Results 71 to 80 of about 2,932,261 (286)

Escape from TGF‐β‐induced senescence promotes aggressive hallmarks in epithelial hepatocellular carcinoma cells

Molecular Oncology, EarlyView.
Chronic TGF‐β exposure drives epithelial HCC cells from a senescent state to a TGF‐β resistant mesenchymal phenotype. This transition is characterized by the loss of Smad3‐mediated signaling, escape from senescence, enhanced invasiveness and metastatic potential, and upregulation of key resistance modulators such as MARK1 and GRM8, ultimately promoting
Minenur Kalyoncu, Dilara Demirci, Sude Eris, Bengisu Dayanc, Ece Cakiroglu, Merve Basol, Merve Uysal, Gulcin Cakan‐Akdogan, Fang Liu, Mehmet Ozturk, Gökhan Karakülah, Serif Senturk   +11 more
wiley   +1 more source

The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples

Journal of Cheminformatics, 2023
Metabolomics by gas chromatography/mass spectrometry (GC/MS) provides a standardized and reliable platform for understanding small molecule biology. Since 2005, the West Coast Metabolomics Center at the University of California at Davis has collated GC ...
Parker Ladd Bremer, Gert Wohlgemuth, Oliver Fiehn   +2 more
doaj   +1 more source

Information-theoretic Interestingness Measures for Cross-Ontology Data Mining [PDF]

arXiv, 2015
Community annotation of biological entities with concepts from multiple bio-ontologies has created large and growing repositories of ontology-based annotation data with embedded implicit relationships among orthogonal ontologies. Development of efficient data mining methods and metrics to mine and assess the quality of the mined relationships has not ...
arxiv  

Targeting the AKT/mTOR pathway attenuates the metastatic potential of colorectal carcinoma circulating tumor cells in a murine xenotransplantation model

Molecular Oncology, EarlyView.
Dual targeting of AKT and mTOR using MK2206 and RAD001 reduces tumor burden in an intracardiac colon cancer circulating tumor cell xenotransplantation model. Analysis of AKT isoform‐specific knockdowns in CTC‐MCC‐41 reveals differentially regulated proteins and phospho‐proteins by liquid chromatography coupled mass spectrometry. Circulating tumor cells
Daniel J. Smit, Thais Pereira‐Veiga, Helena Brauer, Michael Horn, Paula Nissen, Thomas Mair, Bente Siebels, Hannah Voß, Ruimeng Zhuang, Marie‐Therese Haider, Desiree Loreth, Margarita Iskhakova, Bele Lindemann, Julian Kött, Laure Cayrefourcq, Jasmin Wellbrock, Hartmut Schlüter, Klaus Pantel, Catherine Alix‐Panabières, Manfred Jücker   +19 more
wiley   +1 more source

OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web [PDF]

arXiv, 2015
The delineation of logical definitions for each class in an ontology and the consistent application of these definitions to the assignment of instances to classes are important criteria for ontology evaluation. If ontologies are specified with property-based restrictions on class membership, then such consistency can be checked automatically.
arxiv  

DDeMON: Ontology-based function prediction by Deep Learning from Dynamic Multiplex Networks [PDF]

arXiv, 2023
Biological systems can be studied at multiple levels of information, including gene, protein, RNA and different interaction networks levels. The goal of this work is to explore how the fusion of systems' level information with temporal dynamics of gene expression can be used in combination with non-linear approximation power of deep neural networks to ...
arxiv  

Inhibitor of DNA binding‐1 is a key regulator of cancer cell vasculogenic mimicry

Molecular Oncology, EarlyView.
Elevated expression of transcriptional regulator inhibitor of DNA binding 1 (ID1) promoted cancer cell‐mediated vasculogenic mimicry (VM) through regulation of pro‐angiogenic and pro‐cancerous genes (e.g. VE‐cadherin (CDH5), TIE2, MMP9, DKK1). Higher ID1 expression also increased metastases to the lung and the liver.
Emma J. Thompson, Emma L. Dorward, Kristyn Jurrius, Nathalie Nataren, Markus Tondl, Kay K. Myo Min, Michaelia P. Cockshell, Anahita Fouladzadeh, John Toubia, Mark DeNichilo, Delphine Merino, Claudine S. Bonder   +11 more
wiley   +1 more source

Developing and using ontologies in behavioural science: addressing issues raised [version 2; peer review: 2 approved, 1 approved with reservations]

Wellcome Open Research, 2023
Ontologies are ways of representing aspects of the world in terms of uniquely defined classes of ‘entities’ and relationships between them. They are widely used in biological science, data science and commerce because they provide clarity, consistency ...
Nelli Hankonen, Robert West, Janna Hastings, Susan Michie, Marie Johnston, Alison J. Wright   +5 more
doaj  

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case

BMC Bioinformatics, 2006
Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field.
Taylor Chris, Stevens Robert, Rocca-Serra Philippe, Castro Alexander, Nashar Karim, Ragan Mark A, Sansone Susanna-Assunta   +6 more
doaj   +1 more source

Identifying Essential Hub Genes and Protein Complexes in Malaria GO Data using Semantic Similarity Measures [PDF]

arXiv, 2023
Hub genes play an essential role in biological systems because of their interaction with other genes. A vocabulary used in bioinformatics called Gene Ontology (GO) describes how genes and proteins operate. This flexible ontology illustrates the operation of molecular, biological, and cellular processes (Pmol, Pbio, Pcel).
arxiv