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).

• Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

  PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

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  Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

  pestis combined dental contemporary spacer phylogenetic pcr

• Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

  PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally

  plasmid genomic bacterial real-time methylation-specific

• Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

  PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

  activated skeletal muscle altered affymetrix quantitative sirna

• Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

  PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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  MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

  genitalium clinical urine pairwise pcr serial

• Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

  PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

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  Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

  hela post-mitotic pulsed fluorescence selective

• Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

  PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

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  DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

  nuclear same sh-sy5y snp haplotype-based quantitative

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

  PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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  The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

  coli se11 rapd whole-genome gene

• Massively parallel pyrosequencing in HIV research.

  PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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  Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

  mammoth hiv hiv-infected honey pyrosequencing pcr 16s

• Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

  PMID 20043151 · PMC2825322 · Applied microbiology and biotechnology · 2010 · 8 claims · 8 setups

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  Aerobic biodegradation of branched NP in polluted river sediment occurs within 8 days after a 2-day lag phase at 30°C

  np-polluted sediment-derived fourth-generation extracted biodegradation serial metabolite

• Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

  PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

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  Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

  breast hek293 erβ1 allelic luciferase stability

• LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture.

  PMID 41489510 · PMC13040219 · Cancer discovery · 2026 · 8 claims · 8 setups

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  LINE-1 RNAs are primarily chromatin-associated nascent transcripts rather than cytosolic mRNAs

  mcf7 cancer qrt-pcr single-molecule chirp-seq

• Retentive Network promotes efficient RNA language modeling of long sequences.

  PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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  RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

  million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna

• 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

• NCBI Reference Sequences: current status, policy and new initiatives.

  PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

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  RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

  microbial bacterial prokaryotic refseq spliced structural functional

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups

  Has reproduction

  Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas

  alteromonas trichodesmium differential classical smrt

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

  holacanthella duospinosa genome transcriptome phylogenomics

• Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.

  PMID 38909031 · PMC11193758 · Scientific data · 2024 · 7 claims · 8 setups

  Has reproduction · 80

  A chromosome-level genome of P. ornatus was assembled spanning 2.65 Gb with contig N50 of 51.05 Mb, with 99.11% of sequence anchored to 73 chromosomes

  muscle eight genomic genome wgs hi-c rna-seq

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Mutational analysis of p80 coilin indicates a functional interaction between coiled bodies and the nucleolus.

  PMID 7490287 · PMC2200013 · The Journal of cell biology · 1995 · 8 claims · 7 setups

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  p80 coilin plays an important role in subnuclear organization and there is a functional interaction between coiled bodies and nucleoli

  multi-tissue rabbit hela northern transcription western