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).

• Adaptively inferring human transcriptional subnetworks.

  PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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  A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

  liver proximal hela predicted microarray computational novo

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• p53 mutation is a poor prognostic indicator for survival in patients with hepatocellular carcinoma undergoing surgical tumour ablation.

  PMID 9514057 · PMC2149958 · British journal of cancer · 1998 · 8 claims · 6 setups

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  p53 mutations were found in 8 of 12 HCCs with cirrhosis due to viral hepatitis and in both patients with sarcomatoid change

  resected exon p53 hcc gc-clamped sscp restriction

• A prospective, cross-sectional survey study of the natural history of Niemann-Pick disease type B.

  PMID 18625664 · PMC2692309 · Pediatrics · 2008 · 8 claims · 8 setups

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  NPD type B involves multisystem disease including hepatosplenomegaly, interstitial lung disease, dyslipidemia, thrombocytopenia, and growth delay

  leukocyte peripheral serum plasma gene enzyme chitotriosidase

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• A high-temporal resolution technology for dynamic proteomic analysis based on 35S labeling.

  PMID 18714357 · PMC2500177 · PloS one · 2008 · 6 claims · 6 setups

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  35S pulse-labeling (phosphor-imaging) detects more protein spots with higher sensitivity than CBB staining on the same 2-DE gels

  a549 liver 35s electrophoresis paired

• Metabolomics applied to diabetes research: moving from information to knowledge.

  PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups

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  Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status

  ins-1-derived pancreatic liver stedman 13c targeted ms-based

• 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