02248nas a2200253   4500008004100000022001400041245009900055210006900154260010300223300002500326490000600351520128400357653002701641653002601668653001801694653002401712653002301736653002501759653002701784653001701811100002001828700002101848856012501869       2015                        eng d  a1664-302X00aCell scale host-pathogen modeling: another branch in the evolution of constraint-based methods0 aCell scale hostpathogen modeling another branch in the evolution  aPO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015, SWITZERLANDbFRONTIERS MEDIA SAcOCT  aArticle Number: 10320 v63 a<p>Constraint-based models have become popular methods for systems biology as they enable the integration of complex, disparate datasets in a biologically cohesive framework that also supports the description of biological processes in terms of basic physicochemical constraints and relationships. The scope, scale, and application of genome scale models have grown from single cell bacteria to multi cellular interaction modeling; host-pathogen modeling represents one of these examples at the current horizon of constraint-based methods. There are now a small number of examples of host-pathogen constraint-based models in the literature, however there has not yet been a definitive description of the methodology required for the functional integration of genome scale models in order to generate simulation capable host-pathogen models. Herein we outline a systematic procedure to produce functional host-pathogen models, highlighting steps which require debugging and iterative revisions in order to successfully build a functional model. The construction of such models will enable the exploration of host-pathogen interactions by leveraging the growing wealth of omic data in order to better understand mechanism of infection and identify novel therapeutic strategies.</p>10aconstraint-based model10aflux balance analysis10ahost-pathogen10amathematical models10aomics-technologies10aoptimization methods10asalmonella typhimurium10atuberculosis1 aJamshidi, Neema1 aRaghunathan, Anu  uhttps://library.ncl.res.in/content/cell-scale-host-pathogen-modeling-another-branch-evolution-constraint-based-methods-101531nas a2200145   4500008004100000245005500041210005400096260000800150300001200158490000900170520107500179100002101254700002001275856009001295       2018                        eng d00aIntegrated host-pathogen metabolic reconstructions0 aIntegrated hostpathogen metabolic reconstructions  cJAN  a197-2170 v17163 aThe science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious disease is complex due to the multifactorial response of the host to the pathogen. Systems biology approaches and modeling allow one to study, understand, and predict emergent properties of such complex responses. The integration of the host and pathogen metabolic networks and the subsequent merger of their stoichiometric matrices is nontrivial and requires understanding of both pathogen and host metabolism and physiologies. The protocol here describes the detailed process of network and stoichiometric matrix merger using a salmonella-mouse macrophage model. The protocol also discusses the interfacial and objective functions required to actually embark on the analysis of host-pathogen interaction models.1 aRaghunathan, Anu1 aJamshidi, Neema  uhttps://library.ncl.res.in/content/integrated-host-pathogen-metabolic-reconstructions