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Software   Open Access

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Zinovyev BMC Systems Biology 2013, 7:18 (1 March 2013)

Abstract | Provisional PDF

Research article   Open Access

Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol, Aljoscha Wahl BMC Systems Biology 2013, 7:17 (28 February 2013)

Abstract | Provisional PDF

Research article   Open Access

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

Kamil Erguler, Myrtani Pieri, Constantinos Deltas BMC Systems Biology 2013, 7:16 (21 February 2013)

Abstract | Provisional PDF | PubMed

Methodology article   Open Access

Precise generation of systems biology models from KEGG pathways

Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell BMC Systems Biology 2013, 7:15 (21 February 2013)

Abstract | Provisional PDF | PubMed

Methodology article   Open Access

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini BMC Systems Biology 2013, 7:14 (19 February 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

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

Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov BMC Systems Biology 2013, 7:13 (15 February 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

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

Gaurav Kumar, Edmond J Breen, Shoba Ranganathan BMC Systems Biology 2013, 7:12 (6 February 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

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

Anna Bershteyn, Philip A Eckhoff BMC Systems Biology 2013, 7:11 (4 February 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access Highly Accessed

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 BMC Systems Biology 2013, 7:9 (22 January 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

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

Jennifer E Dent, Christine Nardini BMC Systems Biology 2013, 7:10 (22 January 2013)

Abstract | Provisional PDF | PubMed

Methodology article   Open Access Highly Accessed

A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model

Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels, Mats Jirstrand BMC Systems Biology 2013, 7:8 (19 January 2013)

Abstract | Provisional PDF | PubMed

Database   Open Access Highly Accessed

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 BMC Systems Biology 2013, 7:7 (18 January 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access Highly Accessed

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

Marc Weber, Javier Buceta BMC Systems Biology 2013, 7:6 (16 January 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

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

Dario Ghersi, Mona Singh BMC Systems Biology 2013, 7:5 (16 January 2013)

Abstract | Provisional PDF | PubMed

Software   Open Access

EnRICH: Extraction and Ranking using Integration and Criteria Heuristics

Xia Zhang, M Heather West Greenlee, Jeanne M Serb BMC Systems Biology 2013, 7:4 (15 January 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT

Ulf W Liebal, Thomas Millat, Jon Marles-Wright, Richard J Lewis, Olaf Wolkenhauer BMC Systems Biology 2013, 7:3 (15 January 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

A kinetic model for RNA-interference of focal adhesions

Max Hoffmann, Ulrich S Schwarz BMC Systems Biology 2013, 7:2 (12 January 2013)

Abstract | Provisional PDF | PubMed

Methodology article   Open Access Highly Accessed

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 BMC Systems Biology 2013, 7:1 (2 January 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

Metabolic Flux-Based Modularity using Shortest Retroactive distances

Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee BMC Systems Biology 2012, 6:155 (27 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access

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 BMC Systems Biology 2012, 6:154 (15 December 2012)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access Highly Accessed

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

Yuliang Wang, James A Eddy, Nathan D Price BMC Systems Biology 2012, 6:153 (13 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

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 BMC Systems Biology 2012, 6:152 (10 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access

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 BMC Systems Biology 2012, 6:151 (7 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

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

Ali Navid, Eivind Almaas BMC Systems Biology 2012, 6:150 (6 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access

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 BMC Systems Biology 2012, 6:149 (6 December 2012)

Abstract | Full text | PDF | PubMed

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