Stephen R Lasky

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. pmc Transcriptional responses to fatty acid are coordinated by combinatorial control
    Jennifer J Smith
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 3:115. 2007
  2. pmc The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control
    David J Dilworth
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 171:955-65. 2005
  3. pmc Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 181:281-92. 2008
  4. pmc Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane
    Marcello Marelli
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 167:1099-112. 2004
  5. pmc Systems cell biology of the mitotic spindle
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 188:7-9. 2010
  6. pmc Transcriptome profiling to identify genes involved in peroxisome assembly and function
    Jennifer J Smith
    The Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103 8904, USA
    J Cell Biol 158:259-71. 2002
  7. pmc Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing
    Jennifer J Smith
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 7:455. 2011
  8. pmc Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues
    Alexander V Ratushny
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS Comput Biol 7:e1002091. 2011
  9. pmc A regression model approach to enable cell morphology correction in high-throughput flow cytometry
    Theo A Knijnenburg
    Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109 5234, USA
    Mol Syst Biol 7:531. 2011
  10. pmc Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing
    Yakun Wan
    Institute for Systems Biology, Seattle, WA 98103, USA
    Nucleic Acids Res 38:1431-40. 2010

Collaborators

Detail Information

Publications36

  1. pmc Transcriptional responses to fatty acid are coordinated by combinatorial control
    Jennifer J Smith
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 3:115. 2007
    ..Together, these data suggest a network mechanism involving dynamic combinatorial control for coordinating transcriptional responses...
  2. pmc The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control
    David J Dilworth
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 171:955-65. 2005
    ....
  3. pmc Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 181:281-92. 2008
    ..Our study represents the first global study of signaling networks regulating the biogenesis of an organelle...
  4. pmc Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane
    Marcello Marelli
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 167:1099-112. 2004
    ..Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis...
  5. pmc Systems cell biology of the mitotic spindle
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 188:7-9. 2010
    ..doi:10.1083/jcb.200909013), have combined systems genetics with high-throughput and high-content imaging to comprehensively identify and classify novel components that contribute to the morphology and function of the mitotic spindle...
  6. pmc Transcriptome profiling to identify genes involved in peroxisome assembly and function
    Jennifer J Smith
    The Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103 8904, USA
    J Cell Biol 158:259-71. 2002
    ..These studies demonstrate the utility of comparative gene profiling as an alternative to functional assays to identify genes with roles in peroxisome biogenesis...
  7. pmc Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing
    Jennifer J Smith
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 7:455. 2011
    ..This study reveals a path for the coordination of subtelomeric silencing with cellular environment, and with activities of other cellular processes...
  8. pmc Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues
    Alexander V Ratushny
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS Comput Biol 7:e1002091. 2011
    ....
  9. pmc A regression model approach to enable cell morphology correction in high-throughput flow cytometry
    Theo A Knijnenburg
    Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109 5234, USA
    Mol Syst Biol 7:531. 2011
    ..We identify a group of epigenetic regulators and nucleoporins that, by maintaining an 'unresponsive population,' may provide the population with the advantage of diversified bet hedging...
  10. pmc Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing
    Yakun Wan
    Institute for Systems Biology, Seattle, WA 98103, USA
    Nucleic Acids Res 38:1431-40. 2010
    ..Taken together, the results demonstrate a novel role for Chz1p in epigenetic regulation, through H2B de-ubiquitination by Ubp10p...
  11. pmc Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism
    Jennifer J Smith
    Institute for Systems Biology, Yeast Group, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:2006.0009. 2006
    ..Statistical analyses of these and other global data sets suggest that the utilization of distinct control mechanisms for the execution of morphological versus metabolic responses is widespread...
  12. pmc Asymmetric positive feedback loops reliably control biological responses
    Alexander V Ratushny
    Institute for Systems Biology, Seattle, WA, USA
    Mol Syst Biol 8:577. 2012
    ..This study reveals evolutionary advantages for the ASSURE motif, and mechanisms for control, that are relevant to pharmacologic intervention and synthetic biology applications...
  13. pmc The yeast nuclear pore complex and transport through it
    John D Aitchison
    Institute for Systems Biology and Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Genetics 190:855-83. 2012
    ....
  14. pmc Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex
    D J Dilworth
    Institute for Systems Biology, Seattle, Washington, 98105, USA
    J Cell Biol 153:1465-78. 2001
    ..Together, our data support a model in which Nup2p movement facilitates the transition between the import and export phases of nucleocytoplasmic transport...
  15. pmc Inventories to insights
    John D Aitchison
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    J Cell Biol 161:465-9. 2003
    ..We have entered the cell, the Mansion of our birth and started the inventory of our acquired wealth." (Albert Claude, Nobel lecture, 1974)...
  16. pmc Regulation of peroxisome dynamics
    Jennifer J Smith
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Curr Opin Cell Biol 21:119-26. 2009
    ..This review focuses on the biogenesis of peroxisomes with an emphasis on the regulation of peroxisome formation and the import of peroxisomal matrix proteins in the model organism Saccharomyces cerevisiae...
  17. pmc POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer
    Christopher Lausted
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Genome Biol 5:R58. 2004
    ..We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays...
  18. pmc Genome-wide analysis of effectors of peroxisome biogenesis
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, Washington, USA
    PLoS ONE 5:e11953. 2010
    ..By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function...
  19. ncbi request reprint Printing your own inkjet microarrays
    Christopher G Lausted
    Institute for Systems Biology, Seattle, Washington, USA
    Methods Enzymol 410:168-89. 2006
    ..A benchtop inkjet arrayer-nicknamed POSAM-can be built by most skilled molecular biology laboratories. Inkjet arrays can fulfill the changing needs of those studying the complex network of relationships in systems biology...
  20. doi request reprint Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes
    Marcello Marelli
    Homestead Clinical Corporation, Seattle, WA, USA
    Methods Mol Biol 432:357-71. 2008
    ..The methods for the analyses of the yeast peroxisome are described in detail; however, these concepts are generally applicable to the study of other organelles...
  21. doi request reprint Systems biology at the Institute for Systems Biology
    Leroy Hood
    Institute for Systems Biology, Seattle, WA 98103, USA
    Brief Funct Genomic Proteomic 7:239-48. 2008
    ..The Institute for Systems Biology has aspired to pioneer and seamlessly integrate each of these concepts...
  22. pmc Control of transcriptional variability by overlapping feed-forward regulatory motifs
    Alexander V Ratushny
    Institute for Systems Biology, Seattle, Washington, USA
    Biophys J 95:3715-23. 2008
    ..The OFFNM is highly overrepresented in the yeast regulome, suggesting that the specific functions described for the OFFNM, or other properties of this motif, provide a selective advantage...
  23. ncbi request reprint Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software
    Patrick G A Pedrioli
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Methods 3:533-9. 2006
    ..Notably, our method is theoretically applicable to any type of modification or chemical moiety generating a unique fragment ion pattern...
  24. ncbi request reprint Approaching complete peroxisome characterization by gas-phase fractionation
    Eugene C Yi
    The Institute for Systems Biology, Seattle, WA 98103, USA
    Electrophoresis 23:3205-16. 2002
    ....
  25. pmc Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast
    Deena M Leslie
    Institute for Systems Biology, Seattle, Washington 98105, USA
    Mol Cell Biol 22:2544-55. 2002
    ..Together these data demonstrate that Ste12p is imported into nuclei by Kap121p and that mating and differentiation defects associated with kap121 mutants are primarily attributable to the mislocalization of Ste12p...
  26. pmc QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments
    David J Dilworth
    Institute for Systems Biology, Seattle, Washington 98103, USA
    J Am Soc Mass Spectrom 21:1417-22. 2010
    ..This method has general utility for multiple applications where isotopic labeling is used for quantification in mass spectrometry...
  27. pmc Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import
    Deena M Leslie
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Biol 24:8487-503. 2004
    ..Together, our data elucidate additional levels of complexity in these nuclear transport pathways...
  28. pmc Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress
    Sunhee Jung
    Institute for Systems Biology, Seattle, Washington 98103, USA
    J Biol Chem 285:6739-49. 2010
    ....
  29. pmc Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein
    Yaroslav Sydorskyy
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Biochem J 388:819-26. 2005
    ....
  30. pmc Deterministic and stochastic models of genetic regulatory networks
    Ilya Shmulevich
    Institute for Systems Biology, Seattle, Washington, USA
    Methods Enzymol 467:335-56. 2009
    ..For each combination of these categories, a model is presented and discussed in the context of the yeast cell cycle, illustrating how different types of questions can be addressed by different model classes...
  31. pmc Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes
    Yakun Wan
    Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
    Mol Cell Biol 29:2346-58. 2009
    ..While these new nucleosomes do not incorporate Htz1p, the initial presence of Htz1p appears to mark the promoter for sustained gene expression and the recruitment of TATA-binding protein...
  32. ncbi request reprint Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
    Stephen A Ramsey
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Genet 38:1082-7. 2006
    ....
  33. ncbi request reprint Studying nuclear protein import in yeast
    Deena M Leslie
    Institute for Systems Biology, 1141 N 34th St, Seattle, WA 98103, USA
    Methods 39:291-308. 2006
    ....
  34. pmc Proteomic and genomic characterization of chromatin complexes at a boundary
    Alan J Tackett
    Rockefeller University, New York, NY 10021, USA
    J Cell Biol 169:35-47. 2005
    ..We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states...
  35. ncbi request reprint Comprehensive analysis of diverse ribonucleoprotein complexes
    Marlene Oeffinger
    Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nat Methods 4:951-6. 2007
    ..Our method overcomes many of the previous limitations to produce large RNP interactomes with almost no contamination...
  36. ncbi request reprint Cell biology: pore puzzle
    John D Aitchison
    Nature 450:621-2. 2007

Research Grants10

  1. The Role of Novel Peroxins in Peroxisomal Biogenesis
    John Aitchison; Fiscal Year: 2003
    ..Preliminary results applying these techniques demonstrate that the first these proteins is a previously unknown peroxin required for peroxisome size regulation and segregation during cell division. ..
  2. Oleate-responsive gene regulatory networks governing peroxisome proliferation
    John D Aitchison; Fiscal Year: 2010
    ..Understanding peroxisome dynamics, biogenesis and function are critical to understanding these numerous human conditions and to their future treatment. ..
  3. Oleate-responsive gene regulatory networks governing peroxisome proliferation
    John Aitchison; Fiscal Year: 2009
    ..Understanding peroxisome dynamics, biogenesis and function are critical to understanding these numerous human conditions and to their future treatment. ..
  4. The Role of Novel Peroxins in Peroxisomal Biogenesis
    John Aitchison; Fiscal Year: 2007
    ..Preliminary results applying these techniques demonstrate that the first these proteins is a previously unknown peroxin required for peroxisome size regulation and segregation during cell division. ..
  5. High-throughput cell manipulation and quantitative imaging
    John Aitchison; Fiscal Year: 2007
    ....
  6. The Role of Novel Peroxins in Peroxisomal Biogenesis
    John Aitchison; Fiscal Year: 2006
    ..Preliminary results applying these techniques demonstrate that the first these proteins is a previously unknown peroxin required for peroxisome size regulation and segregation during cell division. ..
  7. The Role of Novel Peroxins in Peroxisomal Biogenesis
    John Aitchison; Fiscal Year: 2005
    ..Preliminary results applying these techniques demonstrate that the first these proteins is a previously unknown peroxin required for peroxisome size regulation and segregation during cell division. ..
  8. The Role of Novel Peroxins in Peroxisomal Biogenesis
    John Aitchison; Fiscal Year: 2004
    ..Preliminary results applying these techniques demonstrate that the first these proteins is a previously unknown peroxin required for peroxisome size regulation and segregation during cell division. ..
  9. Oleate-responsive gene regulatory networks governing peroxisome proliferation
    John D Aitchison; Fiscal Year: 2010
    ..Understanding peroxisome dynamics, biogenesis and function are critical to understanding these numerous human conditions and to their future treatment. ..