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).

• Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella.

  PMID 41684216 · PMC12902445 · Microbial biotechnology · 2026 · 7 claims · 5 setups

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  Structured, recurrent promoter variation in epigenetically regulated operons is a novel layer of functional adaptation in Salmonella, complementing genetic and epigenetic mechanisms.

  complete annotated 220-nucleotide opvab comparative correlation blastn

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Biodefense versus bioterrorism.

  PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

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  Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

  bacillus ancestral cultures anthrax whole-genome comparative colony

• First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

  PMID 41436027 · PMC12958814 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

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  This study produced the first genome assemblies of Neotropical Bombus (Thoracobombus) species, B. pauloensis and B. pullatus

  pauloensis masked long-read k-mer novo

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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  Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

  viruses virus coli soluble large-scale bioinformatic recombinant

• Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.

  PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups

  Has reproduction · 92

  Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.

  sciuri bacterial assembled 2254a long-read maldi-tof genome

• The genome sequence of the leafhopper, Arthaldeus pascuellus (Fallén, 1826) (Hemiptera: Cicadellidae).

  PMID 41625988 · PMC12859417 · Wellcome open research · 2026 · 6 claims · 8 setups

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  A chromosome-level genome assembly was generated for Arthaldeus pascuellus, the first high-quality genome for the genus Arthaldeus

  organism pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the Gold Spangle, Autographa bractea (Denis & Schiffermüller), 1775 (Lepidoptera: Noctuidae).

  PMID 41710118 · PMC12910202 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level, haplotype-resolved genome assembly was produced for Autographa bractea (Gold Spangle)

  autographa pacbio hi-c k-mer

• The genome sequence of the Spanish Festoon, Zerynthia rumina (Linnaeus, 1758) (Lepidoptera: Papilionidae).

  PMID 41769331 · PMC12946699 · Wellcome open research · 2026 · 8 claims · 7 setups

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  A genome assembly for Zerynthia rumina was produced, containing two haplotypes of 852.84 Mb and 775.60 Mb

  organism genomic assembled haplotype pacbio hi-c k-mer

• The genome sequence of the Mediterranean Skipper, Gegenes nostrodamus (Fabricius, 1793) (Lepidoptera: Hesperiidae).

  PMID 41908929 · PMC13019046 · Wellcome open research · 2026 · 6 claims · 7 setups

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  A chromosome-level genome assembly was generated for Gegenes nostrodamus (Mediterranean Skipper) as part of Project Psyche.

  gegenes pacbio hi-c k-mer

• The genome sequence of the Oriental Meadow Brown, Cercyonis lupina (Lepidoptera: Nymphalidae).

  PMID 41924386 · PMC13036442 · Wellcome open research · 2026 · 8 claims · 8 setups

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  Genome of Cercyonis lupina assembled into two haplotypes with total lengths of 508.65 Mb (haplotype 1) and 467.75 Mb (haplotype 2)

  organism pacbio assembled scaffolded pacbio hi-c k-mer

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• Population genomics: diversity and virulence in the Neisseria.

  PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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  Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

  neisseria meningitidis meningococcal multi-locus microarray genome

• The genome sequence of the Chalk Yellow-face Bee, Hylaeus dilatatus (Kirby, 1802) (Hymenoptera: Colletidae).

  PMID 41657665 · PMC12881847 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A two-haplotype genome assembly of Hylaeus dilatatus was produced, with total lengths of 307.38 Mb (haplotype 1) and 314.32 Mb (haplotype 2)

  hylaeus pacbio assembled barcoding pacbio hi-c

• The genome sequence of the Basking Shark, Cetorhinus maximus (Gunnerus, 1765) (Lamniformes: Cetorhinidae).

  PMID 41938266 · PMC13044535 · Wellcome open research · 2026 · 8 claims · 7 setups

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  The Cetorhinus maximus genome was assembled into two haplotypes with total lengths of 3993.85 Mb (hap1) and 3817.33 Mb (hap2)

  heart pacbio assembled pacbio hi-c rna-seq

• 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

• The genome sequence of the Provence Hairstreak, Tomares ballus (Fabricius, 1787) (Lepidoptera: Lycaenidae).

  PMID 41710119 · PMC12910201 · Wellcome open research · 2026 · 7 claims · 8 setups

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  A genome assembly was produced for a male Tomares ballus specimen consisting of two haplotypes (839.94 Mb and 831.10 Mb)

  organism pacbio assembled pacbio hi-c k-mer

• The genome sequence of the soldier beetle, Malthodes minimus (Linnaeus, 1758) (Coleoptera: Cantharidae).

  PMID 41769330 · PMC12949377 · Wellcome open research · 2026 · 8 claims · 8 setups

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  The Malthodes minimus genome assembly has a total length of 583.60 Mb, with 97.75% scaffolded into 7 chromosomal pseudomolecules including X and Y sex chromosomes

  malthodes pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the Osiris Blue, Cupido osiris (Meigen, 1830) (Lepidoptera: Lycaenidae).

  PMID 41798706 · PMC12963831 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly was produced for Cupido osiris (Osiris Blue butterfly)

  cupido pacbio hi-c k-mer