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).

• High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

  PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

  Has reproduction · 85

  SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

  atlantic low-coverage genotyping genome

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.

  PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups

  Full-text index only

  rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution

  enterobacterales illumina aeruginosa pneumoniae whole-genome wgs amr

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

  Has reproduction · 91

  175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

  one sinensis small-molecular-weight leaves small genome mirna

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

  PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 7 claims · 5 setups

  Has reproduction · 78

  Genomic profiling can identify malignant transformation in MGUS/SMM patients, distinguishing 'genomic MM' from 'genomic MGUS' despite identical clinical/morphologic presentation

  cd138+ mgus whole-exome whole-genome copy-number

• CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

  PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

  Has reproduction · 97

  CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

  simulated wgs reference same novo blast-based k-mer

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

  Full-text index only

  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.

  PMID 42206012 · PMC13202175 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups

  Full-text index only

  AVITI and NovaSeq X Plus are highly comparable overall for variant-calling performance in WGS

  tumor mm1s aviti chr20 whole-genome pacbio small

• Integrative Multiomic Classification Reveals Distinct Origins and Evolutionary Trajectories of Thymic Epithelial Tumors.

  PMID 41671387 · PMC13012242 · Cancer research · 2026 · 8 claims · 8 setups

  Full-text index only

  TETs stratify into three molecular subgroups with distinct origins: GTF2I-type thymomas, CN-type thymomas, and thymic carcinomas

  tet thymic hek293t whole-exome whole-genome bulk

• DDBJ in collaboration with mass-sequencing teams on annotation.

  PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data

  chimpanzee silkworm mus homo whole-chromosome whole-genome cage

• A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• 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 Genetic and Morphological Basis of Local Adaptation to Elevational Extremes in an Alpine Finch.

  PMID 41624103 · PMC12853319 · Ecology and evolution · 2026 · 8 claims · 6 setups

  Full-text index only

  Birds in the warmer Piute Pass population were predicted to have longer wings and larger beaks per Allen's rule

  sierra body blood same morphometric feather whole-genome

• The dynamic distribution of genetic tandem amplifications in a heteroresistant Escherichia coli population revealed by ultra-deep long read sequencing.

  PMID 41760616 · PMC12953903 · Nature communications · 2026 · 8 claims · 6 setups

  Full-text index only

  Ultra-deep Nanopore sequencing of I-SceI-linearized plasmid DNA can detect and quantify full tandem amplification arrays at single-molecule resolution down to frequencies of 10^-5

  coli ultra-deep short-read digital

• Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.

  PMID 42046229 · PMC13171174 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  Duplex-Indel is a Snakemake pipeline for somatic Indel calling from Tn5 transposase-based duplex sequencing data that requires consensus support from both DNA strands to minimize technical artifacts.

  colo829-t colo829-bl colo829-blt duplex tn5 bulk cosine

• A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

  PMID 41514053 · PMC12858409 · Nature cancer · 2026 · 8 claims · 6 setups

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  Generated a single-cell Immune Atlas of 1,397,272 BM cells from 337 NDMM participants (263 discovery, 74 validation) using scRNA-seq

  cd138 bone ndmm single-cell cytogenetic disease

• Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

  PMID 41532847 · PMC13056296 · Cancer discovery · 2026 · 8 claims · 8 setups

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  High-depth targeted sequencing of >1,500 IM samples from six countries identified 47 significantly mutated driver genes, including ARID1A, KRAS/MAPK pathway genes, and PIGR

  subset matched saliva hek293t high-depth whole-genome genome-wide