Jean Marc Schwartz

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. doi request reprint Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii
    Stephen P Chapman
    Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK School of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK Current address Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerrddan, Aberystwyth, SY23 3EE, UK
    Biosystems 162:119-127. 2017
  2. doi request reprint PathNER: a tool for systematic identification of biological pathway mentions in the literature.
    Chengkun Wu
    BMC Syst Biol 7 Suppl 3:S2. 2013
  3. doi request reprint Molecular profiling of thyroid cancer subtypes using large-scale text mining.
    Chengkun Wu
    BMC Med Genomics 7 Suppl 3:S3. 2014
  4. pmc Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae
    Thomas Williamson
    Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 3:70. 2009
  5. pmc A global view of drug-therapy interactions
    Jose C Nacher
    Department of Complex Systems, Future University Hakodate, Hokkaido 041 8655, Japan
    BMC Pharmacol 8:5. 2008
  6. pmc Observing metabolic functions at the genome scale
    Jean Marc Schwartz
    Bioinformatics Center, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Biol 8:R123. 2007
  7. pmc Local and global modes of drug action in biochemical networks
    Jean Marc Schwartz
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
    BMC Chem Biol 9:4. 2009
  8. doi request reprint Genome-scale integrative data analysis and modeling of dynamic processes in yeast
    Jean Marc Schwartz
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    Methods Mol Biol 759:427-43. 2011
  9. ncbi request reprint A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes
    Jean Marc Schwartz
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto, Japan
    Bioinformatics 21:ii204-5. 2005
  10. doi request reprint Streamlining the construction of large-scale dynamic models using generic kinetic equations
    Delali A Adiamah
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    Bioinformatics 26:1324-31. 2010

Collaborators

Detail Information

Publications19

  1. doi request reprint Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii
    Stephen P Chapman
    Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK School of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK Current address Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerrddan, Aberystwyth, SY23 3EE, UK
    Biosystems 162:119-127. 2017
    ..These results show how the decomposition of metabolic flux into cyclic and acyclic components helps to understand the impact of metabolic cycling on organismal behaviour at the genome scale...
  2. doi request reprint PathNER: a tool for systematic identification of biological pathway mentions in the literature.
    Chengkun Wu
    BMC Syst Biol 7 Suppl 3:S2. 2013
    ..PathNER is implemented in Java and made freely available online at http://sourceforge.net/projects/pathner/...
  3. doi request reprint Molecular profiling of thyroid cancer subtypes using large-scale text mining.
    Chengkun Wu
    BMC Med Genomics 7 Suppl 3:S3. 2014
    ..Source code used for this study is made freely available online at https://github.com/chengkun-wu/GenesThyCan...
  4. pmc Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae
    Thomas Williamson
    Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 3:70. 2009
    ..A stochastic model of the pathway has been reported...
  5. pmc A global view of drug-therapy interactions
    Jose C Nacher
    Department of Complex Systems, Future University Hakodate, Hokkaido 041 8655, Japan
    BMC Pharmacol 8:5. 2008
    ....
  6. pmc Observing metabolic functions at the genome scale
    Jean Marc Schwartz
    Bioinformatics Center, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Biol 8:R123. 2007
    ....
  7. pmc Local and global modes of drug action in biochemical networks
    Jean Marc Schwartz
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
    BMC Chem Biol 9:4. 2009
    ..To make this change possible, the interaction networks connecting drug targets to all components of biological systems must be identified and characterized...
  8. doi request reprint Genome-scale integrative data analysis and modeling of dynamic processes in yeast
    Jean Marc Schwartz
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    Methods Mol Biol 759:427-43. 2011
    ..We subsequently discuss principles of such models and describe a series of approaches that open perspectives toward the construction of genome-scale dynamic models...
  9. ncbi request reprint A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes
    Jean Marc Schwartz
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto, Japan
    Bioinformatics 21:ii204-5. 2005
    ..However, little understanding has been achieved so far in how individual elementary modes contribute to the reconstruction of actual physiological flux distributions...
  10. doi request reprint Streamlining the construction of large-scale dynamic models using generic kinetic equations
    Delali A Adiamah
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    Bioinformatics 26:1324-31. 2010
    ..Furthermore, the integration of gene expression and protein levels into kinetic models is not straightforward...
  11. pmc Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis
    Jean Marc Schwartz
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 7:186. 2006
    ....
  12. ncbi request reprint Identification of metabolic units induced by environmental signals
    Jose C Nacher
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji Kyoto 611 0011, Japan
    Bioinformatics 22:e375-83. 2006
    ....
  13. pmc Exploring the genetic control of glycolytic oscillations in Saccharomyces cerevisiae
    Thomas Williamson
    Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 6:108. 2012
    ..To our knowledge there has not been a genetic approach to elucidate the regulatory role of the different enzymes of the glycolytic pathway...
  14. pmc Modeling the Mechanism of GR/c-Jun/Erg Crosstalk in Apoptosis of Acute Lymphoblastic Leukemia
    Daphne Wei Chen Chen
    Faculty of Life Sciences, University of Manchester Manchester, UK Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester Manchester, UK
    Front Physiol 3:410. 2012
    ..We also demonstrate the importance of using a systematic approach to translate human disease processes into computational models in order to derive information-driven new hypotheses...
  15. pmc Comprehensive modelling of the Neurospora circadian clock and its temperature compensation
    Yu Yao Tseng
    University of Manchester, Manchester, United Kingdom
    PLoS Comput Biol 8:e1002437. 2012
    ..Furthermore, simulations enabled us to propose a mechanism for temperature compensation, which is achieved by simultaneously increasing the translation of frq RNA and decreasing the nuclear import of FRQ protein...
  16. pmc Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis
    Jose C Nacher
    Department of Information Science, Faculty of Science, Toho University, Miyama 2 2 1, Funabashi, Chiba 274 8510, Japan, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
    Proc Biol Sci 281:20132907. 2014
    ..These results suggest that similar disease-connected modules may exist in different human disorders, which could lead to systematic identification of genes or proteins that have a joint role in specific disease phenotypes. ..
  17. pmc Dynamics of DNA damage induced pathways to cancer
    Kun Tian
    Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
    PLoS ONE 8:e72303. 2013
    ....
  18. pmc Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
    Karin Radrich
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
    BMC Syst Biol 4:114. 2010
    ..This process is further complicated by occurrences of missing or conflicting information and the absence of common annotation standards between different data sources...
  19. doi request reprint Quantitative analysis and modeling of glucocorticoid-controlled gene expression
    Daphne Wei Chen Chen
    Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, UK
    Pharmacogenomics 11:1545-60. 2010
    ....