<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jamshidi, Neema</style></author><author><style face="normal" font="default" size="100%">Raghunathan, Anu</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods</style></title><secondary-title><style face="normal" font="default" size="100%">Frontiers in Microbiology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">constraint-based model</style></keyword><keyword><style  face="normal" font="default" size="100%">flux balance analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">host-pathogen</style></keyword><keyword><style  face="normal" font="default" size="100%">mathematical models</style></keyword><keyword><style  face="normal" font="default" size="100%">omics-technologies</style></keyword><keyword><style  face="normal" font="default" size="100%">optimization methods</style></keyword><keyword><style  face="normal" font="default" size="100%">salmonella typhimurium</style></keyword><keyword><style  face="normal" font="default" size="100%">tuberculosis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">OCT</style></date></pub-dates></dates><publisher><style face="normal" font="default" size="100%">FRONTIERS MEDIA SA</style></publisher><pub-location><style face="normal" font="default" size="100%">PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015, SWITZERLAND</style></pub-location><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">Article Number: 1032</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">4.165</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Raghunathan, Anu</style></author><author><style face="normal" font="default" size="100%">Jamshidi, Neema</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integrated host-pathogen metabolic reconstructions</style></title><secondary-title><style face="normal" font="default" size="100%">Methods in Molecular Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JAN</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1716</style></volume><pages><style face="normal" font="default" size="100%">197-217</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The 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.</style></abstract><custom4><style face="normal" font="default" size="100%">Not Available</style></custom4></record></records></xml>