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ISSN: 2333-9721
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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

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

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Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT

Ulf W Liebal, Thomas Millat, Jon Marles-Wright, Richard J Lewis, Olaf Wolkenhauer

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

Michael Weber, Sebastian G Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J van Zoelen, Dominik Driesch

Precise generation of systems biology models from KEGG pathways

Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dr？ger, Andreas Zell

Multilevel omic data integration in cancer celllines: advanced annotation and emergentproperties

Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini

A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis

Kamil Erguler, Myrtani Pieri, Constantinos Deltas

SignaLink 2 -- a signaling pathway resource with multi-layered regulatory networks

Dávid Fazekas, Mihály Koltai, Dénes Türei, Dezs？ Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Bek？, Katalin Lenti, Illés J Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros

A continuous-time adaptive particle filter forestimations under measurement time uncertaintieswith an application to a plasma-leucine mixedeffects model

Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels, Mats Jirstrand

Model composition through model reduction: a combined model of CD95 and NF-kappaB signaling pathways

Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov

Dynamics of the quorum sensing switch: stochastic and non-stationary effects

Marc Weber, Javier Buceta

A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns

Anna Bershteyn, Philip A Eckhoff

EnRICH: Extraction and Ranking using Integration and Criteria Heuristics

Xia Zhang, M Heather West Greenlee, Jeanne M Serb

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

Gaurav Kumar, Edmond J Breen, Shoba Ranganathan

Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells

Hyunju Cho, Ming Wu, Linxia Zhang, Ryan Thompson, Aritro Nath, Christina Chan

From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials

Jennifer E Dent, Christine Nardini

A kinetic model for RNA-interference of focal adhesions

Max Hoffmann, Ulrich S Schwarz

Disentangling function from topology to infer the network properties of disease genes

Dario Ghersi, Mona Singh

Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique

Nizamul Morshed, Madhu Chetty, Nguyen Xuan Vinh

A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network

Changki Hong, Minho Lee, Dongsup Kim, Dongsan Kim, Kwang-Hyun Cho, Insik Shin

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

Ralph Patrick, Kim-Anh Cao, Melissa Davis, Bostjan Kobe, Mikael Bodén

Tav4SB: integrating tools for analysis of kinetic models of biological systems

Miko？aj Rybiński, Micha？ Lula, Pawe？ Banasik, S？awomir Lasota, Anna Gambin

An optimally evolved connective ratio of neural networks that maximizes the occurrence of synchronized bursting behavior

Chao-Yi Dong, Kwang-Hyun Cho

Stochastic simulations of a synthetic bacteria-yeast ecosystem

Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N Kaznessis

From networks of protein interactions to networks of functional dependencies

Davide Luciani, Gianfranco Bazzoni

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud, David Sherman

Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level

Wenting Li, Rui Wang, Linfu Bai, Zhangming Yan, Zhirong Sun

Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences

Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee

Frequency-based time-series gene expression recomposition using PRIISM

Bruce A Rosa, Yuhua Jiao, Sookyung Oh, Beronda L Montgomery, Wensheng Qin, Jin Chen

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

Arvind K Chavali, Anna S Blazier, Jose L Tlaxca, Paul A Jensen, Richard D Pearson, Jason A Papin

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

An investigation of spatial signal transduction in cellular networks

Aiman Alam-Nazki, J Krishnan

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

Jason E McDermott, Deborah L Diamond, Courtney Corley, Angela L Rasmussen, Michael G Katze, Katrina M Waters

A variational approach to parameter estimation in ordinary differential equations

Daniel Kaschek, Jens Timmer

Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae

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

FAME, the Flux Analysis and Modeling Environment

Joost Boele, Brett G Olivier, Bas Teusink

Combinatorial network of transcriptional regulation and microRNA regulation in human cancer

Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li

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

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

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

Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation

Barbara Szomolay, Vahid Shahrezaei

Metabolic Flux-Based Modularity using Shortest Retroactive distances

Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee

Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency

Vijay Chickarmane, Victor Olariu, Carsten Peterson

Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing

Bor-Sen Chen, Chih-Yuan Hsu

An integer optimization algorithm for robust identification of non-linear gene regulatory networks

Nishanth Chemmangattuvalappil, Keith Task, Ipsita Banerjee

Spice: discovery of phenotype-determining component interplays

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

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

Larry Croft, Damian Szklarczyk, Lars Jensen, Jan Gorodkin

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

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

Jason E Shoemaker, Satoshi Fukuyama, Amie J Eisfeld, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Yukiko Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka

Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease

Michael C Oldham, Peter Langfelder, Steve Horvath

Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models

Kristin T？ndel, Ulf G Indahl, Arne B Gjuvsland, Stig W Omholt, Harald Martens

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

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