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 chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• 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

• Searching for SNPs with cloud computing.

  PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

  Full-text index only

  Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

  han local short simulated whole-genome cloud

• HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

  PMID 34025601 · PMC8134036 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Full-text index only

  ABAA reduces the number of false-positives with all metabarcoding methods tested

  fungal same mock raw its1 blastn hierarchical

• A chromosome-level reference genome and pangenome for barn swallow population genomics.

  PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data

  single barn bhirrus1 rustica genome cytogenetic reference-free

• Multi-context seeds enable fast and high-accuracy read mapping.

  PMID 41764549 · PMC13059148 · Genome biology · 2026 · 7 claims · 5 setups

  Full-text index only

  Multi-context seeds (MCS) allow storage of seeds with different lengths in the same index structure by splitting hash bits among strobes, enabling full and partial matches

  simulated chm13 same sequence seed simulated

• DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

  PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

  Full-text index only

  Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

  validation cns healthy genes methylation copy-number gene-set

• 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

• Germline sequence variation within the ribosomal DNA is associated with human complex traits.

  PMID 41966685 · PMC13261666 · Cell genomics · 2026 · 8 claims · 5 setups

  Full-text index only

  Germline rDNA sequence variant frequencies associate with multiple human complex traits in the UK Biobank, independently of rDNA copy number

  biobank genomes synthetic 28s whole-genome short-read genome-wide

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

  PMID 35046988 · PMC8761809 · Frontiers in plant science · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  SLDMS is a novel method for computing overlapping regions of sequencing reads using suffix array (SA), longest common prefix (LCP) array, document array (DA), and a monotonic stack.

  sequencing concatenated pacbio-hifi third-generation running-time suffix overlap

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig