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).

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

  Full-text index only

  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• pmid-42038403

  PMID 42038403 · PMC13106539 · 7 claims · 7 setups

  Full-text index only

  Meta-analysis integration of three independent RNA-seq drought studies identifies 472 robust differentially expressed genes (274 up, 198 down) that remain significant across the full meta-analysis and all leave-one-out Jackknife iterations

  grandis computational consistently bulk differential leave-one-out

• ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.

  PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.

  pc9 paired-end sorted atac-seq quality read

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.

  PMID 41631412 · PMC12885427 · mAbs · 2026 · 8 claims · 8 setups

  Full-text index only

  alpseq is an open-source, end-to-end workflow combining a PCR-free sequencing library prep protocol with a Nextflow pre-processing pipeline and an R-based analysis/reporting module for nanobody NGS data.

  nanobody raw hanke candidate pcr-free bioinformatic comparison

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence With Existing Human Data.

  PMID 41566898 · PMC12824456 · Brain and behavior · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  A meta-analysis of 6 public PFC transcriptional profiling datasets (n=117 mice, 8 stress vs control contrasts) identified 133 genes consistently differentially expressed across chronic stress studies and paradigms (FDR<0.05)

  c57 c57bl post-weaning pooled microarray rna-seq random-effects

• Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features.

  PMID 41667493 · PMC13002996 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  6-base-CUT&Tag (6B-C&T) simultaneously maps G, A, T, C, 5mC, and 5hmC at antibody-targeted chromatin features on the same DNA fragment

  e14tg2a synthetic mescs mesc 6-base-cut&tag standard exonuclease

• Centromere organization and epigenetic regulation in Aristolochia fimbriata.

  PMID 41761339 · PMC13049873 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  A complete gapless telomere-to-telomere (T2T) genome assembly of A. fimbriata was constructed, substantially improving on the previous v1 assembly.

  aristolochia fimbriata pacbio hi-c cenh3

• chromIDEAS reveals epigenetic dynamics via multi-dimensional clustering of chromatin states.

  PMID 41816913 · PMC12980073 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  chromIDEAS groups chromatin states into functionally coherent clusters by jointly analyzing epigenetic composition and genomic distribution

  thp1 cd34+ chromideas chip-seq atac-seq