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).

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data.

  PMID 29420797 · PMC5961211 · Nucleic acids research · 2018 · 7 claims · 5 setups

  Has reproduction · 68

  Octopus-toolkit is a stand-alone application that automatically retrieves and processes large sets of epigenomic and transcriptomic NGS data from GEO in a single step

  mammary liver saccharomyces chip-seq rna-seq

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 8 setups

  Has reproduction · 59

  382 genomic regions contain SNPs whose frequencies are consistently zonated (vary with intertidal position) across all surveyed North Atlantic habitats (Maine, Rhode Island, Norway)

  semibalanus rocky individual ld-thinned pool-seq field morphometric

• Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1-adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE.

  PMID 41540017 · PMC12890961 · NPJ genomic medicine · 2026 · 6 claims · 7 setups

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  POSTRE correctly classified all 34 GPR101-associated duplications (27 pathogenic X-LAG, 7 non-pathogenic) as pathogenic or benign

  anterior embryonic patient-derived genome h3k27ac atac-seq rna-seq

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

  PMID 41535307 · PMC12913623 · Nature communications · 2026 · 8 claims · 8 setups

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  e2MPRA, combining lentiviral integration-based MPRA with CUT&Tag or ATAC-seq, enables simultaneous measurement of regulatory activity, protein binding, and epigenetic modification of the same synthetic CRE sequences.

  hepg2 lentimpra atac-seq h3k27ac

• Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

  PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

  Has reproduction · 75

  rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

  saccharomyces model ribose-seq emriboseq rhii-hyden-seq

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• How negative sampling shapes the performance of transcription factor binding site prediction models.

  PMID 41601205 · PMC12910371 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups

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  Negative sampling technique significantly impacts TFBS prediction model performance and interpretation of results

  encode same genome chip-seq atac-seq deep

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• Sequential sequencing reveals the architecture and complexity of genomic variants in patients with Alport syndrome.

  PMID 41872207 · PMC13171879 · Nature communications · 2026 · 8 claims · 7 setups

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  A sequential sequencing strategy (WES→WGS→RNA-seq→NLR-seq) identifies COL4A3/COL4A4/COL4A5 variants in 509/555 (91.7%) of Alport syndrome patients

  chinese prediction-negative randomly minigene whole-exome whole-genome sequencing

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

  PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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  Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

  mcf7 arabidopsis specified different chip-seq microarray array-based

• Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

  PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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  Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

  tissues genomic gtex hgmd long-read variant splice

• The chromosome-scale genome assembly and annotation of Rosa bracteata (Macartney Rose).

  PMID 41794947 · PMC13096426 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of R. bracteata totaling 540.63 Mb with contig N50 of 35.97 Mb was generated, with 501.06 Mb anchored onto seven pseudochromosomes.

  genomic root pacbio young pacbio hi-c rna-seq

• Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.

  PMID 41802886 · PMC13014123 · Molecular biology and evolution · 2026 · 8 claims · 8 setups

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  Genomic structural variations and gene family expansions contributed little to morphological (mimicry) evolution in Epicopeiidae

  epicopeiidae mencia ancestral chromosome-level whole-genome hi-c comparative

• Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.

  PMID 34471117 · PMC8410849 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  Chromosome structure correlates with genetic compartmentalization during exponential phase in S. ambofaciens

  ambofaciens comparative antismash rna-seq

• Genome-wide prediction of DNase I hypersensitivity using gene expression.

  PMID 29051481 · PMC5715040 · Nature communications · 2017 · 8 claims · 5 setups

  Has reproduction · 79

  Gene expression can, to a large extent, predict genome-wide DNase I hypersensitivity (chromatin accessibility)

  distinct same training encode dnase-seq exon bird