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).

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature

• In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

  PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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  This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

  vastus skeletal spectra identified phosphopeptide in-solution strong

• Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

  PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups

  Full-text index only

  Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS

  adipocytes jurkat mammary specified antiphosphotyrosine phosphospecific comparative

• Phosphoproteomics: new insights into cellular signaling.

  PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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  Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

  yeast hela beta2-adrenergic erk phosphopeptide targeted silac

• Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

  PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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  CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

  cerevisiae cycle reanalysis statistical optimal

• Sequence and structure signatures of cancer mutation hotspots in protein kinases.

  PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

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  Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

  kinase common egfr autoinhibited database-driven structure-informed evolutionary

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Patterns of somatic mutation in human cancer genomes.

  PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

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  Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

  cancers additional computational combined targeted follow-up statistical

• Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

  PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

  serous same lmp braf-mutant gene hotspot erbb2

• Integrated omics in Drosophila uncover a circadian kinome.

  PMID 32483184 · PMC7264355 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 98

  iCMod, a computational pipeline integrating transcriptomic, proteomic, and phosphoproteomic circadian data, was developed to accurately identify normalized circadian p-sites (NCPs)

  drosophila analysis tmt-based sequencing western

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

  PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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  Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems

  hela jurkat exposed yeast quantitative antibody-based analog-sensitive

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

  PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 59

  Short-term stress and long-term adaptations share common metabolic pathways

  great embryonic gef mapk1 bulk gene transcription

• A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

  PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups

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  HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin

  hela computational living halochip halochip-chip chip-chip

• A European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

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  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms