Bruce Conklin

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptor
    Wei 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
  2. pmc Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000553. 2009
  3. pmc Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and mice
    Edward C Hsiao
    Gladstone Institute of Cardiovascular Disease, 1650 Owens St, San Francisco, CA 94158, USA
    Stem Cell Res Ther 2:11. 2011
  4. pmc Time- and exercise-dependent gene regulation in human skeletal muscle
    Alexander C Zambon
    Gladstone Institute of Cardiovascular Disease, Department of Medicine, University of California, San Francisco, CA 94141, USA
    Genome Biol 4:R61. 2003
  5. pmc MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
    Scott W Doniger
    Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141 9100, USA
    Genome Biol 4:R7. 2003
  6. pmc Identifying genetic networks underlying myometrial transition to labor
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Genome Biol 6:R12. 2005
  7. pmc Engineered G protein coupled receptors reveal independent regulation of internalization, desensitization and acute signaling
    Kimberly 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
  8. pmc The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
    Martijn P van Iersel
    Department of Bioinformatics BiGCaT, Maastricht University, Maastricht, The Netherlands
    BMC Bioinformatics 11:5. 2010
  9. pmc GenMAPP 2: new features and resources for pathway analysis
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
    BMC Bioinformatics 8:217. 2007
  10. pmc Presenting and exploring biological pathways with PathVisio
    Martijn P van Iersel
    Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
    BMC Bioinformatics 9:399. 2008

Research Grants

  1. GenMAPP: A tool for pathway analysis of genomic data
    Bruce Conklin; Fiscal Year: 2006
  2. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2007
  3. Tissue engineering with a complete RASSL toolbox
    Bruce Conklin; Fiscal Year: 2007
  4. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2009
  5. Tissue Engineering with a Modular RASSL Toolbox
    Bruce Conklin; Fiscal Year: 2009
  6. Tissue Engineering with a Modular RASSL Toolbox
    Bruce R Conklin; Fiscal Year: 2010
  7. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce R Conklin; Fiscal Year: 2010
  8. COLLABORATIVE R01--ROLES OF G PROTEINS IN CARDIOMYOPATHY
    Bruce Conklin; Fiscal Year: 2002
  9. GI SIGNALING AND CARDIOMYOPATHY
    Bruce Conklin; Fiscal Year: 2002
  10. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2009

Collaborators

Detail Information

Publications38

  1. pmc Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptor
    Wei 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...
  2. pmc Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000553. 2009
    ....
  3. pmc Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and mice
    Edward C Hsiao
    Gladstone Institute of Cardiovascular Disease, 1650 Owens St, San Francisco, CA 94158, USA
    Stem Cell Res Ther 2:11. 2011
    ....
  4. pmc Time- and exercise-dependent gene regulation in human skeletal muscle
    Alexander C Zambon
    Gladstone Institute of Cardiovascular Disease, Department of Medicine, University of California, San Francisco, CA 94141, USA
    Genome Biol 4:R61. 2003
    ..Both exercise-induced remodeling and circadian rhythms rely on the transcriptional regulation of key genes...
  5. pmc MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
    Scott 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...
  6. pmc Identifying genetic networks underlying myometrial transition to labor
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Genome Biol 6:R12. 2005
    ..Although several marker genes have been identified, little is known about the underlying global gene expression patterns and pathways that orchestrate these striking changes...
  7. pmc Engineered G protein coupled receptors reveal independent regulation of internalization, desensitization and acute signaling
    Kimberly 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...
  8. pmc The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
    Martijn 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...
  9. pmc GenMAPP 2: new features and resources for pathway analysis
    Nathan 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...
  10. pmc Presenting and exploring biological pathways with PathVisio
    Martijn 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...
  11. pmc Engineering GPCR signaling pathways with RASSLs
    Bruce 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...
  12. pmc New tools to build synthetic hormonal pathways
    Bruce 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
  13. pmc Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humans
    Supriya 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...
  14. pmc Reporter-based isolation of induced pluripotent stem cell- and embryonic stem cell-derived cardiac progenitors reveals limited gene expression variance
    Linda W Van Laake
    Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 94158, USA
    Circ Res 107:340-7. 2010
    ....
  15. doi request reprint Cloning mice and men: prohibiting the use of iPS cells for human reproductive cloning
    Bernard 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...
  16. pmc SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
    Alexander 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...
  17. pmc Gs G protein-coupled receptor signaling in osteoblasts elicits age-dependent effects on bone formation
    Edward 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...
  18. pmc G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies
    Kenta 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...
  19. pmc Ligand-mediated activation of an engineered gs g protein-coupled receptor in osteoblasts increases trabecular bone formation
    Edward 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...
  20. pmc Marking embryonic stem cells with a 2A self-cleaving peptide: a NKX2-5 emerald GFP BAC reporter
    Edward 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...
  21. pmc Osteoblast expression of an engineered Gs-coupled receptor dramatically increases bone mass
    Edward 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...
  22. pmc Engineering the melanocortin-4 receptor to control constitutive and ligand-mediated G(S) signaling in vivo
    Supriya 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...
  23. ncbi request reprint Engineering the melanocortin-4 receptor to control G(s) signaling in vivo
    Supriya 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...
  24. ncbi request reprint Regression approaches for microarray data analysis
    Mark 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...
  25. ncbi request reprint Cardiac transgenesis with the tetracycline transactivator changes myocardial function and gene expression
    Diana 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...
  26. pmc The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse
    Alex S Nord
    University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 34:D642-8. 2006
    ....
  27. pmc Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation
    Nathan 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...
  28. pmc MicroRNA regulation of cell lineages in mouse and human embryonic stem cells
    Kathryn 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...
  29. pmc Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulation
    Whittemore 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...
  30. pmc Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A
    Alexander 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...
  31. ncbi request reprint Sustained preconditioning induced by cardiac transgenesis with the tetracycline transactivator
    Lynne 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...
  32. ncbi request reprint Tools for dissecting signaling pathways in vivo: receptors activated solely by synthetic ligands
    Kimberly 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
  33. pmc Canonical Wnt signaling is a positive regulator of mammalian cardiac progenitors
    Chulan 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...
  34. ncbi request reprint GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    Kam D Dahlquist
    Nat Genet 31:19-20. 2002
  35. pmc mGluR2 acts through inhibitory Galpha subunits to regulate transmission and long-term plasticity at hippocampal mossy fiber-CA3 synapses
    Russell 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...
  36. ncbi request reprint Development of hydrocephalus in mice expressing the G(i)-coupled GPCR Ro1 RASSL receptor in astrocytes
    Elizabeth 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...
  37. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa 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...
  38. pmc Gene expression signatures of cAMP/protein kinase A (PKA)-promoted, mitochondrial-dependent apoptosis. Comparative analysis of wild-type and cAMP-deathless S49 lymphoma cells
    Lingzhi 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...

Research Grants27

  1. GenMAPP: A tool for pathway analysis of genomic data
    Bruce 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. ..
  2. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2007
    ..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
  3. Tissue engineering with a complete RASSL toolbox
    Bruce 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. ..
  4. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2009
    ..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
  5. Tissue Engineering with a Modular RASSL Toolbox
    Bruce 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. ..
  6. Tissue Engineering with a Modular RASSL Toolbox
    Bruce 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. ..
  7. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce R Conklin; Fiscal Year: 2010
    ..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..
  8. COLLABORATIVE R01--ROLES OF G PROTEINS IN CARDIOMYOPATHY
    Bruce 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) ..
  9. GI SIGNALING AND CARDIOMYOPATHY
    Bruce Conklin; Fiscal Year: 2002
    ....
  10. GenMAPP-CS, a dynamic resource pathway analysis
    Bruce Conklin; Fiscal Year: 2009
    ..The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS. ..