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).

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

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  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.

  PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups

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  omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem

  renal microarray qrt-pcr computational

• Survival analysis with high-dimensional covariates.

  PMID 19654171 · PMC4806549 · Statistical methods in medical research · 2010 · 8 claims · 1 setups

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  The classical Cox proportional hazards model cannot be fit when p >> n because the partial likelihood maximizer is not unique and the matrix X^T A X is singular in the IRLS procedure

  renal gene

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• Patterns of somatic mutation in human cancer genomes.

  PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

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  Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

  cancers additional computational combined targeted follow-up statistical

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• The 32nd Annual Congress of the Society of Critical Care Medicine, 28 January - 2 February 2003, San Antonio, USA.

  PMID 12720569 · PMC270663 · Critical care (London, England) · 2003 · 8 claims · 8 setups

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  Proteomics is more useful than genomics for identifying regulatory pathways and druggable targets in disease because transcriptional responses to different stimuli often converge while protein interaction networks reveal distinct regulatory nodes

  macrophages patients animal ards gene histological mechanical

• Two novel mutations in the aquaporin 2 gene in a girl with congenital nephrogenic diabetes insipidus.

  PMID 16361827 · PMC2779314 · Journal of Korean medical science · 2005 · 8 claims · 5 setups

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  The patient carries a compound heterozygous missense mutation in AQP2: A70D (exon 1, paternal) and R187H (exon 3, maternal)

  3-year-old serum genomic clinical hormone water

• Understanding sex differences in environmental health: a thought leaders' roundtable.

  PMID 15064168 · PMC1241928 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  Dioxin and corticosteroids both cause thymic atrophy but via distinct mechanisms; dioxin's atrophy kinetics resemble those induced by estrogen despite acting through a different receptor.

  laboratory mice nzb c57bl thymus radiation autoimmune

• Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

  PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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  Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

  genomic pcr-amplified tsc healthy dhplc direct pcr

• A genome search for primary vesicoureteral reflux shows further evidence for genetic heterogeneity.

  PMID 18197425 · PMC2259258 · Pediatric nephrology (Berlin, Germany) · 2008 · 8 claims · 7 setups

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  Genome-wide linkage analysis identifies several novel loci for primary VUR on chromosomes 1, 3, 4, and 22, supporting genetic heterogeneity.

  patients multiplex index pedigree genome-wide fine-mapping haplotype