[ { "key": "D7QAARAH", "version": 1, "library": { "type": "group", "id": 26369, "name": "TheseGZEBib", "links": { "alternate": { "href": "https://www.zotero.org/groups/thesegzebib", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/26369/items/D7QAARAH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/thesegzebib/items/D7QAARAH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 187829, "username": "zohim", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/zohim", "type": "text/html" } } }, "creatorSummary": "Khanin and Vinciotti", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "D7QAARAH", "version": 1, "itemType": "journalArticle", "title": "Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs", "creators": [ { "creatorType": "author", "firstName": "Raya", "lastName": "Khanin" }, { "creatorType": "author", "firstName": "Veronica", "lastName": "Vinciotti" } ], "abstractNote": "", "publicationTitle": "Journal of Computational Biology", "publisher": "", "place": "", "date": "04/2008", "volume": "15", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "305-316", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Journal of Computational Biology", "DOI": "10.1089/cmb.2007.0184", "citationKey": "", "url": "http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0184", "accessDate": "2010-09-30T11:09:20Z", "PMID": "", "PMCID": "", "ISSN": "1066-5277", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NSTGFG8W" ], "relations": {}, "dateAdded": "2010-09-30T11:09:20Z", "dateModified": "2010-09-30T11:09:20Z" } }, { "key": "897J2EK7", "version": 1, "library": { "type": "group", "id": 26369, "name": "TheseGZEBib", "links": { "alternate": { "href": 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"firstName": "B.", "lastName": "Guy" }, { "creatorType": "author", "firstName": "C.", "lastName": "Lambert" } ], "abstractNote": "", "publicationTitle": "Journal of Computational Biology", "publisher": "", "place": "", "date": "01/2008", "volume": "15", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "105-128", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Journal of Computational Biology", "DOI": "10.1089/cmb.2007.0125", "citationKey": "", "url": "http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0125", "accessDate": "2010-09-30T11:09:16Z", "PMID": "", "PMCID": "", "ISSN": "1066-5277", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NSTGFG8W" ], "relations": {}, "dateAdded": "2010-09-30T11:09:16Z", "dateModified": "2010-09-30T11:09:16Z" } }, { "key": "QZPP2IJ9", "version": 1, "library": { "type": "group", "id": 26369, "name": "TheseGZEBib", "links": { "alternate": { "href": "https://www.zotero.org/groups/thesegzebib", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/26369/items/QZPP2IJ9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/thesegzebib/items/QZPP2IJ9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 187829, "username": "zohim", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/zohim", "type": "text/html" } } }, "creatorSummary": "Mariani et al.", "parsedDate": "2004-09", "numChildren": 0 }, "data": { "key": "QZPP2IJ9", "version": 1, "itemType": "journalArticle", "title": "Transcriptional control networks of cell differentiation: insights from helper T lymphocytes", "creators": [ { "creatorType": "author", "firstName": "Luca", "lastName": "Mariani" }, { "creatorType": "author", "firstName": "Max", "lastName": "Löhning" }, { "creatorType": "author", "firstName": "Andreas", "lastName": "Radbruch" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Höfer" } ], "abstractNote": "Coordinated programs of gene expression during cell differentiation can be controlled by master transcription factors. The differentiation of helper T (Th) lymphocytes during the immune response has been shown to occur along alternative pathways designated as Th1 and Th2. Induction of the Th1 and Th2 pathways is associated with the conversely regulated expression of the master factors T-bet and GATA-3, respectively. Both autoactivation and inhibition of GATA-3 play a crucial role in this process. We develop mathematical models of the underlying regulatory networks to provide a framework for the analysis of experimental data. Modeling concepts for gene expression dynamics are introduced, and paradigms for the behavior of gene-regulatory networks are reviewed. A mechanistic model for the regulation of GATA-3 in Th cells is developed that accounts for autoactivation and regulation by external differentiation signals. This system works as a bistable switch that enables the triggering of a differentiation program by transient inductive signals. GATA-3 inhibitors (such as FOG-1 and ROG) modulate GATA-3 expression by yet unidentified mechanisms. Three potential modes of inhibition, sequestration by a binding protein, repression of basal transcription, and repression of autoactivation, are predicted to have distinct, and strongly concentration-dependent, regulatory effects on GATA-3 dynamics. Based on these results, we develop a model for the cross-regulation of the alternative Th1 and Th2 differentiation programs which are governed by the dynamics of T-bet and GATA-3, respectively. The steady states of this model correlate with naïve, Th1-polarized, and Th2-polarized phenotypes. Our analysis makes predictions on the stability of the Th1 and Th2 programs and raises questions on the relation between transcription factor regulation and epigenetic determination in cell differentiation.", "publicationTitle": "Progress in Biophysics and Molecular Biology", "publisher": "", "place": "", "date": "Sep 2004", "volume": "86", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "45-76", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Prog. Biophys. Mol. Biol", "DOI": "10.1016/j.pbiomolbio.2004.02.007", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/15261525", "accessDate": "2010-09-30T10:35:56Z", "PMID": "", "PMCID": "", "ISSN": "0079-6107", "archive": "", "archiveLocation": "", "shortTitle": "Transcriptional control networks of cell differentiation", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 15261525", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Cell Differentiation", "type": 1 }, { "tag": "Computer Simulation", "type": 1 }, { "tag": "DNA-Binding Proteins", "type": 1 }, { "tag": "Feedback", "type": 1 }, { "tag": "GATA3 Transcription Factor", "type": 1 }, { "tag": "Gene Expression Profiling", "type": 1 }, { "tag": "Gene Expression Regulation", "type": 1 }, { "tag": "Homeostasis", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "T-Lymphocytes, Helper-Inducer", "type": 1 }, { "tag": "Trans-Activators", "type": 1 }, { "tag": "Transcription Factors", "type": 1 }, { "tag": "Transcription, Genetic", "type": 1 }, { "tag": "Transcriptional Activation", "type": 1 } ], "collections": [ "NSTGFG8W" ], "relations": {}, "dateAdded": "2010-09-30T10:35:56Z", "dateModified": "2010-09-30T10:35:56Z" } }, { "key": "R6ID9CCS", "version": 1, "library": { "type": "group", "id": 26369, "name": "TheseGZEBib", "links": { "alternate": { "href": "https://www.zotero.org/groups/thesegzebib", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/26369/items/R6ID9CCS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/thesegzebib/items/R6ID9CCS", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/26369/items/TFZ7AX5C", "type": "application/json" } }, "meta": { "createdByUser": { "id": 187829, "username": "zohim", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/zohim", "type": "text/html" } } } }, "data": { "key": "R6ID9CCS", "version": 1, "parentItem": "TFZ7AX5C", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2010-09-30T10:34:56Z", "url": "http://intimm.oxfordjournals.org/content/20/10/1269.full", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "1269.html", "md5": null, "mtime": 2147483647, "tags": [], "relations": {}, "dateAdded": "2010-09-30T10:34:56Z", "dateModified": "2010-09-30T10:34:56Z" } }, { "key": "TFZ7AX5C", "version": 1, "library": { "type": "group", "id": 26369, "name": "TheseGZEBib", "links": { "alternate": { "href": "https://www.zotero.org/groups/thesegzebib", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/26369/items/TFZ7AX5C", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/thesegzebib/items/TFZ7AX5C", "type": "text/html" } }, "meta": { "createdByUser": { "id": 187829, "username": "zohim", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/zohim", "type": "text/html" } } }, "creatorSummary": "van den Ham and de Boer", "parsedDate": "2008-10-01", "numChildren": 1 }, "data": { "key": "TFZ7AX5C", "version": 1, "itemType": "journalArticle", "title": "From the two-dimensional Th1 and Th2 phenotypes to high-dimensional models for gene regulation", "creators": [ { "creatorType": "author", "firstName": "Henk-Jan", "lastName": "van den Ham" }, { "creatorType": "author", "firstName": "Rob J.", "lastName": "de Boer" } ], "abstractNote": "The Th1/Th2 paradigm has been used for decades to characterize phenotypically different immune responses. Recent discoveries, e.g. Th17 cells are adding more dimensions to the helper T cell framework, and the Th1/Th2 paradigm is currently being extended to include these new phenotypes. Previous mathematical models cannot easily be extended to accommodate these new phenotypes, and therefore these discoveries call for a new type of models. We devised a new model of helper T cell differentiation that describes expression of, and interactions between, the master regulators determining the phenotypic polarization of helper T cells. The model is able to describe any number of master regulators and is grounded on transcription factors binding promoter sites and binding each other. The model allows for stable switches between several different phenotypes. Furthermore, the model accounts for the kinetics of FoxP3 and GATA3 mRNA expression measured after stimulating naive helper (CD4+CD45RA+) T cells under various circumstances. Due to its n-dimensional character, this model may easily be applied to other developmental processes that involve master regulators.", "publicationTitle": "International Immunology", "publisher": "", "place": "", "date": "Octobre 01 , 2008", "volume": "20", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1269 -1277", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/intimm/dxn093", "citationKey": "", "url": "http://intimm.oxfordjournals.org/content/20/10/1269.abstract", "accessDate": "2010-09-30T10:34:54Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NSTGFG8W" ], "relations": {}, "dateAdded": "2010-09-30T10:34:54Z", "dateModified": "2010-09-30T10:34:54Z" } } ]