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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Noisy-threshold control of cell death

Jose MG Vilar

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Xin Fang, Anders Wallqvist, Jaques Reifman

Quantifying uncertainty, variability and likelihood for ordinary differential equation models

Andrea Y Wei？e, Richard H Middleton, Wilhelm Huisinga

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

Dominic P Tolle, Nicolas Le Novère

Blood flow controls coagulation onset via the positive feedback of factor VII activation by factor Xa

Alexey M Shibeko, Ekaterina S Lobanova, Mikhail A Panteleev, Fazoil I Ataullakhanov

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

Ana Pop, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N Benfey, Olga G Troyanskaya

Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case

Guy Karlebach, Ron Shamir

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scott Christley, Briana Lee, Xing Dai, Qing Nie

Understanding protein evolutionary rate by integrating gene co-expression with protein interactions

Kaifang Pang, Chao Cheng, Zhenyu Xuan, Huanye Sheng, Xiaotu Ma

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

Ali R Zomorrodi, Costas D Maranas

A multi-level study of recombinant Pichia pastoris in different oxygen conditions

Kristin Baumann, Marc Carnicer, Martin Dragosits, Alexandra B Graf, Johannes Stadlmann, Paula Jouhten, Hannu Maaheimo, Brigitte Gasser, Joan Albiol, Diethard Mattanovich, Pau Ferrer

Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response - a predictive kinetic model

Bernhard Schmierer, Béla Novák, Christopher J Schofield

Mathematical modeling of the dynamic storage of iron in ferritin

J Cristian Salgado, Alvaro Olivera-Nappa, Ziomara P Gerdtzen, Victoria Tapia, Elizabeth C Theil, Carlos Conca, Marco T Nu？ez

Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models

Dietrich Trümbach, Cornelia Graf, Benno Pütz, Claudia Kühne, Marcus Panhuysen, Peter Weber, Florian Holsboer, Wolfgang Wurst, Gerhard Welzl, Jan M Deussing

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F Urchueguía, Kiran Patil

Regulation patterns in signaling networks of cancer

Gunnar Schramm, Nandakumar Kannabiran, Rainer K？nig

Predicting functional associations from metabolism using bi-partite network algorithms

Balaji Veeramani, Joel S Bader

Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling

Shouguo Gao, John L Hartman IV, Justin L Carter, Martin J Hessner, Xujing Wang

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells

Huilei Xu, Ihor R Lemischka, Avi Ma'ayan

Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation

Li Shen, Iouri Chepelev, Jie Liu, Wei Wang

Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach

Moritz von Stosch, Joana Peres, Sebasti？o de Azevedo, Rui Oliveira

Genotype networks in metabolic reaction spaces

Areejit Samal, Jo？o F Matias Rodrigues, Jürgen Jost, Olivier C Martin, Andreas Wagner

Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression

Zhiao Shi, Catherine K Derow, Bing Zhang

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation

Subir K Nandy, Paula Jouhten, Jens Nielsen

Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes

Dokyun Na, Sunjae Lee, Doheon Lee

On finite-horizon control of genetic regulatory networks with multiple hard-constraints

Yang Cong,Wai-Ki Ching,Nam-Kiu Tsing,Ho-Yin Leung

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

Wang Liangjiang,Huang Caiyan,Yang Mary,Yang Jack Y

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar

Optimal drug combinations and minimal hitting sets

Alexei Vazquez

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

Heiko Neuweger, Marcus Persicke, Stefan P Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, J？rn Winnebald, Jessica Schneider, J？rn Kalinowski, Alexander Goesmann

Specialized or flexible feed-forward loop motifs: a question of topology

Javier Macía, Stefanie Widder, Ricard Solé

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network

Clemens Kühn, Christoph Wierling, Alexander Kühn, Edda Klipp, Georgia Panopoulou, Hans Lehrach, Albert J Poustka

The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Harald Martens, Siren R Veflingstad, Erik Plahte, Magni Martens, Dominique Bertrand, Stig W Omholt

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis

Rafal Zielinski, Pawel F Przytycki, Jie Zheng, David Zhang, Teresa M Przytycka, Jacek Capala

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

Osnat Atias, Benny Chor, Daniel A Chamovitz

A computational approach to resolve cell level contributions to early glandular epithelial cancer progression

Sean HJ Kim, Jayanta Debnath, Keith Mostov, Sunwoo Park, C Anthony Hunt

Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli

Rishi Jain, Ranjan Srivastava

An evaluation of minimal cellular functions to sustain a bacterial cell

Yusuke Azuma, Motonori Ota

DASMiner: discovering and integrating data from DAS sources

Diogo FT Veiga, Helena F Deus, Caner Akdemir, Ana Vasconcelos, Jonas S Almeida

Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis

Shun-Fu Chen, Yue-Li Juang, Wei-Kang Chou, Jin-Mei Lai, Chi-Ying F Huang, Cheng-Yan Kao, Feng-Sheng Wang

Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase

Carmen Pin, Matthew D Rolfe, Marina Mu？oz-Cuevas, Jay CD Hinton, Michael W Peck, Nicholas J Walton, József Baranyi

A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

Xin Fang, Anders Wallqvist, Jaques Reifman

Using the ratio of means as the effect size measure in combining results of microarray experiments

Pingzhao Hu, Celia MT Greenwood, Joseph Beyene

A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides

Mark AJ Roberts, Elias August, Abdullah Hamadeh, Philip K Maini, Patrick E McSharry, Judith P Armitage, Antonis Papachristodoulou

Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties

Guido Melzer, Manely Esfandabadi, Ezequiel Franco-Lara, Christoph Wittmann

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

Einat Sprinzak, Shawn J Cokus, Todd O Yeates, David Eisenberg, Matteo Pellegrini

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

Reed Taffs, John E Aston, Kristen Brileya, Zackary Jay, Christian G Klatt, Shawn McGlynn, Natasha Mallette, Scott Montross, Robin Gerlach, William P Inskeep, David M Ward, Ross P Carlson

Ranges of control in the transcriptional regulation of Escherichia coli

Nikolaus Sonnenschein, Marc-Thorsten Hütt, Helga Stoyan, Dietrich Stoyan

Human synthetic lethal inference as potential anti-cancer target gene detection

Nuria Conde-Pueyo, Andreea Munteanu, Ricard V Solé, Carlos Rodríguez-Caso

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