AVI MA'AYAN

Summary

Affiliation: Mount Sinai School of Medicine
Country: USA

Publications

  1. ncbi Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
    Edward Y Chen
    Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L, Levy Place, Box 1215, New York, NY, 10029, USA
    BMC Bioinformatics 14:128. 2013
  2. ncbi Neuro2A differentiation by Galphai/o pathway
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 2:cm1. 2009
  3. ncbi SNAVI: Desktop application for analysis and visualization of large-scale signaling networks
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    BMC Syst Biol 3:10. 2009
  4. ncbi Network integration and graph analysis in mammalian molecular systems biology
    A MA'AYAN
    Mount Sinai School of Medicine, Department of Pharmacology and Systems Therapeutics, New York, NY 10029 6574, USA
    IET Syst Biol 2:206-21. 2008
  5. ncbi Insights into the organization of biochemical regulatory networks using graph theory analyses
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 284:5451-5. 2009
  6. ncbi Toward predictive models of mammalian cells
    AVI MA'AYAN
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Annu Rev Biophys Biomol Struct 34:319-49. 2005
  7. ncbi Proximity of intracellular regulatory networks to monotone systems
    A MA'AYAN
    Mount Sinai School of Medicine, Department of Pharmacology and Systems Therapeutics, USA
    IET Syst Biol 2:103-12. 2008
  8. ncbi From components to regulatory motifs in signalling networks
    AVI MA'AYAN
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA
    Brief Funct Genomic Proteomic 5:57-61. 2006
  9. ncbi PubMedAlertMe--standalone Windows-based PubMed SDI software application
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Comput Biol Med 38:620-2. 2008
  10. ncbi Introduction to network analysis in systems biology
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 4:tr5. 2011

Detail Information

Publications103 found, 100 shown here

  1. ncbi Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
    Edward Y Chen
    Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L, Levy Place, Box 1215, New York, NY, 10029, USA
    BMC Bioinformatics 14:128. 2013
    ..While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement...
  2. ncbi Neuro2A differentiation by Galphai/o pathway
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 2:cm1. 2009
    ..Components in the Science Signaling Connections Map are linked to Nature Molecule Pages. This interoperability provides ready access to detail that includes information about specific states for the nodes...
  3. ncbi SNAVI: Desktop application for analysis and visualization of large-scale signaling networks
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    BMC Syst Biol 3:10. 2009
    ..The emergence of large-scale signaling networks provides an opportunity for topological statistical analysis while visualization of such networks represents a challenge...
  4. ncbi Network integration and graph analysis in mammalian molecular systems biology
    A MA'AYAN
    Mount Sinai School of Medicine, Department of Pharmacology and Systems Therapeutics, New York, NY 10029 6574, USA
    IET Syst Biol 2:206-21. 2008
    ..This review highlights the currently available varieties of mammalian biomolecular networks, and surveys methods and tools to construct, compare, integrate, visualise and analyse such networks...
  5. ncbi Insights into the organization of biochemical regulatory networks using graph theory analyses
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 284:5451-5. 2009
    ..These insights show that graph theory is a valuable tool for gaining an understanding of global regulatory features of biochemical networks...
  6. ncbi Toward predictive models of mammalian cells
    AVI MA'AYAN
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Annu Rev Biophys Biomol Struct 34:319-49. 2005
    ..The use of deterministic, stochastic, and hybrid models to represent cellular processes is reviewed, and an initial integrated approach for the development of large-scale predictive models of a mammalian cell is presented...
  7. ncbi Proximity of intracellular regulatory networks to monotone systems
    A MA'AYAN
    Mount Sinai School of Medicine, Department of Pharmacology and Systems Therapeutics, USA
    IET Syst Biol 2:103-12. 2008
    ..These observations suggest that intracellular regulatory networks are 'close-to-monotone', a characteristic that could contribute to the dynamical stability observed in cellular behaviour...
  8. ncbi From components to regulatory motifs in signalling networks
    AVI MA'AYAN
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA
    Brief Funct Genomic Proteomic 5:57-61. 2006
    ..The integration of high-throughput experimental results and information from legacy literature is expected to produce computational models that would rapidly enhance our understanding of the detail workings of mammalian cells...
  9. ncbi PubMedAlertMe--standalone Windows-based PubMed SDI software application
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Comput Biol Med 38:620-2. 2008
    ..The program is standalone. Thus, it does not require a remote mail server or user registration. PubMedAlertMe is free software, and can be downloaded from: http://amp.pharm.mssm.edu/PubMedAlertMe/PubMedAlertMe_setup.zip...
  10. ncbi Introduction to network analysis in systems biology
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 4:tr5. 2011
    ..The third lecture discusses methods for analyzing lists of genes and experimental data in the context of prior knowledge networks to make predictions...
  11. ncbi Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format
    Ryan L Webb
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York SBCNY, Mount Sinai School of Medicine, New York NY 10029, USA
    Source Code Biol Med 6:5. 2011
    ..abstract:..
  12. ncbi Protein kinase target discovery from genome-wide messenger RNA expression profiling
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY, USA
    Mt Sinai J Med 77:345-9. 2010
    ....
  13. ncbi Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
    Seth I Berger
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, 10029, New York, USA
    BMC Bioinformatics 8:372. 2007
    ....
  14. ncbi Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes
    Amin R Mazloom
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York SBCNY, Mount Sinai School of Medicine, New York, New York, United States of America
    PLoS Comput Biol 7:e1002319. 2011
    ..The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/...
  15. ncbi GATE: software for the analysis and visualization of high-dimensional time series expression data
    Ben D MacArthur
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA
    Bioinformatics 26:143-4. 2010
    ..AVAILABILITY: GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm..
  16. ncbi Renoprotective effect of combined inhibition of Angiotensin-converting enzyme and histone deacetylase
    Yifei Zhong
    Department of Medicine, Division of Nephrology, Mount Sinai School of Medicine, One Gustave L Levy Place, Box 1243, New York, NY 10029, or Dr Avi Ma ayan computational part, Department of Pharmacology and Systems Therapeutics, One Gustave L Levy Place, Box 1215, Mount Sinai School of Medicine, New York, NY 10029
    J Am Soc Nephrol 24:801-11. 2013
    ..In addition, this study provides proof-of-concept that drug-induced expression signatures have potential use in predicting the effects of combination drug therapy...
  17. ncbi Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers
    Edward Y Chen
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA
    Bioinformatics 28:105-11. 2012
    ..AVAILABILITY: The software and source code are freely available at: http://www.maayanlab.net/X2K. CONTACT: avi.maayan@mssm.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  18. ncbi ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
    Alexander Lachmann
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York SBCNY, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
    Bioinformatics 26:2438-44. 2010
    ..Such experiments provide hundreds to thousands of potential binding sites for a given transcription factor in proximity to gene coding regions...
  19. ncbi Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth
    Kenneth D Bromberg
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Science 320:903-9. 2008
    ....
  20. ncbi AVIS: AJAX viewer of interactive signaling networks
    Seth I Berger
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York 10029, USA
    Bioinformatics 23:2803-5. 2007
    ..Simple web-based visualization tools can allow for improved data presentation and collaboration. Researchers studying cell signaling would benefit from having the ability to embed dynamic cell signaling maps in web pages...
  21. ncbi A systems approach identifies HIPK2 as a key regulator of kidney fibrosis
    Yuanmeng Jin
    Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
    Nat Med 18:580-8. 2012
    ..We therefore conclude that HIPK2 is a potential target for anti-fibrosis therapy...
  22. ncbi Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons
    Raphael Rozenfeld
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, United States of America
    PLoS ONE 7:e29239. 2012
    ....
  23. ncbi Systems biology of kidney diseases
    John Cijiang He
    Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA
    Kidney Int 81:22-39. 2012
    ..This integration of experimental approaches and computational modeling is expected to generate new knowledge that can help to identify marker sets to guide the diagnosis, monitor disease progression, and identify new therapeutic targets...
  24. ncbi Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis
    Noura S Abul-Husn
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, United States of America
    PLoS ONE 6:e25535. 2011
    ....
  25. ncbi Lists2Networks: integrated analysis of gene/protein lists
    Alexander Lachmann
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
    BMC Bioinformatics 11:87. 2010
    ..In addition, linking high-content multilayered experimental results with prior biological knowledge can be useful for identifying functional themes and form novel hypotheses...
  26. ncbi Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 105:19235-40. 2008
    ..This topology provides more dynamic stability in large networks...
  27. ncbi Retinoic acid utilizes CREB and USF1 in a transcriptional feed-forward loop in order to stimulate MKP1 expression in human immunodeficiency virus-infected podocytes
    Ting Chi Lu
    Department of Medicine, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY 10029, USA
    Mol Cell Biol 28:5785-94. 2008
    ..The mechanism involves a feed-forward loop where activation of one transcription factor (TF) (CREB) leads to induction of a second TF (USF1)...
  28. ncbi Expression of HIV transgene aggravates kidney injury in diabetic mice
    Sandeep K Mallipattu
    Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
    Kidney Int 83:626-34. 2013
    ..Thus, our study found that expression of HIV-1 genes aggravates diabetic kidney disease...
  29. ncbi Functions of bifans in context of multiple regulatory motifs in signaling networks
    Azi Lipshtat
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York 10029, USA
    Biophys J 94:2566-79. 2008
    ..These results indicate that bifan motifs in cell signaling networks can contribute to signal processing capability both intrinsically and by enabling the functions of other regulatory motifs...
  30. ncbi Systems approach to explore components and interactions in the presynapse
    Noura S Abul-Husn
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proteomics 9:3303-15. 2009
    ....
  31. ncbi Sets2Networks: network inference from repeated observations of sets
    Neil R Clark
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center of New York SBCNY, Mount Sinai School of Medicine, One Gustave L, Levy Place, Box 1215, New York, NY 10029, USA
    BMC Syst Biol 6:89. 2012
    ..This type of data is ubiquitous in the field of systems biology and in other areas of complex systems research. Hence, such methods would be of great utility and value...
  32. ncbi Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
    Emmanuel L Gautier
    Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
    Nat Immunol 13:1118-28. 2012
    ..We further identified how these transcripts and the proteins they encode facilitated distinguishing macrophages from dendritic cells...
  33. ncbi Kruppel-like factor 15 (KLF15) is a key regulator of podocyte differentiation
    Sandeep K Mallipattu
    Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029 6574, USA
    J Biol Chem 287:19122-35. 2012
    ..These results indicate a critical role of KLF15 in mediating podocyte differentiation and in protecting podocytes against injury...
  34. ncbi KEA: kinase enrichment analysis
    Alexander Lachmann
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center in New York, Icahn Medical Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
    Bioinformatics 25:684-6. 2009
    ..Such analysis can assist in producing hypotheses that can explain how the kinome is involved in the maintenance of different cellular states and can be manipulated to modulate cells towards a desired phenotype...
  35. ncbi Toward a complete in silico, multi-layered embryonic stem cell regulatory network
    Huilei Xu
    Department of Gene and Cell Medicine and The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Wiley Interdiscip Rev Syst Biol Med 2:708-33. 2010
    ..This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature...
  36. ncbi Systems biology of stem cell fate and cellular reprogramming
    Ben D MacArthur
    Department of Gene and Cell Medicine and Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    Nat Rev Mol Cell Biol 10:672-81. 2009
    ....
  37. ncbi Formation of regulatory patterns during signal propagation in a Mammalian cellular network
    Sherry L Jenkins
    Department of Pharmacology and Biological Chemistry Mount Sinai School of Medicine, New York, NY 10029, USA
    Science 309:1078-83. 2005
    ..Key regulators of plasticity were highly connected nodes required for the formation of regulatory motifs, indicating the potential importance of such motifs in determining cellular choices between homeostasis and plasticity...
  38. ncbi Modeling cell signaling networks
    Narat J Eungdamrong
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Biol Cell 96:355-62. 2004
    ..Different mathematical approaches that are currently used to model signaling networks are described, and future challenges including the need for databases as well as enhanced computing environments are discussed...
  39. ncbi Activation of alternate prosurvival pathways accounts for acquired sunitinib resistance in U87MG glioma xenografts
    Qingyu Zhou
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY, USA
    J Pharmacol Exp Ther 343:509-19. 2012
    ....
  40. ncbi FNV: light-weight flash-based network and pathway viewer
    Ruth Dannenfelser
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York SBCNY, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
    Bioinformatics 27:1181-2. 2011
    ..To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways...
  41. ncbi Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis
    Neil R Clark
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 4:tr4. 2011
    ..GSEA is a statistical functional enrichment analysis commonly applied to identify enrichment of biological functional categories in sets of ranked differentially expressed genes from genome-wide mRNA expression data sets...
  42. ncbi Network analysis of FDA approved drugs and their targets
    AVI MA'AYAN
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York 10029, USA
    Mt Sinai J Med 74:27-32. 2007
    ..These initial observations allow for development of an integrated research methodology to identify general principles of the drug discovery process...
  43. ncbi Systems pharmacology of arrhythmias
    Seth I Berger
    Department of Pharmacology and Systems Therapeutics and Systems Biology Center New York, Mount Sinai School of Medicine, One Gustave L Levy Place, Box 1215, New York, NY 10029, USA
    Sci Signal 3:ra30. 2010
    ....
  44. ncbi Mesenchymal and haematopoietic stem cells form a unique bone marrow niche
    Simon Mendez-Ferrer
    Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA
    Nature 466:829-34. 2010
    ..These results uncover an unprecedented partnership between two distinct somatic stem-cell types and are indicative of a unique niche in the bone marrow made of heterotypic stem-cell pairs...
  45. ncbi Flotillin-mediated endocytic events dictate cell type-specific responses to semaphorin 3A
    Ioana Carcea
    Fishberg Department of Neuroscience and Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Neurosci 30:15317-29. 2010
    ....
  46. ncbi Signaling in regulation of podocyte phenotypes
    Peter Y Chuang
    Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
    Nephron Physiol 111:p9-15. 2009
    ..At the level of intracellular signaling, it appears that different extracellular signals can converge onto a few pathways to induce changes in the phenotype of podocytes...
  47. ncbi Up-regulation of the homophilic adhesion molecule sidekick-1 in podocytes contributes to glomerulosclerosis
    Lewis Kaufman
    Division of Nephrology, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 285:25677-85. 2010
    ..We conclude that the up-regulation of sdk-1 in podocytes is an important pathogenic factor in FSGS and that the mechanism involves disruption of the actin cytoskeleton possibly via alterations in MAGI-1 function...
  48. ncbi Teaching resources. Introduction: Overview of pathways and networks and GPCR signaling
    Ravi Iyengar
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci STKE 2005:tr4. 2005
    ..A description of the lecture, along with a set of slides (http://stke.sciencemag.org/cgi/content/full/sigtrans;2005/270/tr4/DC1) used to present this information, is provided...
  49. ncbi Teaching resources. Cell signaling systems: a course for graduate students
    Ravi Iyengar
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci STKE 2005:tr3. 2005
    ..Each lecture is 2 hours. After each set of lectures, there is a 2-hour discussion period during which students present an in-depth analysis of a primary literature article, selected in consultation with the lecturer...
  50. ncbi Teaching resources. Structure of G-protein-coupled receptors and G proteins
    Ravi Iyengar
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci STKE 2005:tr10. 2005
    ..quot; The lecture begins with a discussion of the crystal structure of rhodopsin and G protein subunits and then proceeds to describe the molecular mechanisms of receptor activation and the subsequent release of G proteins...
  51. ncbi Nef stimulates proliferation of glomerular podocytes through activation of Src-dependent Stat3 and MAPK1,2 pathways
    John Cijiang He
    Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
    J Clin Invest 114:643-51. 2004
    ..These data suggest that Nef-induced activation of Stat3 and Ras-MAPK1,2 via Src-dependent pathways is responsible for podocyte proliferation and dedifferentiation, a characteristic finding in collapsing FSGS of HIVAN...
  52. ncbi Cannabinoid 1 receptor and interleukin-6 receptor together induce integration of protein kinase and transcription factor signaling to trigger neurite outgrowth
    Yana Zorina
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 285:1358-70. 2010
    ..These results provide a mechanism where multiple protein kinases and transcription factors interact to integrate signals from G protein-coupled and cytokine receptor to evoke neurite outgrowth in Neuro2A cells...
  53. ncbi Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues
    Azi Lipshtat
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 107:1247-52. 2010
    ..We conclude that the emergence of ultrasensitivity from coupled first-order reactions provides a versatile mechanism for the design of biochemical switches...
  54. ncbi Modelling cellular signalling systems
    Padmini Rangamani
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, U S A
    Essays Biochem 45:83-94. 2008
    ..This is followed by a brief summary of some recent modelling successes and the state of future models...
  55. ncbi Inquiry learning. Integrating content detail and critical reasoning by peer review
    Ravi Iyengar
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Science 319:1189-90. 2008
  56. ncbi Regulation of neurite outgrowth by G(i/o) signaling pathways
    Kenneth D Bromberg
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Front Biosci 13:4544-57. 2008
    ....
  57. ncbi HIV-1 Nef disrupts the podocyte actin cytoskeleton by interacting with diaphanous interacting protein
    Ting Chi Lu
    Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
    J Biol Chem 283:8173-82. 2008
    ..We conclude that in HIV-infected podocytes, Nef, through the recruitment of DIP and p190RhoAGAP to Nef-Src complex, activates p190RhoAGAP and down-regulates RhoA activity...
  58. ncbi Role of the Go/i signaling network in the regulation of neurite outgrowth
    John Cijiang He
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY 10029, USA
    Can J Physiol Pharmacol 84:687-94. 2006
    ..We also analyze the role neurotransmitters, which stimulate Go/i to activate a complex signaling network controlling neurite outgrowth, play in regeneration after neuronal injury...
  59. ncbi Retinoic acid inhibits HIV-1-induced podocyte proliferation through the cAMP pathway
    John Cijiang He
    Department of Medicine, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY 10029, USA
    J Am Soc Nephrol 18:93-102. 2007
    ..These results demonstrate the mechanism by which atRA reverses the proliferation of podocytes that is induced by HIV-1...
  60. ncbi Teaching resources. Using web-based discussion forums as a model of the peer-review process and a tool for assessment
    Sherry L Jenkins
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 1:tr2. 2008
    ....
  61. ncbi Modelling spatio-temporal interactions within the cell
    Padmini Rangamani
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY 10029, USA
    J Biosci 32:157-67. 2007
    ..This review describes the capability and limitations of the approaches used to study spatio-temporal dynamics of cell signalling components...
  62. ncbi Teaching resource. Quantitative models of mammalian cell signaling pathways
    Ravi Iyengar
    Department of Pharmacology and SystemsTherapeutics, Mount Sinai School ofMedicine, New York, NY 10029, USA
    Sci Signal 1:tr1. 2008
    ..The lecture concludes with a description of how models can be tested experimentally and modified when the details of the models and the resultant predictive behavior are not confirmed by experimentation...
  63. ncbi Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling
    Dung Fang Lee
    Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Cell Stem Cell 11:179-94. 2012
    ..Our studies demonstrate an essential role for Aurka-p53 signaling in the regulation of self-renewal, differentiation, and somatic cell reprogramming...
  64. ncbi Oct4 links multiple epigenetic pathways to the pluripotency network
    Junjun Ding
    Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Cell Res 22:155-67. 2012
    ..Our study establishes a solid biochemical basis for genetic and epigenetic regulation of stem cell pluripotency and provides a framework for exploring alternative factor-based reprogramming strategies...
  65. ncbi SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells
    Huilei Xu
    Department of Pharmacology and System Therapeutics, Mount Sinai School of Medicine, 1 Gustave L, Levy Place, New York, New York 10029, USA
    BMC Syst Biol 4:173. 2010
    ....
  66. ncbi Adenovirus-directed expression of Q227L-G alpha(s) inhibits growth of established tumors of later-stage human breast cancer cells in athymic mice
    Tara Ann Santore
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029
    Proc Natl Acad Sci U S A 99:1671-6. 2002
    ..These results raise the possibility that sustained elevation of cAMP may have therapeutic value in the treatment of estrogen-resistant later stage breast cancers...
  67. ncbi Computational approaches for modeling regulatory cellular networks
    Narat J Eungdamrong
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Trends Cell Biol 14:661-9. 2004
    ..Finally, the modeling approach is expanded to describe how signaling networks might regulate cellular machines and evoke phenotypic behaviors...
  68. ncbi The G alpha(o/i)-coupled cannabinoid receptor-mediated neurite outgrowth involves Rap regulation of Src and Stat3
    John Cijiang He
    Department of Pharmacology, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 280:33426-34. 2005
    ..Overall, this study demonstrated that G alpha(o/i)-coupled CB1R triggers neurite outgrowth in Neuro-2A through the activation of a signaling network containing two pathways that bifurcate at Src and converge at Stat3...
  69. ncbi Transforming growth factor β signaling controls activities of human intestinal CD8(+)T suppressor cells
    Keren M Rabinowitz
    Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Gastroenterology 144:601-612.e1. 2013
    ..Disruption of Ts cell activities can lead to mucosal inflammation. We investigated what factors were required for expansion of the Ts cell population or loss of their activity in patients with Crohn's disease (CD)...
  70. ncbi Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability
    Yan Kou
    Department of Psychiatry, Mount Sinai School of Medicine, One Gustave L Levy Place, Box 1668, New York, NY 10029, USA
    Am J Med Genet C Semin Med Genet 160:130-42. 2012
    ..Our methods can be applied broadly to other diseases helping in prioritizing newly identified genetic variation that emerge from disease gene discovery based on WES and WGS...
  71. ncbi Introduction to statistical methods to analyze large data sets: principal components analysis
    Neil R Clark
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Sci Signal 4:tr3. 2011
    ..The lecture describes how to handle large data sets with correlation methods and unsupervised clustering with this popular method of analysis, PCA...
  72. ncbi Genes2FANs: connecting genes through functional association networks
    Ruth Dannenfelser
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center of New York, Mount Sinai School of Medicine, New York, NY 10029, USA
    BMC Bioinformatics 13:156. 2012
    ....
  73. ncbi Compartment-specific feedback loop and regulated trafficking can result in sustained activation of Ras at the Golgi
    Narat J Eungdamrong
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    Biophys J 92:808-15. 2007
    ....
  74. ncbi Calpain as an effector of the Gq signaling pathway for inhibition of Wnt/beta -catenin-regulated cell proliferation
    Guangnan Li
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 99:13254-9. 2002
    ..We conclude that Gq signaling promotes nuclear export and calpain-mediated degradation of beta-catenin, which therefore contributes to the inhibition of Wnt/beta-catenin pathway...
  75. ncbi Role of dynamic interactions in effective signal transfer for Gbeta stimulation of phospholipase C-beta 2
    Elizabeth Buck
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
    J Biol Chem 277:49707-15. 2002
    ....
  76. ncbi HIV-1 upregulates VEGF in podocytes
    Sonal Navin Korgaonkar
    Department of, New York, Mount Sinai School of Medicine, New York, USA
    J Am Soc Nephrol 19:877-83. 2008
    ..In conclusion, HIV-1 induces VEGF and VEGFR2 expression in podocytes, and this may be a critical step in the pathogenesis of HIVAN...
  77. ncbi Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks
    Susana R Neves
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, One Gustave L Levy Place, Box 1215, New York, NY 10029, USA
    Cell 133:666-80. 2008
    ....
  78. ncbi Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors
    Carlos Clavel
    Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Dev Cell 23:981-94. 2012
    ..Collectively, our data identify Sox2 as a key regulator of hair growth that controls progenitor migration by fine-tuning BMP-mediated mesenchymal-epithelial crosstalk...
  79. ncbi Microdynamics and criticality of adaptive regulatory networks
    Ben D MacArthur
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, New York 10029, USA
    Phys Rev Lett 104:168701. 2010
    ..We show analytically that the observed criticality results from the formation and breaking of transient feedback loops during the adaptive process...
  80. ncbi Local protein synthesis mediates a rapid increase in dendritic elongation factor 1A after induction of late long-term potentiation
    Panayiotis Tsokas
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Neurosci 25:5833-43. 2005
    ..These results suggest a mechanism whereby synaptic stimulation, by signaling through the mTOR pathway, produces an increase in dendritic translational capacity that contributes to LTP maintenance...
  81. ncbi Quantitative information management for the biochemical computation of cellular networks
    Fabien Campagne
    Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
    Sci STKE 2004:pl11. 2004
    ..We anticipate that, when appropriately populated, such a system will be useful for large-scale quantitative studies of cell-signaling networks and other cellular networks. SigPath is distributed under the GNU General Public License...
  82. ncbi Topology of resultant networks shaped by evolutionary pressure
    Azi Lipshtat
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 73:061912. 2006
    ..This analysis provides initial insights into distribution of pathways in naturally evolving complex systems that have defined input-output relationships...
  83. ncbi Cannabinoid receptor-induced neurite outgrowth is mediated by Rap1 activation through G(alpha)o/i-triggered proteasomal degradation of Rap1GAPII
    J Dedrick Jordan
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 280:11413-21. 2005
    ..Thus, the G(alpha)o/i-coupled cannabinoid receptor, by regulating the proteasomal degradation of Rap1GAPII, activates Rap1 to induce neurite outgrowth...
  84. ncbi G protein pathways
    Susana R Neves
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Science 296:1636-9. 2002
    ..These cellular processes in turn regulate systemic functions such as embryonic development, gonadal development, learning and memory, and organismal homeostasis...
  85. ncbi Mitogen-activated protein kinase upregulates the dendritic translation machinery in long-term potentiation by controlling the mammalian target of rapamycin pathway
    Panayiotis Tsokas
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Neurosci 27:5885-94. 2007
    ..The role of ERK in regulating PDK1 and Akt, with their extensive effects on cellular function, has important implications for the coordinated response of the neuron to LTP-inducing stimulation...
  86. ncbi Use of peptide probes to determine function of interaction sites in G protein interactions with effectors
    Elizabeth Buck
    Department of Pharmacology, Mount Sinai School of Medicine, New York, New York 10029, USA
    Methods Enzymol 344:513-21. 2002
  87. ncbi Network analyses in systems pharmacology
    Seth I Berger
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
    Bioinformatics 25:2466-72. 2009
    ..Taken together, these types of analyses can lead to new therapeutic options while improving the safety and efficacy of existing medications...
  88. ncbi Oral glycotoxins determine the effects of calorie restriction on oxidant stress, age-related diseases, and lifespan
    Weijing Cai
    Department of Geriatrics, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
    Am J Pathol 173:327-36. 2008
    ..Therefore, the beneficial effects of a CR diet may be partly related to reduced oxidant intake, a principal determinant of oxidant status in aging mice, rather than decreased energy intake...
  89. ncbi Advanced glycation end product (AGE) receptor 1 suppresses cell oxidant stress and activation signaling via EGF receptor
    Weijing Cai
    Division of Experimental Diabetes and Aging, Brookdale Department of Geriatrics, and Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 103:13801-6. 2006
    ..AGER1 could serve as a model for developing therapeutic targets against vascular and kidney disorders related to diabetes and aging...
  90. ncbi Expression of adenovirus-directed expression of activated G alpha s in rat hippocampal slices
    George P Brown
    Department of Pharmacology, Mount Sinai School of Medicine, New York, New York 10029, USA
    Methods Enzymol 344:343-9. 2002
  91. ncbi Modeling of signaling networks
    Susana R Neves
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
    Bioessays 24:1110-7. 2002
    ..These types of complex behavior from relatively simple networks highlight the necessity of using theoretical approaches in understanding higher order biological functions...
  92. ncbi Organization and functions of interacting domains for signaling by protein-protein interactions
    Elizabeth Buck
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA
    Sci STKE 2003:re14. 2003
    ..Other binding regions may be arranged within the protein to impart specificity of recognition and thereby maintain overall contact between the partners during the conformational dynamics that occur in the signal-transfer process...
  93. ncbi Postsynaptic signaling networks: cellular cogwheels underlying long-term plasticity
    Robert D Blitzer
    Department of Psychiatry, Mount Sinai School of Medicine, New York, New York 10029, USA
    Biol Psychiatry 57:113-9. 2005
    ..It is posited that local translation at the synapse, in a self-sustaining manner, mediates the persistence of long-term changes despite constant turnover of the synaptic components...
  94. ncbi Systems approaches to polypharmacology and drug discovery
    Aislyn D W Boran
    Mount Sinai School of Medicine, Department of Pharmacology and Systems Therapeutics, One Gustave L Levy Place, New York, NY 10029, USA
    Curr Opin Drug Discov Devel 13:297-309. 2010
    ..Drug-target networks can be used to identify multiple targets and to determine suitable combinations of drug targets or drugs. Thus, the discovery of new drug therapies for complex diseases may be greatly aided by systems biology...
  95. ncbi Functional analysis of the interface regions involved in interactions between the central cytoplasmic loop and the C-terminal tail of adenylyl cyclase
    Barney Yoo
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 279:13925-33. 2004
    ....
  96. ncbi Specification of spatial relationships in directed graphs of cell signaling networks
    Azi Lipshtat
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, USA
    Ann N Y Acad Sci 1158:44-56. 2009
    ..We suggest that such mixed graphs will provide more accurate descriptions of functional cellular networks and their regulatory capabilities and aid in the development of large-scale predictive models of cellular behavior...
  97. ncbi The cognitive phenotype of Down syndrome: insights from intracellular network analysis
    Katheleen Gardiner
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
    NeuroRx 3:396-406. 2006
    ..We propose how these methods could be integrated with creation and manipulation of mouse models of DS to advance our understanding of the perturbed cell signaling pathways in DS. This understanding could lead to potential therapeutics...
  98. ncbi Galphao/i-stimulated proteosomal degradation of RGS20: a mechanism for temporal integration of Gs and Gi pathways
    Mario Pagano
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, United States
    Cell Signal 20:1190-7. 2008
    ..These observations suggest that G(o/i)-coupled receptors, by stimulating the degradation of RGS20, can regulate how subsequent activation of the G(s) and G(i) pathways controls cellular cAMP levels, thus allowing for signal integration...
  99. ncbi An androgen-IL-6-Stat3 autocrine loop re-routes EGF signal in prostate cancer cells
    David S Aaronson
    Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY, USA
    Mol Cell Endocrinol 270:50-6. 2007
    ..Understanding interactions and changes in signal flow within the cell is important to our understanding of signaling networks as well as our ability to identify cellular targets for novel therapies to inhibit cancer progression...
  100. ncbi MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
    Upinder S Bhalla
    National Center for Biological Sciences, Bangalore 560065 India
    Science 297:1018-23. 2002
    ..Thus, the MAPK 1, 2/PKC controller network is flexibly designed, and MAPK phosphatase may be critical for this flexible response...
  101. ncbi Computational analysis of isoform-specific signal regulation by CEACAM1-A cell adhesion molecule expressed in PC12 cells
    Björn Obrink
    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
    Ann N Y Acad Sci 971:597-607. 2002
    ....