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 14

System / cell line: e.g ✕ Assay: global ✕ Clear

Application of functional genomics to primate endometrium: insights into biological processes.

PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

endometrial uterus whole-genome cdna oligonucleotide
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
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
Inverse symmetry in complete genomes and whole-genome inverse duplication.

PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups

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Reverse and complement symmetries are essentially absent in genomic sequences at all scales.

complete coli individual coding k-mer comparison segmental
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 4 setups

Has reproduction · 76

DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities

prostate global gene metabolomic computational
Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

hadv-37 predicted select genome cpg global
The role of genomics in tracking the evolution of influenza A virus.

PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

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Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

Has reproduction · 83

Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

species microrna atlas microarray rna-seq microrna
Stemming cancer: functional genomics of cancer stem cells in solid tumors.

PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

solid fetal cd133+ breast facs neurosphere genome-wide
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
Having a BLAST with bioinformatics (and avoiding BLASTphemy).

PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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BLAST is the most widely used tool for searching biological sequences for regions of local similarity

superfamilies blocks query pairwise phylogenetic sequence heuristic
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
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
iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

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Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

membrane-enriched xenograft homogenate quantified itraq western bradford

Experiments

Application of functional genomics to primate endometrium: insights into biological processes.

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

Use of functional genomics to understand influenza-host interactions.

Inverse symmetry in complete genomes and whole-genome inverse duplication.

Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

The role of genomics in tracking the evolution of influenza A virus.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Stemming cancer: functional genomics of cancer stem cells in solid tumors.

Novel insights into adipogenesis from omics data.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.