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Jake Y Chen - One of the best experts on this subject based on the ideXlab platform.

  • HPD: an online integrated human pathway database enabling systems Biology Studies
    BMC Bioinformatics, 2009
    Co-Authors: Sudhir R Chowbina, Peter M Li, Ragini Pandey, Harini N Kasamsetty, Xiaogang Wu, Fan Zhang, Jake Y Chen
    Abstract:

    Background Pathway-oriented experimental and computational Studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gene regulation events, and metabolic reaction events. A pathway consists of a series of molecular pathway events that link molecular entities such as proteins, genes, and metabolites. There are approximately 300 biological pathway resources as of April 2009 according to the Pathguide database; however, these pathway databases generally have poor coverage or poor quality, and are difficult to integrate, due to syntactic-level and semantic-level data incompatibilities. Results We developed the Human Pathway Database (HPD) by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web sites. Integration of pathway data at syntactic, semantic, and schematic levels was based on a unified pathway data model and data warehousing-based integration techniques. HPD provides a comprehensive online view that connects human proteins, genes, RNA transcripts, enzymes, signaling events, metabolic reaction events, and gene regulatory events. At the time of this writing HPD includes 999 human pathways and more than 59,341 human molecular entities. The HPD software provides both a user-friendly Web interface for online use and a robust relational database backend for advanced pathway querying. This pathway tool enables users to 1) search for human pathways from different resources by simply entering genes/proteins involved in pathways or words appearing in pathway names, 2) analyze pathway-protein association, 3) study pathway-pathway similarity, and 4) build integrated pathway networks. We demonstrated the usage and characteristics of the new HPD through three breast cancer case Studies. Conclusion HPD http://bio.informatics.iupui.edu/HPD is a new resource for searching, managing, and studying human biological pathways. Users of HPD can search against large collections of human biological pathways, compare related pathways and their molecular entity compositions, and build high-quality, expanded-scope disease pathway models. The current HPD software can help users address a wide range of pathway-related questions in human disease Biology Studies.

  • HPD: an online integrated human pathway database enabling systems Biology Studies.
    BMC bioinformatics, 2009
    Co-Authors: Sudhir R Chowbina, Ragini Pandey, Harini N Kasamsetty, Fan Zhang, Jake Y Chen
    Abstract:

    Pathway-oriented experimental and computational Studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gene regulation events, and metabolic reaction events. A pathway consists of a series of molecular pathway events that link molecular entities such as proteins, genes, and metabolites. There are approximately 300 biological pathway resources as of April 2009 according to the Pathguide database; however, these pathway databases generally have poor coverage or poor quality, and are difficult to integrate, due to syntactic-level and semantic-level data incompatibilities. We developed the Human Pathway Database (HPD) by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web sites. Integration of pathway data at syntactic, semantic, and schematic levels was based on a unified pathway data model and data warehousing-based integration techniques. HPD provides a comprehensive online view that connects human proteins, genes, RNA transcripts, enzymes, signaling events, metabolic reaction events, and gene regulatory events. At the time of this writing HPD includes 999 human pathways and more than 59,341 human molecular entities. The HPD software provides both a user-friendly Web interface for online use and a robust relational database backend for advanced pathway querying. This pathway tool enables users to 1) search for human pathways from different resources by simply entering genes/proteins involved in pathways or words appearing in pathway names, 2) analyze pathway-protein association, 3) study pathway-pathway similarity, and 4) build integrated pathway networks. We demonstrated the usage and characteristics of the new HPD through three breast cancer case Studies. HPD http://bio.informatics.iupui.edu/HPD is a new resource for searching, managing, and studying human biological pathways. Users of HPD can search against large collections of human biological pathways, compare related pathways and their molecular entity compositions, and build high-quality, expanded-scope disease pathway models. The current HPD software can help users address a wide range of pathway-related questions in human disease Biology Studies.

  • hpd an online integrated human pathway database enabling systems Biology Studies
    BMC Bioinformatics, 2009
    Co-Authors: Sudhir R Chowbina, Ragini Pandey, Harini N Kasamsetty, Jake Y Chen, Fan Zhang
    Abstract:

    Pathway-oriented experimental and computational Studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gene regulation events, and metabolic reaction events. A pathway consists of a series of molecular pathway events that link molecular entities such as proteins, genes, and metabolites. There are approximately 300 biological pathway resources as of April 2009 according to the Pathguide database; however, these pathway databases generally have poor coverage or poor quality, and are difficult to integrate, due to syntactic-level and semantic-level data incompatibilities.

  • proteolens a visual analytic tool for multi scale database driven biological network data mining
    BMC Bioinformatics, 2008
    Co-Authors: Jake Y Chen, Tianxiao Huan, Andrey Sivachenko, Scott H Harrison
    Abstract:

    Background New systems Biology Studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed.

John E.g. Mccarthy - One of the best experts on this subject based on the ideXlab platform.

  • Protein production in Saccharomyces cerevisiae for systems Biology Studies.
    Methods in enzymology, 2011
    Co-Authors: Naglis Malys, Stephen G. Oliver, Jill A. Wishart, John E.g. Mccarthy
    Abstract:

    Proteins together with metabolites, nucleic acids, lipids, and other intracellular molecules form biological systems that involve networks of functional and physical interactions. To understand these interactions and the many other characteristics of proteins in the context of biochemical networks and systems Biology, research aimed at studying medium and large sets of proteins is required. This either involves an investigation focused on individual protein activities in the mixture (e.g., cell extracts) or a protein characterization in the isolated form. This chapter provides an overview on the currently available resources and strategies for isolation of proteins from Saccharomyces cerevisiae. The use of standardized gene expression systems is discussed, and protein production protocols applied to the data generation pipeline for systems Biology are described in detail.

Anthony Trewavas - One of the best experts on this subject based on the ideXlab platform.

Gregory A. Nelson - One of the best experts on this subject based on the ideXlab platform.

  • Caenorhabditis elegans: a model system for space Biology Studies.
    Experimental gerontology, 1991
    Co-Authors: Thomas E. Johnson, Gregory A. Nelson
    Abstract:

    Abstract The utility of the nematode Caenorhabditis elegans in Studies spanning aspects of development, aging, and radioBiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space Biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induced changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for Studies of development and senscence. The current and future opportunities for such space-flight experimentation are presented.

Yannick Saintigny - One of the best experts on this subject based on the ideXlab platform.

  • In vitro engineering of human 3D chondrosarcoma: a preclinical model relevant for investigations of radiation quality impact
    BMC Cancer, 2015
    Co-Authors: Dounia Hamdi, Sofia Barbieri, François Chevalier, Jean-emmanuel Groetz, Florence Legendre, Magali Demoor, Philippe Galera, Jean-louis Lefaix, Yannick Saintigny
    Abstract:

    Background: The benefit of better ballistic and higher efficiency of carbon ions for cancer treatment (hadron-therapy) is asserted since decades, especially for unresectable or resistant tumors like sarcomas. However, hadron-therapy with carbon ions stays underused and raises some concerns about potential side effects for patients. Chondrosarcoma is a cartilaginous tumor, chemo-and radiation-resistant, that lacks reference models for basic and pre-clinical Studies in radiation-Biology. Most Studies about cellular effects of ionizing radiation, including hadrons, were performed under growth conditions dramatically different from human homeostasis. Tridimensional in vitro models are a fair alternative to animal models to approach tissue and tumors microenvironment. Methods: By using a collagen matrix, standardized culture conditions, physiological oxygen tension and a well defined chondrosarcoma cell line, we developed a pertinent in vitro 3D model for hadron-Biology Studies. Low-and high-Linear Energy Transfer (LET) ionizing radiations from GANIL facilities of ~1 keV/μm and 103 ± 4 keV/μm were used respectively, at 2 Gy single dose. The impact of radiation quality on chondrosarcoma cells cultivated in 3D was analyzed on cell death, cell proliferation and DNA repair. Results: A fair distribution of chondrosarcoma cells was observed in the whole 3D scaffold. Moreover, LET distribution in depth, for ions, was calculated and found acceptable for radiation-Biology Studies using this kind of scaffold. No difference in cell toxicity was observed between low-and high-LET radiations but a higher rate of proliferation was displayed following high-LET irradiation. Furthermore, 3D models presented a higher and longer induction of H2AX phosphorylation after 2 Gy of high-LET compared to low-LET radiations. Conclusions: The presented results show the feasibility and usefulness of our 3D chondrosarcoma model in the study of the impact of radiation quality on cell fate. The observed changes in our tissue-like model after ionizing radiation exposure may explain some discrepancies between radiation-Biology Studies and clinical data.