Pathways and biological systems modelling group

List of publications

2017

Bakker E, Tian K, Mutti L, Demonacos C, Schwartz JM, Krstic-Demonacos M (2017). Insight into glucocorticoid receptor signalling through interactome model analysis. PLoS Computational Biology 13: e1005825.
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Chapman S, Trindade dos Santos M, Johnson G, Kritz M, Schwartz JM (2017). Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii. Biosystems 162: 119-27.
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Gioia R, Tonelli F, Ceppi I, Biggiogera M, Leikin S, Fisher S, Tenedini E, Yorgan TA, Schinke T, Tian K, Schwartz JM, Forte F, Wagener R, Villani S, Rossi A, Forlino A (2017). The chaperone activity of 4PBA ameliorates the skeletal phenotype of Chihuahua, a zebrafish model for dominant osteogenesis imperfecta. Human Molecular Genetics 26: 2897-2911.
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Strangward P, Haley MJ, Shaw TN, Schwartz JM, Greig R, Mironov A, Brian de Souza J, Cruickshank SM, Craig AG, Milner DA, Allan SM, Couper KN (2017). A quantitative brain map of experimental cerebral malaria pathology. PLoS Pathogens 13: e1006267.
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2016

Hetmanski JH, Schwartz JM, Caswell PT (2016). Modelling GTPase dynamics to understand RhoA-driven cancer cell invasion. Biochemical Society Transactions 44: 1695-1700.
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Soul J, Dunn SL, Hardingham TE, Boot-Handford RP, Schwartz JM (2016). PhenomeScape: a Cytoscape app to identify differentially regulated sub-networks using known disease associations. Bioinformatics 32: 3847-9.
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Dunn SL, Soul J, Anand S, Schwartz JM, Boot-Handford RP, Hardingham TE (2016). Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. Osteoarthritis and Cartilage 24: 1431-40.
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Hetmanski JHR, Zindy E, Schwartz JM, Caswell PT (2016). A MAPK-driven feedback loop suppresses Rac activity to promote RhoA-driven cancer cell invasion. PLoS Computational Biology 12: e1004909.
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2015

Stoney R, Ames R, Nenadic G, Robertson DL, Schwartz JM (2015). Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology 9(Suppl 6): S3.
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Wu C, Schwartz JM, Brabant G, Peng SL, Nenadic G (2015). Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events. BMC Systems Biology 9(Suppl 6): S5.
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Schwartz JM, Barber M, Soons Z (2015). Metabolic flux prediction in cancer cells with altered substrate uptake. Biochem Soc Trans 43: 1177-81.
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Hussain M, Tian K, Mutti L, Krstic-Demonacos M, Schwartz JM (2015). The expanded p53 interactome as a predictive model for cancer therapy. Genomics and Computational Biology 1: e20.
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Jarnuczak AF, Eyers CE, Schwartz JM, Grant CM, Hubbard SJ (2015). Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae. Proteomics 15: 3126-39.
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Chapman SP, Paget CM, Johnson GN, Schwartz JM (2015). Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii. Frontiers in Plant Science 6: 474.
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Oyeyemi OJ, Davies O, Robertson DL, Schwartz JM (2015). A logical model of HIV-1 interactions with the T-cell activation signalling pathway. Bioinformatics 31: 1075-83.
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Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM (2015). PhenomeExpress: A refined network analysis of expression datasets by inclusion of known disease phenotypes. Scientific Reports 5: 8117.
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2014

Wu C, Schwartz JM, Brabant G, Nenadic G (2014). Molecular profiling of thyroid cancer subtypes using large-scale text-mining. BMC Medical Genomics 7(Suppl 3): S3.
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Paget CM, Schwartz JM, Delneri D (2014). Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. Molecular Ecology 23: 5241-57.
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Schwartz JM, Taylor PN (2014). In silico prediction of elementary mode fluxes. Proceedings International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) 1: 183-91.
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Hussain M, Stutchbury B, Tian K, Atalay R, Schwartz JM, Krstic-Demonacos M (2014). Applications of p53 interactome analysis to personalised drug discovery. Proceedings International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) 1: 192-203.
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Nacher JC, Keith B, Schwartz JM (2014). Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis. Proceedings of the Royal Society B 281: 20132907.
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2013

Wu C, Schwartz JM, Nenadic G (2013). PathNER: A tool for systematic identification of biological pathway mentions in the literature. BMC Systems Biology 7(Suppl 3): S2.
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Tian K, Rajendran R, Doddananjaiah M, Krstic-Demonacos M, Schwartz JM (2013). Dynamics of DNA damage induced pathways to cancer. PLoS One 8: e72303.
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Chen DWC, Saha V, Liu JZ, Schwartz JM, Krstic-Demonacos M (2013). Erg and AP-1 as determinants of glucocorticoid response in acute lymphoblastic leukemia. Oncogene 32: 3039-48.
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Schwartz JM, Nacher JC (2013). Systems pharmacology, drug disease interactions. In: Encyclopedia of Systems Biology, Springer, ed. W. Dubitzky, O. Wolkenhauer, K.H. Cho, H. Yokota: 2103-6.
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Nacher JC, Schwartz JM (2013). Systems pharmacology, drug-target networks. In: Encyclopedia of Systems Biology, Springer, ed. W. Dubitzky, O. Wolkenhauer, K.H. Cho, H. Yokota: 2106-8.
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2012

Chen DWC, Krstic-Demonacos M, Schwartz JM (2012). Modeling the mechanism of GR/c-Jun/Erg crosstalk in apoptosis of acute lymphoblastic leukemia. Frontiers in Physiology 3: 410.
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Williamson T, Adiamah DA, Schwartz JM, Stateva L (2012). Exploring the genetic control of glycolytic oscillations in Saccharomyces cerevisiae. BMC Systems Biology 6: 108.
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Adiamah DA, Schwartz JM (2012). Construction of a genome-scale kinetic model of Mycobacterium tuberculosis using generic rate equations. Metabolites 2: 382-97.
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Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM (2012). Comprehensive modelling of the Neurospora circadian clock and its temperature compensation. PLoS Computational Biology 8: e1002437.
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Nacher JC, Schwartz JM (2012). Modularity in protein complex and drug interactions reveals new polypharmacological properties. PLoS One 7: e30028.
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2011

Schwartz JM, Gaugain C (2011). Genome-scale integrative data analysis and modeling of dynamic processes in yeast. In: Yeast Systems Biology, Springer, ed. J.I. Castrillo, S.G. Oliver, Methods in Molecular Biology 759: 427-43.
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2010

Chen DWC, Lynch JT, Demonacos C, Krstic-Demonacos M, Schwartz JM (2010). Quantitative analysis and modeling of glucocorticoid-controlled gene expression. Pharmacogenomics 11: 1545-60.
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Radrich K, Tsuruoka Y, Dobson P, Gevorgyan A, Swainston N, Baart G, Schwartz JM (2010). Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Systems Biology 4: 114.
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Adiamah DA, Handl J, Schwartz JM (2010). Generic dynamic modeling of metabolic systems. Proceedings Dynamic Days South America 2010: International Conference on Chaos and Nonlinear Dynamics.
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Kritz MV, Trindade dos Santos M, Urrutia S, Schwartz JM (2010). Organising metabolic networks: cycles in flux distributions. Journal of Theoretical Biology 265: 250-60.
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Adiamah DA, Handl J, Schwartz JM (2010). Streamlining the construction of large-scale dynamic models using generic kinetic equations. Bioinformatics 26: 1324-31.
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2009

Williamson T, Schwartz JM, Kell DB, Stateva L (2009). Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. BMC Systems Biology 3: 70.
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Schwartz JM, Nacher JC (2009). Local and global modes of drug action in biochemical networks. BMC Chemical Biology 9: 4.
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2008

Nacher JC, Schwartz JM (2008). A global view of drug-therapy interactions. BMC Pharmacology 8: 5.
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2007

Schwartz JM, Gaugain C, Nacher JC, de Daruvar A, Kanehisa M (2007). Observing metabolic functions at the genome scale. Genome Biology 8: R123.
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Schwartz JM, Laurendeau D, Denninger M, Rancourt D, Simo C (2007). Modeling techniques for liver tissue properties and their application in surgical treatment of liver cancer. In: Biomechanical Systems Technology, World Scientific, ed. C.T. Leondes, 4: 45-81.
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2006

Nacher JC, Schwartz JM, Kanehisa M, Akutsu T (2006). Identification of metabolic units induced by environmental signals. Bioinformatics 22: e375-83.
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Schwartz JM, Kanehisa M (2006). Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7: 186.
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2005

Schwartz JM, Kanehisa M (2005). A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 21: ii204-5.
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Schwartz JM, Denninger M, Rancourt D, Moisan C, Laurendeau D (2005). Modelling liver tissue properties using a non-linear visco-elastic model for surgery simulation. Medical Image Analysis 9: 103-12.
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2004

Schwartz JM, Kanehisa M (2004). Decomposition of kinetically feasible metabolic flux distributions onto elementary modes. Genome Informatics 15(2): P069.
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Schwartz JM, Kanehisa M (2004). Combining kinetics and network-based pathway analysis. Genome Informatics 15(1): 59-60.
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Schwartz JM, Laurendeau D, Denninger M, Rancourt D (2004). Geometrically and physically non-linear models for soft tissue simulation. Proceedings 6th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (CMBBE 2004): 48C.
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Mokhtari M, Bernier F, Lemieux F, Martel H, Schwartz JM, Laurendeau D, Branzan-Albu A (2004). Virtual environment and sensori-motor activities: haptic, audition and olfaction. Proceedings International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision (WSCG 2004): 109-12.
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2003

Branzan Albu A, Schwartz JM, Laurendeau D, Moisan C (2003). Integrating geometric and biomechanical models of a liver tumour for cryosurgery simulation. Lecture Notes in Computer Science 2673: 121-31.
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2002

Schwartz JM, Denninger M, Rancourt D, Moisan C, Laurendeau D (2002). Modelling liver tissue properties using a non-linear viscoelastic model for surgery simulation. ESAIM Proceedings 12: 146-53.
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2001

Schwartz JM, Langelier È, Moisan C, Laurendeau D (2001). Non-linear soft tissue deformations for the simulation of percutaneous surgeries. Lecture Notes in Computer Science 2208: 1271-2.
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2000

Schneider N, Schwartz JM, Köhler J, Becker M, Schwarz H, Gerisch G (2000). Golvesin-GFP fusions as distinct markers for Golgi and post-Golgi vesicles in Dictyostelium cells. Biology of the Cell 92: 495-511.
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1999

Koonce MP, Köhler J, Neujahr R, Schwartz JM, Tikhonenko I, Gerisch G (1999). Dynein motor regulation stabilizes interphase microtubule arrays and determines centrosome position. EMBO Journal 18: 6786-92.
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Gabriel D, Hacker U, Köhler J, Müller-Taubenberger A, Schwartz JM, Westphal M, Gerisch G (1999). The contractile vacuole network of Dictyostelium as a distinct organelle: its dynamics visualized by a GFP marker protein. Journal of Cell Science 112: 3995-4005.
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Weber I, Gerisch G, Heizer C, Murphy J, Badelt K, Stock A, Schwartz JM, Faix J (1999). Cytokinesis mediated through the recruitment of cortexillins into the cleavage furrow. EMBO Journal 18: 586-94.
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1998

Peracino B, Borleis J, Jin T, Westphal M, Schwartz JM, Wu L, Bracco E, Gerisch G, Devreotes P, Bozzaro S (1998). G protein beta subunit-null mutants are impaired in phagocytosis and chemotaxis due to inappropriate regulation of the actin cytoskeleton. Journal of Cell Biology 141: 1529-37.
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Neujahr R, Albrecht R, Köhler J, Matzner M, Schwartz JM, Westphal M, Gerisch G (1998). Microtubule-mediated centrosome motility and the positioning of cleavage furrows in multinucleate myosin II-null cells. Journal of Cell Science 111: 1227-40.
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1997

Neujahr R, Heizer C, Albrecht R, Ecke M, Schwartz JM, Weber I, Gerisch G (1997). Three-dimensional patterns and redistribution of myosin II and actin in mitotic Dictyostelium cells. Journal of Cell Biology 139: 1793-804.
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Westphal M, Jungbluth A, Heidecker M, Mühlbauer B, Heizer C, Schwartz JM, Marriott G, Gerisch G (1997). Microfilament dynamics during cell movement and chemotaxis monitored using a GFP-actin fusion protein. Current Biology 7: 176-83.
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