BMC Systems Biology | Empirical systems biology section

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Empirical systems biology

This section covers the conduct of experiments or use of empirical data to improve the understanding of the structure and function of biological systems.

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	1.	Research article The last generation of bacterial growth in limiting nutrient Anat Bren, Yuval Hart, Erez Dekel, Daniel Koster, Uri Alon BMC Systems Biology 2013, 7:27 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	2.	Research article In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Muzi Falconi, Daniela Besozzi, Paolo Plevani BMC Systems Biology 2013, 7:24 (20 March 2013) Abstract \| Provisional PDF \| PubMed
	3.	Research article 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
	4.	Research article Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells Mariano Beguerisse-Dıaz, Mercedes C Hernández-Gómez, Alessandro M Lizzul, Mauricio Barahona, Radhika Desikan BMC Systems Biology 2012, 6:146 (25 November 2012) Abstract \| Full text \| PDF \| PubMed
	5.	Research article Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast Leandra M Brettner, Joanna Masel BMC Systems Biology 2012, 6:128 (27 September 2012) Abstract \| Full text \| PDF \| PubMed
	6.	Research article Nuclear Factor kappa B is central to Marek’s Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo Shyamesh Kumar, Dusan Kunec, Joram J Buza, Hsin-I Chiang, Huaijun Zhou, Sugalesini Subramaniam, Ken Pendarvis, Hans H Cheng, Shane C Burgess BMC Systems Biology 2012, 6:123 (14 September 2012) Abstract \| Full text \| PDF \| PubMed
	7.	Research article Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike, Boris N Kholodenko BMC Systems Biology 2012, 6:109 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bimodal signaling response of individual cells in a population in response to stimulation need not imply a digital cellular response, but can arise from a combination of protein expression noise and negative feedback.
	8.	Research article Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz, Lubomira Stateva BMC Systems Biology 2012, 6:108 (24 August 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Research article Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang BMC Systems Biology 2012, 6:105 (20 August 2012) Abstract \| Full text \| PDF \| PubMed
	10.	Research article Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak BMC Systems Biology 2012, 6:100 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
	11.	Software The Cell Collective: Toward an open and collaborative approach to systems biology Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers BMC Systems Biology 2012, 6:96 (7 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new web-based platform, The Cell Collective, allows scientists from across the globe to collaboratively build, analyze and simulate large-scale biological systems in real time enabling efficient transfer of laboratory data into models for complex networks.
	12.	Research article A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations Rohan D Gidvani, Peter Sudmant, Grace Li, Lance F DaSilva, Brendan J McConkey, Bernard P Duncker, Brian P Ingalls BMC Systems Biology 2012, 6:78 (27 June 2012) Abstract \| Full text \| PDF \| PubMed
	13.	Research article A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegans development Brandilyn Stigler, Helen M Chamberlin BMC Systems Biology 2012, 6:77 (26 June 2012) Abstract \| Full text \| PDF \| PubMed
	14.	Research article Modeling of human factor Va inactivation by activated protein C Maria Bravo, Thomas Orfeo, Kenneth G Mann, Stephen J Everse BMC Systems Biology 2012, 6:45 (20 May 2012) Abstract \| Full text \| PDF \| PubMed
	15.	Research article Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions Jeffrey D Orth, BernhardØ Palsson BMC Systems Biology 2012, 6:30 (1 May 2012) Abstract \| Full text \| PDF \| PubMed
	16.	Research article Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis Tian Xia, Jiansong Tong, Shailendra S Rathore, Xun Gu, Julie A Dickerson BMC Systems Biology 2012, 6:19 (16 March 2012) Abstract \| Full text \| PDF \| PubMed
	17.	Research article Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach Jörg Linde, Peter Hortschansky, Eugen Fazius, Axel A Brakhage, Reinhard Guthke, Hubertus Haas BMC Systems Biology 2012, 6:6 (19 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18.	Research article Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies Bettina M Länger, Cristina Pou-Barreto, Carlos González-Alcón, Basilio Valladares, Bettina Wimmer, Néstor V Torres BMC Systems Biology 2012, 6:1 (5 January 2012) Abstract \| Full text \| PDF \| PubMed
	19.	Research article Heterogeneity reduces sensitivity of cell death for TNF-Stimuli Monica Schliemann, Eric Bullinger, Steffen Borchers, Frank Allgöwer, Rolf Findeisen, Peter Scheurich BMC Systems Biology 2011, 5:204 (28 December 2011) Abstract \| Full text \| PDF \| PubMed
	20.	Research article More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli Anna-Katharina Göhler, Öznur Kökpinar, Wolfgang Schmidt-Heck, Robert Geffers, Reinhard Guthke, Ursula Rinas, Stefan Schuster, Knut Jahreis, Christoph Kaleta BMC Systems Biology 2011, 5:197 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
	21.	Research article Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles Uma K Aryal, Jana Stöckel, Ravi K Krovvidi, Marina A Gritsenko, Matthew E Monroe, Ronald J Moore, David W Koppenaal, Richard D Smith, Himadri B Pakrasi, Jon M Jacobs BMC Systems Biology 2011, 5:194 (1 December 2011) Abstract \| Full text \| PDF \| PubMed
	22.	Research article Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes Celine Diaz, Miyako Kusano, Ronan Sulpice, Mitsutaka Araki, Henning Redestig, Kazuki Saito, Mark Stitt, Ryoung Shin BMC Systems Biology 2011, 5:192 (21 November 2011) Abstract \| Full text \| PDF \| PubMed
	23.	Research article The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene Rafael Silva-Rocha, Hidde de Jong, Javier Tamames, Víctor de Lorenzo BMC Systems Biology 2011, 5:191 (11 November 2011) Abstract \| Full text \| PDF \| PubMed
	24.	Research article Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems Jason E McDermott, Harish Shankaran, Amie J Eisfeld, Sarah E Belisle, Gabriele Neuman, Chengjun Li, Shannon McWeeney, Carol Sabourin, Yoshihiro Kawaoka, Michael G Katze, Katrina M Waters BMC Systems Biology 2011, 5:190 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25.	Research article Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1 Rémi Peyraud, Kathrin Schneider, Patrick Kiefer, Stéphane Massou, Julia A Vorholt, Jean-Charles Portais BMC Systems Biology 2011, 5:189 (10 November 2011) Abstract \| Full text \| PDF \| PubMed