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).

• Human metapneumovirus, Australia, 2001-2004.

  PMID 16965711 · PMC3291208 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

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  HMPV had a 7.1% average annual incidence among 10,025 respiratory samples tested over 4 years

  nasopharyngeal npa hmpv-positive reverse direct multiplex

• Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

  PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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  Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

  individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

  Has reproduction · 66

  A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

  zygotes aorta genomic aortae crispr prime quantitative

• BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

  PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts

  barley pacbio illumina read

• Overlapping gene mutations of hepatitis B virus in a chronic hepatitis B patient with hepatitis B surface antigen loss during lamivudine therapy.

  PMID 15953865 · PMC2782199 · Journal of Korean medical science · 2005 · 7 claims · 5 setups

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  Serum HBsAg became negative after 36 months of lamivudine therapy while HBeAg and HBV DNA remained positive

  serum hbv serologic hbv pcr

• Genomic view of the evolution of the complement system.

  PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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  Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

  chicken complement sponge shark comparative phylogenetic reverse

• Recurring mutations found by sequencing an acute myeloid leukemia genome.

  PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

  aml-m1 tumor bone additional whole-genome snp gene-expression

• Structural genomics: a new era for pharmaceutical research.

  PMID 11864367 · PMC139010 · Genome biology · 2002 · 8 claims · 6 setups

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  Automation of crystal mounting, diffraction data collection, and structure determination/refinement is a critical factor enabling large-scale structural genomics projects.

  proteins target hiv x-ray thermal initio

• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

  PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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  The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

  genomic predicted cdna tissues genomic sequence pcr

• Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

  PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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  Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

  genomic huvec microarray solid-phase real-time

• Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

  PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

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  50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

  genomic α-gal cos-7 transcripts pcr southern microsatellite

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

  PMID 18433472 · PMC2386800 · BMC molecular biology · 2008 · 7 claims · 6 setups

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  Co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves gives high-level transient expression of active, mismatch-specific ENDO1 via a simple purification protocol

  benthamiana test genomic hiv-1 transient heteroduplex mutation