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 304

System / cell line: biological ✕ Clear

Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

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Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

cervical independent computational long real-time gene
Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional protein-protein
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
Molecular markers of preterm labor in the choriodecidua.

PMID 20009011 · PMC2852874 · Reproductive sciences (Thousand Oaks, Calif.) · 2010 · 8 claims · 4 setups

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Preterm choriodecidua displays distinct gene and protein expression patterns associated with preterm labor

choriodecidual excised differentially microarray two-dimensional mass
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

Has reproduction · 58

Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

dissected concatenated yakuba reference whole-transcriptome novo read
Network properties of complex human disease genes identified through genome-wide association studies.

PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

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Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

complex interactome gene disease-sharing gene protein-protein
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

cerevisiae mitocarta mitochondrial tissues comparative subcellular gene
Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

maternal tryptic scx-fractionated identified itraq immunodepletion strong
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

lung gene differentially significantly laser histology principal
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups

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31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis

rh9 hiv-infected identified subtractive mass enzyme-linked
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

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JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

tumor degs cancer jag bulk proteomics gene
Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

abdominal gingival overlapping interacting microarray weighted kegg
CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

arabidopsis bulk rna-seq-based rna-seq
Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

tcga tssb blca mirna-seq bulk kegg
Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.

PMID 41636304 · PMC12918712 · Environmental science & technology · 2026 · 7 claims · 6 setups

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Reclaimed effluents show lower AMR exposure (<0.5 ARGs/cell) than typically reported for secondary effluents

influent card pubmlst targeted shotgun arg

Experiments

Dissecting microregulation of a master regulatory network.

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

Of mice and men: comparative proteomics of bronchoalveolar fluid.

Human synthetic lethal inference as potential anti-cancer target gene detection.

Molecular markers of preterm labor in the choriodecidua.

Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

Network properties of complex human disease genes identified through genome-wide association studies.

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.