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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

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

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

Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini

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

EnRICH: Extraction and Ranking using Integration and Criteria Heuristics

Xia Zhang, M Heather West Greenlee, Jeanne M Serb

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

Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov

Precise generation of systems biology models from KEGG pathways

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

A kinetic model for RNA-interference of focal adhesions

Max Hoffmann, Ulrich S Schwarz

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

Jennifer E Dent, Christine Nardini

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

Dario Ghersi, Mona Singh

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

Marc Weber, Javier Buceta

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

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

Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT

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

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

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

Anna Bershteyn, Philip A Eckhoff

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

Gaurav Kumar, Edmond J Breen, Shoba Ranganathan

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

Kamil Erguler, Myrtani Pieri, Constantinos Deltas

Gene autoregulation via intronic microRNAs and its functions

Carla Bosia, Matteo Osella, Mariama Baroudi, Davide Corà, Michele Caselle

A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation

Mark T Mc Auley, Darren J Wilkinson, Janette JL Jones, Thomas BL Kirkwood

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

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

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

Nizamul Morshed, Madhu Chetty, Nguyen Xuan Vinh

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

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

Barbara Szomolay, Vahid Shahrezaei

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

Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

Leandra M Brettner, Joanna Masel

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

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

Daniela Beisser, Markus A Grohme, Joachim Kopka, Marcus Frohme, Ralph O Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W Klau, Marcus Dittrich, Tobias Müller

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

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

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

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

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

Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach

Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li

Multi-compartmental modeling of SORLA’s influence on amyloidogenic processing in Alzheimer’s disease

Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E Willnow, Olaf Wolkenhauer

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

Redox balance is key to explaining full vs. partial switching to low-yield metabolism

Milan JA van Hoek, Roeland MH Merks

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Daniel C Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M Burke, Douglas A Lauffenburger, Peter K Sorger

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

Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach

Tatiana A Karelina, Kirill V Zhudenkov, Oleg O Demin, Dmitry V Svetlichny, Balaji Agoram, David Fairman, Oleg V Demin

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Camille D A Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel Gon？alves, Melody K Morris, Martijn van Iersel, Douglas A Lauffenburger, Julio Saez-Rodriguez

A reaction–diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts

Lei Zhang, Arthur D Lander, Qing Nie

HINT: High-quality protein interactomes and their applications in understanding human disease

Jishnu Das, Haiyuan Yu

Sets2Networks: network inference from repeated observations of sets

Neil R Clark, Ruth Dannenfelser, Christopher M Tan, Michael E Komosinski, Avi Ma'ayan

Estimation of dynamic flux profiles from metabolic time series data

I-Chun Chou, Eberhard O Voit

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

Iain Hepburn, Weiliang Chen, Stefan Wils, Erik De Schutter

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

Jeffrey D Orth, Bernhard？ Palsson

Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster

Man-Sun Kim, Jeong-Rae Kim, Dongsan Kim, Arthur D Lander, Kwang-Hyun Cho

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

Hendrik Rohn, Anja Hartmann, Astrid Junker, Bj？rn H Junker, Falk Schreiber

A multiscale approximation in a heat shock response model of E. coli

Hye-Won Kang

GraphAlignment: Bayesian pairwise alignment of biological networks

Michal Kolá？, J？rn Meier, Ville Mustonen, Michael L？ssig, Johannes Berg

Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis

Eduardo Tejera, Jo？o Bernardes, Irene Rebelo

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