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).

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups

  Has reproduction · 78

  An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.

  proteins microarray ad-associated pahs target differential wgcna

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page

• Identification and characterization of insect-specific proteins by genome data analysis.

  PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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  Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

  drosophila insect-core locusta insect-specific comparative est functional

• Cellular proteins in influenza virus particles.

  PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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  Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

  influenza deglycosylated sucrose lc-ms mudpit electron

• Novel insights into adipogenesis from omics data.

  PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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  Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

  3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

• Back to basics.

  PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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  Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

  chromosome pendrin yeast carbonic genome gene mudpit

• Brown adipose tissue thermogenic adaptation requires Nrf1-mediated proteasomal activity.

  PMID 29400713 · PMC5839993 · Nature medicine · 2018 · 8 claims · 10 setups

  Has reproduction · 88

  Cold adaptation increases proteasomal activity in BAT, which is required for non-shivering thermogenesis

  bat body adipocytes mitochondria proteasomal core qpcr

• Adapting to a changing world: RAG genomics and evolution.

  PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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  RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

  rag-1 patients zebrafish vertebrate comparative site-directed clinical

• Microproteomics: analysis of protein diversity in small samples.

  PMID 18271009 · PMC2743962 · Mass spectrometry reviews · 2008 · 8 claims · 8 setups

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  Changes in gene/mRNA expression often do not correlate well with changes in protein expression, due to precursor cleavage, post-translational modification, localization, and variable protein lifetimes.

  lcm-dissected single few dense gel maldi capillary

• Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

  PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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  Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

  surgical standardized glioma gbm western principal k-means

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

  PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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  Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

  species genomic jmjd6 jmjc reciprocal comparative est

• 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