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 resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

  Full-text index only

  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

  PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

  Has reproduction · 84

  The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

  single glabripennis amino whole-genome gene busco

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

  PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

  Has reproduction · 68

  The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.

  lactobacillus plantarum whole-genome gene comparative

• spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.

  PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups

  Has reproduction · 77

  spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.

  coli simulated net-seq ribosome stochastic

• Human and mouse oligonucleotide-based array CGH.

  PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

  bt474 normal gm01750 mda-mb-468 array fish

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• Wireless sensor network design with reliable and long network lifetime.

  PMID 41981015 · PMC13083951 · Scientific reports · 2026 · 8 claims · 2 setups

  Has reproduction · 65

  Three strategies (Single Copy, Double Copy, Hybrid) jointly address the four WSN design problems (coverage, sink placement/routing, activity scheduling, data routing) together with network reliability in a unified framework.

  simulated large-scale mixed-integer lagrangian

• Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

  PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

  Full-text index only

  CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

  metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

  PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups

  Has reproduction · 80

  Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing

  leishmania whole-genome long-read genome

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

  PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

  Has reproduction · 94

  Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

  novel casei genomes selected whole-genome maximum-likelihood pairwise

• Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

  PMID 41490125 · PMC12768360 · PloS one · 2026 · 6 claims · 5 setups

  Has reproduction · 69

  The original BRAKER3-based NWR annotation was of poor quality: only 51% of transcripts were correctly called, many were assigned uninformative protein names, and some were misassigned to incorrect or bacterial sequences.

  granulosa nwr aligned unassigned bulk reference transcript

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

  PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 52

  A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

  vespid single-copy brain caste-biased bulk orthology principal

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Neuronal Small RNAs Control Behavior Transgenerationally.

  PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

  Has reproduction · 49

  Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

  elegans prab-3 dissected worms small sequencing facs

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome