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Database   Open Access

A comprehensive map of the influenza A virus replication cycle

Yukiko Matsuoka, Hiromi Matsumae, Manami Katoh, Amie J Eisfeld, Gabriele Neumann, Takeshi Hase, Samik Ghosh, Jason E Shoemaker, Tiago JS Lopes, Tokiko Watanabe, Shinji Watanabe, Satoshi Fukuyama, Hiroaki Kitano, Yoshihiro Kawaoka BMC Systems Biology 2013, 7:97 (2 October 2013)

Abstract | Provisional PDF

Research article   Open Access

Reconstruction of the experimentally supported human protein interactome: what can we learn?

Maria I Klapa, Kalliopi Tsafou, Evangelos Theodoridis, Athanasios Tsakalidis, Nicholas K Moschonas BMC Systems Biology 2013, 7:96 (2 October 2013)

Abstract | Provisional PDF

Research article   Open Access

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models

Sirus Palsson, Timothy P Hickling, Erica L Bradshaw-Pierce, Michael Zager, Karin Jooss, Peter J O¿Brien, Mary E Spilker, Bernhard O Palsson, Paolo Vicini BMC Systems Biology 2013, 7:95 (28 September 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

Noise propagation through extracellular signaling leads to fluctuations in gene expression

Omar P Tabbaa, German Nudelman, Stuart C Sealfon, Fernand Hayot, Ciriyam Jayaprakash BMC Systems Biology 2013, 7:94 (25 September 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis

Prashant K Srivastava, Richard P Hull, Jacques Behmoaras, Enrico Petretto, Timothy J Aitman BMC Systems Biology 2013, 7:93 (22 September 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli

Yousuke Nishio, Soichi Ogishima, Masao Ichikawa, Yohei Yamada, Yoshihiro Usuda, Tadashi Masuda, Hiroshi Tanaka BMC Systems Biology 2013, 7:92 (22 September 2013)

Abstract | Provisional PDF | PubMed

Methodology article   Open Access

Identification of parameter correlations for parameter estimation in dynamic biological models

Pu Li, Quoc Dong Vu BMC Systems Biology 2013, 7:91 (22 September 2013)

Abstract | Full text | PDF | PubMed

Review   Open Access

Topology of molecular interaction networks

Wynand Winterbach, Piet Van Mieghem, Marcel Reinders, Huijuan Wang, Dick de Ridder BMC Systems Biology 2013, 7:90 (16 September 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

Saheed Imam, Daniel R Noguera, Timothy J Donohue BMC Systems Biology 2013, 7:89 (13 September 2013)

Abstract | Full text | PDF | PubMed

Software   Open Access Highly Accessed

An online model composition tool for system biology models

Sarp A Coskun, A Ercument Cicek, Nicola Lai, Ranjan K Dash, Z Meral Ozsoyoglu, Gultekin Ozsoyoglu BMC Systems Biology 2013, 7:88 (5 September 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access

Modularity and evolutionary constraints in a baculovirus gene regulatory network

Juliana Oliveira, Anderson de Brito, Carla Braconi, Caio de Melo Freire, Atila Iamarino, Paolo de Andrade Zanotto BMC Systems Biology 2013, 7:87 (4 September 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Identification of upstream regulators for prognostic expression signature genes in colorectal cancer

Taejeong Bae, Kyoohyoung Rho, Jin Woo Choi, Katsuhisa Horimoto, Wankyu Kim, Sunghoon Kim BMC Systems Biology 2013, 7:86 (4 September 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25

Asfar S Azmi, Aliccia Bollig-Fischer, Bin Bao, Bum-Joon Park, Sun-Hye Lee, Gyu Yong-Song, Gregory Dyson, Chandan K Reddy, Fazlul H Sarkar, Ramzi M Mohammad BMC Systems Biology 2013, 7:85 (3 September 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access

Inferring the Effective TOR-Dependent Network: A Computational Study in Yeast

Shahin Mohammadi, Shankar Subramaniam, Ananth Grama BMC Systems Biology 2013, 7:84 (30 August 2013)

Abstract | Provisional PDF | PubMed

Research article   Open Access

Post-translational regulation enables robust p53 regulation

Yong-Jun Shin, Kai-Yuan Chen, Ali H Sayed, Brandon Hencey, Xiling Shen BMC Systems Biology 2013, 7:83 (30 August 2013)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access

Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies

Hannes Hettling, David J C Alders, Jaap Heringa, Thomas W Binsl, A B Groeneveld, Johannes H G M van Beek BMC Systems Biology 2013, 7:82 (21 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

Rule–based regulatory and metabolic model for Quorum sensing in P. aeruginosa

Nadine S Schaadt, Anke Steinbach, Rolf W Hartmann, Volkhard Helms BMC Systems Biology 2013, 7:81 (21 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access

Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder

Ruoting Yang, Bernie J Daigle Jr, Seid Y Muhie, Rasha Hammamieh, Marti Jett, Linda Petzold, Francis J Doyle BMC Systems Biology 2013, 7:80 (20 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study

Yu-Chao Wang, Che Lin, Ming-Ta Chuang, Wen-Ping Hsieh, Chung-Yu Lan, Yung-Jen Chuang, Bor-Sen Chen BMC Systems Biology 2013, 7:79 (16 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

New network topology approaches reveal differential correlation patterns in breast cancer

Michael Bockmayr, Frederick Klauschen, Balazs Györffy, Carsten Denkert, Jan Budczies BMC Systems Biology 2013, 7:78 (15 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access

Transdifferentiation of pancreatic cells by loss of contact-mediated signaling

Walter de Back, Roland Zimm, Lutz Brusch BMC Systems Biology 2013, 7:77 (13 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Methodology article   Open Access Highly Accessed

Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems

Maria Rodriguez-Fernandez, Markus Rehberg, Andreas Kremling, Julio R Banga BMC Systems Biology 2013, 7:76 (12 August 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

Treenut Saithong, Oratai Rongsirikul, Saowalak Kalapanulak, Porntip Chiewchankaset, Wanatsanan Siriwat, Supatcharee Netrphan, Malinee Suksangpanomrung, Asawin Meechai, Supapon Cheevadhanarak BMC Systems Biology 2013, 7:75 (10 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Software   Open Access Highly Accessed

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson, Daniel R Hyduke BMC Systems Biology 2013, 7:74 (8 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

Methodology article   Open Access Highly Accessed

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

Andrea Pinna, Sandra Heise, Robert J Flassig, Alberto Fuente, Steffen Klamt BMC Systems Biology 2013, 7:73 (8 August 2013)

Abstract | Full text | PDF | PubMed

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