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).

• 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

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• SELDI-TOF proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

  PMID 18644101 · PMC2481502 · Breast cancer research : BCR · 2008 · 7 claims · 3 setups

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  SELDI-TOF MS proteomic profiling of breast carcinomas identifies patient subgroups with differential co-expression of protein peaks that are analogous to gene-expression-based classifications (luminal, basal, HER2 subtypes)

  breast seldi-tof hierarchical biomarker

• Personalized medicine: the future is not what it used to be.

  PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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  Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

  sw13 h295r drosophila acc drug synthetic gene

• 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

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• Contribution of oncoproteomics to cancer biomarker discovery.

  PMID 17407558 · PMC1852117 · Molecular cancer · 2007 · 6 claims · 8 setups

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  Oncoproteomic biomarker panels (2-DE/MS-based) show higher sensitivity and specificity than currently used single tumor markers across multiple cancer types (Table 1)

  serum bladder nipple colorectal 2-de isotope-coded immunoblotting

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

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  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case

• Identifying synonymous regulatory elements in vertebrate genomes.

  PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

  genome genes genome-wide gene tissue-specificity

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

  PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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  A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

  upstream co-expression pre-b microarray-based motif gene

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Proteolysis of the endothelial cell protein C receptor by neutrophil proteinase 3.

  PMID 17459006 · PMC1890847 · Journal of thrombosis and haemostasis : JTH · 2007 · 8 claims · 8 setups

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  Activated neutrophils decrease EPCR surface expression on endothelial cells over time

  ea.hy926 peripheral neutrophils recombinant flow luminol-dependent sds-page

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• Application of proteomics in the study of tumor metastasis.

  PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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  Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

  young metastatic hepatocellular lines microarray 2de cdna

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter