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 244

System / cell line: factor ✕ Clear

Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

yeast specified normal coli chip-on-chip chip-sequencing correlation-based
Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

liver saccharomyces mdeg independent microarray transcription chromosomal
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study.

PMID 19963597 · PMC2928997 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 6 claims · 4 setups

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Developed an imaging genomic browsing system allowing whole genome and entire brain analyses via visual exploration

mci same voxel-based snp genotype
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.

PMID 19836472 · PMC2829334 · Biochimica et biophysica acta · 2010 · 8 claims · 7 setups

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Label-free 2D-LC-MS/MS quantitative proteomics identified 476 significantly differentially expressed proteins in kidney tubules of diabetic OVE26 mice versus control mice

kidney hk11 list 2d-lc-ms immunoblot immunohistochemistry
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
Have microarrays failed to deliver for developmental biology?

PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

drosophila caenorhabditis developing xenopus cdna genome-wide microarray
Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic
The changing face of genomics.

PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

yeast drosophila zebrafish elegans chip-chip comparative insertional
Shaken not stirred: a global research cocktail served in Hinxton.

PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

budding caenorhabditis drosophila escherichia two-color double chip-chip
Mathematical models in mammalian cell biology.

PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups

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A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.

culture skin hela mammalian live-cell confocal phosphoprotein
miRGen 2.0: a database of microRNA genomic information and regulation.

PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

lung organ malme embryonic polii small nucleosome
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
The novel duplication HRAS c.186_206dup p.(Glu62_Arg68dup): clinical and functional aspects.

PMID 32499600 · PMC7576819 · European journal of human genetics : EJHG · 2020 · 7 claims · 3 setups

Has reproduction

The novel HRAS c.186_206dup p.(Glu62_Arg68dup) variant was identified in an individual with hypertrophic cardiomyopathy, Chiari 1 malformation and ectodermal findings consistent with a RASopathy.

hras expressing protein-protein phosphorylation growth
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

PMID 39549198 · PMC11979089 · GeroScience · 2025 · 9 claims · 2 setups

Has reproduction · 54

The Multi-State Epigenetic Pacemaker (MSEPM) can accurately model multiple methylation-associated factors (e.g., age, sex, cell-type) simultaneously.

blood simulated methylation simulation
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Onto-Tools: new additions and improvements in 2006.

PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups

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OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files

specified pathway functional example
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

Has reproduction · 80

PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

randomly single-cell single scrna-seq cell-type orthogonal
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

Has reproduction · 91

175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

one sinensis small-molecular-weight leaves small genome mirna

Experiments

Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

Mutation analysis of the MSMB gene in familial prostate cancer.

Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study.

Genetic variation in PARL influences mitochondrial content.

Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.

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

Have microarrays failed to deliver for developmental biology?

Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

The changing face of genomics.

Shaken not stirred: a global research cocktail served in Hinxton.

Mathematical models in mammalian cell biology.

miRGen 2.0: a database of microRNA genomic information and regulation.

Phenotypic variation meets systems biology.

The novel duplication HRAS c.186_206dup p.(Glu62_Arg68dup): clinical and functional aspects.

The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

Web-based resources for comparative genomics.

Onto-Tools: new additions and improvements in 2006.

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.