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).

• Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

  PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 68

  Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.

  cerevisiae colony-forming-unit bulk pooled

• ECgene: genome annotation for alternative splicing.

  PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

  brca2 rgs17 organs cdna genomic genome transcript

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• Autoantibody profiling for the study and treatment of autoimmune disease.

  PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

  Full-text index only

  Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

  serum antigen-antibody antigens fetal spotted elisa microarray

• Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

  PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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  A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

  sheep genome bac sequence randomization

• Genomics in space life sciences.

  PMID 18558380 · PMC5054090 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 6 setups

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  Sudden changes in gravity alter mRNA levels of various genes, indicating molecular-level effects of microgravity

  keratinocyte wi-38 candida rice microarray suppression pathogenicity

• Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

  PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

  one nci60 cerevisiae cancer multidimensional cellular two-color

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Helicobacter pylori: after the genomes, back to biology.

  PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

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  STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

  helicobacter diffuse signature-tagged genome yeast

• Microarray-based DNA methylation profiling: technology and applications.

  PMID 16428248 · PMC1345696 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  A microarray-based method enriching unmethylated and methylated DNA fractions via methylation-sensitive restriction enzymes followed by hybridization enables high-throughput DNA methylation profiling of large genomic regions.

  genomic postmortem ligated custom cpg tiling

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative

• Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

  PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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  Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

  chinese tissues skeletal pk15 full-length real-time gfp

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

  PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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  3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

  brain hbrr topo-cloned tag microarray quantitative

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr

• Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

  PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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  Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

  liver chimpanzee h-invitational tar genome blastn secondary

• Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

  PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

  baumannii ranked lpta representative pooled string mic

• Systems biology approaches for the study of multiple sclerosis.

  PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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  The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

  patients lesion osteopontin monocyte-depleted genetic large-scale gene

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional

• Translation affects mRNA stability in a codon-dependent manner in human cells.

  PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Translation strongly affects mRNA stability in a codon-dependent manner in human cells, with specific codons stabilizing or destabilizing mRNAs.

  293t incl endogenous time-course orfome slam-seq