text index only

  A. haimaensis genome was assembled to chromosome level (4.27 Gb, scaffold N50 195.52 Mb, anchored to 22 chromosomes) using PacBio HiFi, Illumina, and Hi-C sequencing

  acharax haimaensis illumina pacbio hi-c

• The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

  PMID 41765919 · PMC13066037 · Scientific data · 2026 · 8 claims · 8 setups

  Full-text index only

  B. polycarpa genome was assembled de novo using PacBio HiFi reads and Hi-C data to a size of 585.68 Mb with contig N50 of 12.62 Mb

  polycarpa illumina pacbio hi-c

• An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.

  PMID 41792167 · PMC13087180 · Scientific data · 2026 · 8 claims · 8 setups

  Full-text index only

  An improved chromosome-level genome assembly of C. savignyi was generated using Illumina short reads, ONT long reads, and Hi-C data.

  savignyi illumina oxford hi-c

• Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).

  PMID 41824659 · PMC13089509 · Plant physiology · 2026 · 7 claims · 8 setups

  Full-text index only

  A near-complete telomere-to-telomere genome assembly of E. cheiri was generated (244.33 Mb, 6 chromosomes)

  cheiri brassicaceae illumina pacbio hi-c

• The 1000 Chinese Pangenome empowers medical and population genetics.

  PMID 41922767 · PMC13233627 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  1,116 diploid genome assemblies (55 de novo, 1,061 pangenome-informed) were generated as part of the 1KCP project

  genomic diploid benchmark illumina pacbio hi-c

• Chromosome-level genome assembly of the blackchin tilapia (Sarotherodon melanotheron).

  PMID 41942530 · PMC13234295 · Scientific data · 2026 · 7 claims · 7 setups

  Full-text index only

  A chromosome-level genome assembly of blackchin tilapia was generated with total length 1,027.41 Mb and scaffold N50 of 38.87 Mb, with 93.42% of sequence anchored to 22 chromosomes.

  muscle ten illumina assembled illumina ont hi-c

• Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

  PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups

  Has reproduction · 85

  An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.

  salmonella ncbi-pd illumina empirical coverage

• Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

  PMID 18974170 · PMC2638935 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 3 setups

  Full-text index only

  Slider aligns reads using all bases above a probability threshold (baseMinPrb) from prb files, generating all possible read sequences above a read probability threshold (read_0_MinPrb), rather than only the most probable sequence

  illumina uniquely genome sequence snp reference

• Chromosome-level genome assembly of Siberian kale (Brassica napus subsp. pabularia).

  PMID 41760683 · PMC13066399 · Scientific data · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly of Siberian kale variety Beta was generated using PacBio HiFi long reads, Illumina short reads, and Hi-C data

  beta illumina pacbio hi-c