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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

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

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Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

Michael T Klann, Alexei Lapin, Matthias Reuss

A computational model of the hypothalamic - pituitary - gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17β-trenbolone

Zhenhong Li, Kevin J Kroll, Kathleen M Jensen, Daniel L Villeneuve, Gerald T Ankley, Jayne V Brian, María S Sepúlveda, Edward F Orlando, James M Lazorchak, Mitchell Kostich, Brandon Armstrong, Nancy D Denslow, Karen H Watanabe

Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling

Yu-Fang Jin, Hai- Chao Han, Jamie Berger, Qiuxia Dai, Merry L Lindsey

Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

Taewoo Ryu, Charalampos Mavromatis, Till Bayer, Christian R Voolstra, Timothy Ravasi

Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks

Angel Alvarez, Peter J Woolf

PathCase-SB architecture and database design

Ali Cakmak, Xinjian Qi, Sarp A Coskun, Mitali Das, En Cheng, A Cicek, Nicola Lai, Gultekin Ozsoyoglu, Z Ozsoyoglu

Impact of receptor clustering on ligand binding

Bertrand R Caré, Hédi A Soula

Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease

Priyanka Pandey, Shan Qin, Jacqueline Ho, Jing Zhou, Jordan A Kreidberg

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

Jeff Nie, Ron Stewart, Hang Zhang, James A Thomson, Fang Ruan, Xiaoqi Cui, Hairong Wei

Structurally robust biological networks

Franco Blanchini, Elisa Franco

Predicting the points of interaction of small molecules in the NF-κB pathway

Yogendra Patel, Catherine A Heyward, Michael RH White, Douglas B Kell

Codon usage variability determines the correlation between proteome and transcriptome fold changes

Roberto Olivares-Hernández, Sergio Bordel, Jens Nielsen

Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells

Francisco J Azuaje, Haiying Wang, Huiru Zheng, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux, Daniel R Wagner

A new computational method to split large biochemical networks into coherent subnets

Wynand S Verwoerd

Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism

Shakti Gupta, Mano R Maurya, Alfred H Merrill Jr, Christopher K Glass, Shankar Subramaniam

Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity

Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai, Mariko Okada-Hatakeyama

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae

Shengchao Ding, Wei Wang

A computational framework for gene regulatory network inference that combines multiple methods and datasets

Rita Gupta, Anna Stincone, Philipp Antczak, Sarah Durant, Roy Bicknell, Andreas Bikfalvi, Francesco Falciani

Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes - Incorporation of cellular antioxidant response and threshold-dependent behavior

Spyros K Stamatelos, Christopher J Brinkerhoff, Sastry S Isukapalli, Panos G Georgopoulos

Modeling the evolution of a classic genetic switch

Christos Josephides, Alan M Moses

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian J Theis

The logic of kinetic regulation in the thioredoxin system

Ché S Pillay, Jan-Hendrik S Hofmeyr, Johann M Rohwer

Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Antonio Gómez, Juan Cedano, Isaac Amela, Antoni Planas, Jaume Pi？ol, Enrique Querol

When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases

Vincent Navratil, Benoit de Chassey, Chantal Combe, Vincent Lotteau

Network-based scoring system for genome-scale metabolic reconstructions

M ángeles Serrano, Francesc Sagués

Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network

Xin Yao, Han Hao, Yanda Li, Shao Li

A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana

Stuart Meier, Oren Tzfadia, Ratnakar Vallabhaneni, Chris Gehring, Eleanore T Wurtzel

Improved functional overview of protein complexes using inferred epistatic relationships

Colm Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney

Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

Peter E Larsen, Avinash Sreedasyam, Geetika Trivedi, Gopi K Podila, Leland J Cseke, Frank R Collart

A transfer function approach to measuring cell inheritance

Paul Rees, M Rowan Brown, Huw D Summers, Mark D Holton, Rachel J Errington, Sally C Chappell, Paul J Smith

Stochastic adaptation and fold-change detection: from single-cell to population behavior

Tatiana T Marquez-Lago, André Leier

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene

Rafael Silva-Rocha, Hidde de Jong, Javier Tamames, Víctor de Lorenzo

Proteomic patterns of cervical cancer cell lines, a network perspective

Juan Higareda-Almaraz, María Enríquez-Gasca, Magdalena Hernández-Ortiz, Osbaldo Resendis-Antonio, Sergio Encarnación-Guevara

Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells

Marie Beurton-Aimar, Bertrand Beauvoit, Antoine Monier, Fran？ois Vallée, Martine Dieuaide-Noubhani, Sophie Colombié

Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

Steven X Ge

Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

Markus Durzinsky, Annegret Wagler, Wolfgang Marwan

Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis

Rolf O Lindén, Ville-Pekka Eronen, Tero Aittokallio

Genotype networks, innovation, and robustness in sulfur metabolism

Jo？o F Matias Rodrigues, Andreas Wagner

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Ian M Overton, Shirley Graham, Katherine A Gould, Jason Hinds, Catherine H Botting, Sally Shirran, Geoffrey J Barton, Peter J Coote

A General Life History Theory for Effects of Caloric Restriction on Health Maintenance

Chen Hou, Kendra Bolt, Aviv Bergman

Theoretical basis of the community effect in development

Yasushi Saka, Cédric Lhoussaine, Celine Kuttler, Ekkehard Ullner, Marco Thiel

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states

Aarash Bordbar, Neema Jamshidi, Bernhard O Palsson

Combined logical and data-driven models for linking signalling pathways to cellular response

Ioannis N Melas, Alexander Mitsos, Dimitris E Messinis, Thomas S Weiss, Leonidas G Alexopoulos

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Pablo Carbonell, Anne-Ga？lle Planson, Davide Fichera, Jean-Loup Faulon

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Saheed Imam, Safak Yilmaz, Ugur Sohmen, Alexander S Gorzalski, Jennifer L Reed, Daniel R Noguera, Timothy J Donohue

Integrative network analysis reveals active microRNAs and their functions in gastric cancer

Chien-Wei Tseng, Chen-Ching Lin, Chiung-Nien Chen, Hsuan-Cheng Huang, Hsueh-Fen Juan

Exploring pathway interactions in insulin resistant mouse liver

Thomas Kelder, Lars Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris Evelo

Systematic quantitative characterization of cellular responses induced by multiple signals

Ibrahim Al-Shyoukh, Fuqu Yu, Jiaying Feng, Karen Yan, Steven Dubinett, Chih-Ming Ho, Jeff S Shamma, Ren Sun

Transcriptional robustness and protein interactions are associated in yeast

Micha？l Bekaert, Gavin C Conant

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