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).

Publications 1.3k Datasets 392.5k Experiments 523

Assay: model ✕ Clear

Helicobacter Pylori's plasticity zones are novel transposable elements.

PMID 19727398 · PMC2731543 · PloS one · 2009 · 8 claims · 8 setups

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Plasticity zones are a novel class of transposable elements (named TnPZs), flanked by direct repeats of 5'AAGAATG and inserted at multiple discrete chromosomal sites

pylori shimaa model mammalian pcr-based genome pcr
Investigating the genetic association between ERAP1 and ankylosing spondylitis.

PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

patients cases genotype comparison snp meta-analysis resequencing
Network-assisted protein identification and data interpretation in shotgun proteomics.

PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

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Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

yeast organs mammary organ shotgun clique-enrichment microarray
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

missense same synthetic tp53 random support principal
Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

pbmcs blood apoe genes microarray rt-qpcr elisa
Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

PMID 39537633 · PMC11561360 · Nature communications · 2024 · 8 claims · 8 setups

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A pharmacogenomic scoring strategy (OligoScore) combining transcriptomic signatures and curated oligodendrogenesis gene sets identifies compounds with pro-oligodendrogenic transcriptional activity

brain neonatal gene cerebellar bulk transcriptomic pharmacogenomic
MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

PMID 39805182 · PMC11780959 · Translational oncology · 2025 · 6 claims · 8 setups

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A C3 PCLAF+ tumor cell subtype identified by scRNA-seq shows high proliferation/differentiation potential and is linked to aggressive tumor behavior and poor prognosis in HR+BC

hr+bc mda-mb-361 tcga scrna-seq cellchat pyscenic
Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

Has reproduction

SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial
An "omics" approach to uropathogenic Escherichia coli vaccinology.

PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

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An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

upec vaccination comparative two-dimensional
Innate immune modulation by RNA viruses: emerging insights from functional genomics.

PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

embryonic liver brain serial gene-expression computational
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
From single cells to whole organisms.

PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

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The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai
Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

hla-b44 plasma macrophages complement proteomics shotgun cap
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
Lipids join the post-genomic era.

PMID 17076911 · PMC1794566 · Genome biology · 2006 · 8 claims · 8 setups

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Infrared-laser MALDI-MS can image biological tissue while avoiding the matrix-preparation artifacts of UV-laser MALDI

biological intact mixtures yeast maldi esi faims
Genomics--from Neanderthals to high-throughput sequencing.

PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

bacterial ion-channel drosophila arrays next-generation pooled multiplex
PhylomeDB: a database for genome-wide collections of gene phylogenies.

PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

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PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

seed homologous trimmed homology sequence neighbor
NEIBank: genomics and bioinformatics resources for vision research.

PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

dissected eye retina cdna est serial sequence
Addressing the age-old question of old age.

PMID 15287970 · PMC507873 · Genome biology · 2004 · 8 claims · 6 setups

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Dietary restriction and reduced temperature extend Drosophila lifespan via intrinsically different demographic mechanisms: dietary restriction lowers intrinsic frailty, while lower temperature reduces the rate of senescence.

drosophila populations australian centenarians demographic historical peptide
Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

Has reproduction · 51

A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients

tcga candidate cancer univariate weighted lasso

Experiments

Helicobacter Pylori's plasticity zones are novel transposable elements.

Investigating the genetic association between ERAP1 and ankylosing spondylitis.

Network-assisted protein identification and data interpretation in shotgun proteomics.

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

An "omics" approach to uropathogenic Escherichia coli vaccinology.

Innate immune modulation by RNA viruses: emerging insights from functional genomics.

A European focus on proteomics.

From single cells to whole organisms.

Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

Database resources of the National Center for Biotechnology Information.

Lipids join the post-genomic era.

Genomics--from Neanderthals to high-throughput sequencing.

PhylomeDB: a database for genome-wide collections of gene phylogenies.

NEIBank: genomics and bioinformatics resources for vision research.

Addressing the age-old question of old age.

Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.