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).

Publications 1.3k Datasets 392.5k Experiments 301

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HIV-1 sequence evolution in vivo after superinfection with three viral strains.

PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

blood seminal pbmcs biological strain-specific bulk in-house
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

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

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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
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

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The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

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The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

dentium core whole-genome 3d-structure comparative
Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

PMID 19918099 · PMC4155129 · Antiviral therapy · 2009 · 8 claims · 6 setups

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Primary integrase inhibitor resistance mutations (T66I, E92Q, G140S, Y143C/H/R, Q148H/R/K, N155S/H) were absent in 342 drug-naive individuals, indicating these sites are highly constrained.

plasma genomic viral aligned bulk sequence-based quantitative
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

Has reproduction · 93

24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

jatropha geo bulk semi-quantitative quantitative
Human stool contains a previously unrecognized diversity of novel astroviruses.

PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

stool consensus-pcr-positive negative one consensus specific sanger
The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

PMID 41378738 · PMC12758960 · Genome biology and evolution · 2026 · 8 claims · 12 setups

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A chromosome-scale genome assembly of O. macclurei was generated (529.6 Mb, scaffold N50 23.7 Mb, GC 43.49%) using ONT long reads, Illumina short reads, and Hi-C scaffolding.

blood muscle tissues assembled oxford illumina hi-c
CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

PMID 41400832 · PMC12790814 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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CholeraSeq is an automated, V. cholerae-specific Nextflow pipeline that processes WGS outbreak data from raw reads/assemblies to high-quality SNPs and phylogenies in near-real-time.

cholerae recombination-masked pis read reference-based recombination
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
Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae).

PMID 41595526 · PMC12841229 · Genes · 2026 · 8 claims · 7 setups

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The E. seguinii mitogenome is the smallest and has the highest GC content of any known Eriobotrya species

seguinii protein-coding mitogenomes whole-genome mitogenome repeat
NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

PMID 41710890 · PMC12909245 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Dysidea avara has a chromosome-level genome assembly of 575 Mb, N50 41 Mb, 162 scaffolds, and 15 chromosomes.

dysidea avara translated nlrs long-read hi-c genome
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

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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
Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

PMID 41852645 · PMC12993812 · PNAS nexus · 2026 · 8 claims · 8 setups

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The Tokara Islands population is a cryptic species new to science, morphologically similar to but genetically distinct from Ijima's Leaf Warbler on the Izu Islands

museum ijimae phylloscopidae genome-wide morphometric bioacoustic whole-genome
Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae.

PMID 42113870 · PMC13183285 · PLoS pathogens · 2026 · 8 claims · 8 setups

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Each N. gonorrhoeae genome has on average 7 distinct opa alleles at 9-12 opa loci

gonorrhoeae complete opa non-gonorrhoeae long-read custom blast
Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

PMID 42224013 · PMC13225438 · Microbial genomics · 2026 · 8 claims · 6 setups

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The H37Rv_ref reference genome, sequenced in 1998 with early technology, is incomplete relative to modern hybrid-sequenced assemblies

tuberculosis h37rv_cn a2018772 publicly hybrid comparative functional

Experiments

HIV-1 sequence evolution in vivo after superinfection with three viral strains.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

Human stool contains a previously unrecognized diversity of novel astroviruses.

The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

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

Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae).

NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

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

Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae.

Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.