BMC Systems Biology - oalib

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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

主页: http://www.biomedcentral.com/bmcsystbiol

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The Cell Collective: Toward an open and collaborative approach to systems biology

Tomá？ Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak

Morphogengineering roots: comparing mechanisms of morphogen gradient formation

Ver？nica A Grieneisen, Ben Scheres, Paulien Hogeweg, Athanasius F M Marée

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert-Streib

Spice: discovery of phenotype-determining component interplays

Zhengzhang Chen, Kanchana Padmanabhan, Andrea M Rocha, Yekaterina Shpanskaya, James R Mihelcic, Kathleen Scott, Nagiza F Samatova

Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida

Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, Vitor Martins dos Santos, Víctor de Lorenzo

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes

Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, J？rg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

Ali Navid, Eivind Almaas

Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data

Tzu-Hsien Yang, Wei-Sheng Wu

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation

Christian Jungreuthmayer, Jürgen Zanghellini

Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein

Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang

Modeling of human factor Va inactivation by activated protein C

Maria Bravo, Thomas Orfeo, Kenneth G Mann, Stephen J Everse

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure

Dapeng Hao, Cong Ren, Chuanxing Li

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

Philipp Thomas, Arthur V Straube, Ramon Grima

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials

Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen

Gene regulation is governed by a core network in hepatocellular carcinoma

Zuguang Gu, Chenyu Zhang, Jin Wang

Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

Luisa Ana B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade, Walter M van Gulik

Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network

Rachel S Koh, Mary J Dunlop

A specialized ODE integrator for the efficient computation of parameter sensitivities

Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, J？rg Stelling

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

Jong Park, Hye Park, Won Kim, Hyun Kim, Tae Kim, Sang Lee

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

Michael J McAnulty, Jiun Y Yen, Benjamin G Freedman, Ryan S Senger

Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells

Scott B Crown, Woo Ahn, Maciek R Antoniewicz

Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)

Alexander Wentzel, Per Bruheim, Anders ？verby, ？yvind M Jakobsen, H？vard Sletta, Walid A M Omara, David A Hodgson, Trond E Ellingsen

Improving metabolic flux predictions using absolute gene expression data

Dave Lee, Kieran Smallbone, Warwick B Dunn, Ettore Murabito, Catherine L Winder, Douglas B Kell, Pedro Mendes, Neil Swainston

An investigation of spatial signal transduction in cellular networks

Aiman Alam-Nazki, J Krishnan

A network perspective on metabolic inconsistency

Nikolaus Sonnenschein, José Golib Dzib, Annick Lesne, Sebastian Eilebrecht, Sheerazed Boulkroun, Maria-Christina Zennaro, Arndt Benecke, Marc-Thorsten Hütt

The genetic control of growth rate: a systems biology study in yeast

P？nar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B Kell, Nianshu Zhang, Stephen G Oliver

Crosstalk between transcription factors and microRNAs in human protein interaction network

Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang

Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth

Seung Sohn, Tae Kim, Jay H Lee, Sang Lee

Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli

Kevin B Wood, Philippe Cluzel

A systems biology approach reveals common metastatic pathways in osteosarcoma

Ricardo J Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H Rao, Serrine S Lau, Marina Vannucci, Ching C Lau, Tsz-Kwong Man

CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

Anja Karlst？dt, Daniela Fliegner, Georgios Kararigas, Hugo Sanchez Ruderisch, Vera Regitz-Zagrosek, Hermann-Georg Holzhütter

Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback

Yonatan Savir, Nir Waysbort, Yaron E Antebi, Tsvi Tlusty, Nir Friedman

Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks

Jinghang Liang, Jie Han

Topological effects of data incompleteness of gene regulatory networks

Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno

A variational approach to parameter estimation in ordinary differential equations

Daniel Kaschek, Jens Timmer

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm

Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker

Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae

Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz, Lubomira Stateva

Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

Paola Lecca, Daniele Morpurgo, Gianluca Fantaccini, Alessandro Casagrande, Corrado Priami

Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis

Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

Clemens Kreutz, Andreas Raue, Jens Timmer

Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter

Nuclear Factor kappa B is central to Marek’s Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo

Shyamesh Kumar, Dusan Kunec, Joram J Buza, Hsin-I Chiang, Huaijun Zhou, Sugalesini Subramaniam, Ken Pendarvis, Hans H Cheng, Shane C Burgess

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

Yuliang Wang, James A Eddy, Nathan D Price

Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies

Bettina M L？nger, Cristina Pou-Barreto, Carlos González-Alcón, Basilio Valladares, Bettina Wimmer, Néstor V Torres

Analyzing fixed points of intracellular regulation networks with interrelated feedback topology

Nicole Radde

Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer

Giuseppe Facchetti, Mattia Zampieri, Claudio Altafini

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