Research Topics
Genomes and GenesSpecies | Bruce ConklinSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and miceEdward C Hsiao
Gladstone Institute of Cardiovascular Disease, 1650 Owens St, San Francisco, CA 94158, USA
Stem Cell Res Ther 2:11. 2011....- Time- and exercise-dependent gene regulation in human skeletal muscleAlexander C Zambon
Gladstone Institute of Cardiovascular Disease, Department of Medicine, University of California, San Francisco, CA 94141, USA
Genome Biol 4:R61. 2003.... - MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray dataScott W Doniger
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141-9100, USA
Genome Biol 4:R7. 2003..Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged... - Identifying genetic networks underlying myometrial transition to laborNathan Salomonis
Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
Genome Biol 6:R12. 2005..This analysis provides new evidence of multiple parallel mechanisms of uterine contractile regulation and presents new putative targets for regulating myometrial transformation and contraction... - Engineered G protein coupled receptors reveal independent regulation of internalization, desensitization and acute signalingKimberly Scearce-Levie
The Gladstone Institute of Neurological Disease and the Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
BMC Biol 3:3. 2005..This modification allows us to compare receptors that have the same ligands and effectors, but differ only in desensitization and internalization... - The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping servicesMartijn P van Iersel
Department of Bioinformatics BiGCaT, Maastricht University, Maastricht, The Netherlands
BMC Bioinformatics 11:5. 2010..Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services... - GenMAPP 2: new features and resources for pathway analysisNathan Salomonis
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
BMC Bioinformatics 8:217. 2007..Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses... - Presenting and exploring biological pathways with PathVisioMartijn P van Iersel
Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
BMC Bioinformatics 9:399. 2008..The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs... - New tools to build synthetic hormonal pathwaysBruce R Conklin
Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 104:4777-8. 2007 - Engineering GPCR signaling pathways with RASSLsBruce R Conklin
Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, California 94158, USA
Nat Methods 5:673-8. 2008..Currently, RASSLs exist for the three major GPCR signaling pathways (G(s), G(i) and G(q)). We review these advances here to facilitate the use of these powerful and diverse tools... - Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humansSupriya Srinivasan
Gladstone Institute of Cardiovascular Disease, UCSF, San Francisco, California 94143 0540, USA
J Clin Invest 114:1158-64. 2004..Our results also suggest that the tonic satiety signal provided by the constitutive activity of MC4R may be required for maintaining long-term energy homeostasis in humans... - Reporter-based isolation of induced pluripotent stem cell- and embryonic stem cell-derived cardiac progenitors reveals limited gene expression varianceLinda W Van Laake
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 94158, USA
Circ Res 107:340-7. 2010.... 
Cloning mice and men: prohibiting the use of iPS cells for human reproductive cloningBernard Lo
Program in Medical Ethics, Department of Medicine, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
Cell Stem Cell 6:16-20. 2010..Professional standards and laws that ban human reproductive cloning by somatic cell nuclear transfer should be revised to also forbid it by other methods, such as iPSCs via tetraploid complementation...- G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent coloniesKenta Nakamura
Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
PLoS ONE 4:e7780. 2009..We tested the hypothesis that G(i)-coupled GPCR signaling contributes to the characteristic morphology and organization of human pluripotent colonies... - SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization systemAlexander R Pico
Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
Nucleic Acids Res 37:D803-9. 2009..We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data... - Gs G protein-coupled receptor signaling in osteoblasts elicits age-dependent effects on bone formationEdward C Hsiao
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
J Bone Miner Res 25:584-93. 2010..Finally, our model provides a powerful tool for investigating the effects of continuous G(s)-GPCR signaling on dynamic bone growth and remodeling... - Ligand-mediated activation of an engineered gs g protein-coupled receptor in osteoblasts increases trabecular bone formationEdward C Hsiao
Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, California 94158, USA
Mol Endocrinol 24:621-31. 2010..This model provides a powerful tool for investigating the effects of ligand-activated G(s)-GPCR signaling on dynamic bone growth and remodeling... - Marking embryonic stem cells with a 2A self-cleaving peptide: a NKX2-5 emerald GFP BAC reporterEdward C Hsiao
Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
PLoS ONE 3:e2532. 2008..Multiple fluorophores and genetic selection markers exist; however, a system for creating reporter constructs that preserve the regulatory sequences near a gene's native ATG start site has not been widely available... - Osteoblast expression of an engineered Gs-coupled receptor dramatically increases bone massEdward C Hsiao
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 105:1209-14. 2008..This pathway may represent an important determinant of bone mass and may open future avenues for enhancing bone repair and treating metabolic bone diseases... - Engineering the melanocortin-4 receptor to control constitutive and ligand-mediated G(S) signaling in vivoSupriya Srinivasan
Gladstone Institute of Cardiovascular Disease, University of California at San Francisco, San Francisco, California, United States of America
PLoS ONE 2:e668. 2007..Our study also demonstrates the use of human genetic variation for protein engineering... 
Engineering the melanocortin-4 receptor to control G(s) signaling in vivoSupriya Srinivasan
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, California 94141, USA
Ann N Y Acad Sci 994:225-32. 2003..The MC4R G(s) RASSL could be used to control many physiological responses associated with G(s) signaling such as heart rate, energy homeostasis, and cell proliferation...- Regression approaches for microarray data analysisMark R Segal
Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0560, USA
J Comput Biol 10:961-80. 2003..Model selection and solution multiplicity issues are also discussed. The methods are evaluated using a microarray-based study of cardiomyopathy in transgenic mice... - Cardiac transgenesis with the tetracycline transactivator changes myocardial function and gene expressionDiana T McCloskey
Department of Radiology, University of California, San Francisco, USA
Physiol Genomics 22:118-26. 2005..Furthermore, the results raise the possibility that the phenotype conferred by a target gene may be influenced by the modified genetic background of alphaMHC-tTA myocardium... - Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulationWhittemore G Tingley
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 104:8461-6. 2007..Our stem cell-based screen may provide a means of identifying other genes that control heart rhythm... - Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiationNathan Salomonis
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 107:10514-9. 2010..The findings herein illustrate a critical role for AS in the specification of ES cells with differentiation, and highlight the utility of global functional analyses of AS... - Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptorWei Chun Chang
Gladstone Institute of Cardiovascular Disease, University of California at San Francisco, San Francisco, California, United States of America
PLoS ONE 2:e1317. 2007..This G(i)-coupled RASSL, Rs1.3, exhibited no measurable signaling to the G(s) or G(q) pathway. These findings show that the signaling repertoire of Rs1 can be expanded and controlled by receptor engineering and drug selection... - MicroRNA regulation of cell lineages in mouse and human embryonic stem cellsKathryn N Ivey
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA
Cell Stem Cell 2:219-29. 2008..Our findings indicate that muscle-specific miRNAs reinforce the silencing of nonmuscle genes during cell lineage commitment and suggest that miRNAs may have general utility in regulating cell-fate decisions from pluripotent ES cells... - The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouseAlex S Nord
University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
Nucleic Acids Res 34:D642-8. 2006.... - Tools for dissecting signaling pathways in vivo: receptors activated solely by synthetic ligandsKimberly Scearce-Levie
Gladstone Institute of Cardiovascular Disease, Departments of Medicine and Pharmacology, University of California, San Francisco, California 94141, USA
Methods Enzymol 343:232-48. 2002 - Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase AAlexander C Zambon
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141, USA
Proc Natl Acad Sci U S A 102:8561-6. 2005..These transcriptional networks include a primary group of cAMP-response element-containing genes and secondary networks that include the circadian clock... - Sustained preconditioning induced by cardiac transgenesis with the tetracycline transactivatorLynne Turnbull
Department of Radiology, University of California, San Francisco, California 94121, USA
Am J Physiol Heart Circ Physiol 290:H1103-9. 2006..Furthermore, investigations of cardioprotection using the Tet system may be aberrantly influenced by sustained preconditioning induced by cardiac transgenesis with tTA... - Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursorsNathan Salomonis
Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
PLoS Comput Biol 5:e1000553. 2009.... - Canonical Wnt signaling is a positive regulator of mammalian cardiac progenitorsChulan Kwon
Gladstone Institute of Cardiovascular Disease and Department of Pediatrics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 104:10894-9. 2007..Together, these data provide in vivo and in vitro evidence that canonical Wnt signaling promotes the expansion of cardiac progenitors and differentiation of cardiomyocytes... - GenMAPP, a new tool for viewing and analyzing microarray data on biological pathwaysKam D Dahlquist
Nat Genet 31:19-20. 2002 - mGluR2 acts through inhibitory Galpha subunits to regulate transmission and long-term plasticity at hippocampal mossy fiber-CA3 synapsesRussell E Nicholls
Center for Neurobiology and Behavior, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
Proc Natl Acad Sci U S A 103:6380-5. 2006..In addition, the LTP deficit observed in constitutively active Galphai2-expressing mice suggests that mGluR2 activation may serve as a metaplastic switch to permit the induction of LTD by inhibiting LTP... - Development of hydrocephalus in mice expressing the G(i)-coupled GPCR Ro1 RASSL receptor in astrocytesElizabeth J Sweger
Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
J Neurosci 27:2309-17. 2007..This study discovered a new model of hydrocephalus in which the rate of pathogenesis can be controlled enabling the study of the pathogenesis of both juvenile and adult onset hydrocephalus... - Gene expression signatures of cAMP/protein kinase A (PKA)-promoted, mitochondrial-dependent apoptosis. Comparative analysis of wild-type and cAMP-deathless S49 lymphoma cellsLingzhi Zhang
Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA
J Biol Chem 283:4304-13. 2008..The findings indicate that cAMP/PKA-promoted apoptosis of lymphoid cells occurs via mitochondrial-mediated events and imply that such apoptosis involves gene networks in multiple biochemical pathways... - Integration of biological networks and gene expression data using CytoscapeMelissa S Cline
Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
Nat Protoc 2:2366-82. 2007..These steps provide a broad sample of the types of analyses performed by Cytoscape...
Research Grants
- GenMAPP: A tool for pathway analysis of genomic dataBruce Conklin; Fiscal Year: 2006..With the completion these aims, GenMAPP 3.0 will provide a program that is robust, simple to use, and available without charge to the entire biological community. ..
- GenMAPP-CS, a dynamic resource pathway analysisBruce Conklin; Fiscal Year: 2007..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
- Tissue engineering with a complete RASSL toolboxBruce Conklin; Fiscal Year: 2007..A complete set of RASSL targeting vectors will provide biologists with a RASSL toolbox to selectively activate any major GPCR pathway in a wide variety of tissues. ..
- GenMAPP-CS, a dynamic resource pathway analysisBruce Conklin; Fiscal Year: 2009..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
- Tissue Engineering with a Modular RASSL ToolboxBruce Conklin; Fiscal Year: 2009..Finally we are using the cardiac pacemaker as a model system. We hope to gain fundamental insights into cardiac arrhythmias that are a major cause of morbidity and mortality. ..
- Tissue Engineering with a Modular RASSL ToolboxBruce R Conklin; Fiscal Year: 2010..Finally we are using the cardiac pacemaker as a model system. We hope to gain fundamental insights into cardiac arrhythmias that are a major cause of morbidity and mortality. ..
- GenMAPP-CS, a dynamic resource pathway analysisBruce R Conklin; Fiscal Year: 2010..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
- COLLABORATIVE R01--ROLES OF G PROTEINS IN CARDIOMYOPATHYBruce Conklin; Fiscal Year: 2002..3. To selectively activate G protein pathways in the setting of two experimentally induced cardiomyopathy models where G protein signaling has been shown to be altered. (End of Abstract) ..
- GI SIGNALING AND CARDIOMYOPATHYBruce Conklin; Fiscal Year: 2002....
- GenMAPP-CS, a dynamic resource pathway analysisBruce Conklin; Fiscal Year: 2009..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..