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Empirical systems biology

Section edited by Matteo Pellegrini

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

Page 2 of 3

  2. Several dynamic models of a gene regulatory network of the light-induced floral transition process in Arabidopsis have been developed to capture the behavior of gene transcription and infer predictions based on e...

    Authors: Charles CN Wang, Pei-Chun Chang, Ka-Lok Ng, Chun-Ming Chang, Phillip CY Sheu and Jeffrey JP Tsai

    Citation: BMC Systems Biology 2014 8:15

    Content type: Research article

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  3. Muscle development and remodelling, mitochondrial physiology and inflammation are thought to be inter-related and to have implications for metabolism in both health and disease. However, our understanding of t...

    Authors: Aaron B Ingham, Simone A Osborne, Moira Menzies, Suzie Briscoe, Wei Chen, Kritaya Kongsuwan, Antonio Reverter, Angela Jeanes, Brian P Dalrymple, Gene Wijffels, Robert Seymour and Nicholas J Hudson

    Citation: BMC Systems Biology 2014 8:10

    Content type: Research article

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  5. Identifying permissible limits of intracellular parameters such as protein expression provides important information for examining robustness. In this study, we used the TEV protease-mediated induction of prot...

    Authors: Masataka Sasabe, Sayumi Shintani, Reiko Kintaka, Kazunari Kaizu, Koji makanae and Hisao Moriya

    Citation: BMC Systems Biology 2014 8:2

    Content type: Methodology article

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  6. Lag phase is a period of time with no growth that occurs when stationary phase bacteria are transferred to a fresh medium. Bacteria in lag phase seem inert: their biomass does not increase. The low number of c...

    Authors: Daniel Madar, Erez Dekel, Anat Bren, Anat Zimmer, Ziv Porat and Uri Alon

    Citation: BMC Systems Biology 2013 7:136

    Content type: Research article

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  7. Carbon catabolite repression (CCR) is critical for optimal bacterial growth, and in bacterial (and yeast) cells it leads to their selective consumption of a single substrate from a complex environment. However...

    Authors: Yi Zhou, Alexei Vazquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar-Joseph and Zoltán N Oltvai

    Citation: BMC Systems Biology 2013 7:138

    Content type: Research article

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  8. The expansion of cell colonies is driven by a delicate balance of several mechanisms including cell motility, cell–to–cell adhesion and cell proliferation. New approaches that can be used to independently iden...

    Authors: Katrina K Treloar, Matthew J Simpson, Parvathi Haridas, Kerry J Manton, David I Leavesley, DL Sean McElwain and Ruth E Baker

    Citation: BMC Systems Biology 2013 7:137

    Content type: Research article

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  9. The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly ...

    Authors: Soma Ghosh, Priyanka Baloni, Sumanta Mukherjee, Praveen Anand and Nagasuma Chandra

    Citation: BMC Systems Biology 2013 7:132

    Content type: Research article

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  10. Gene regulatory networks (GRNs) are models of molecule-gene interactions instrumental in the coordination of gene expression. Transcription factor (TF)-GRNs are an important subset of GRNs that characterize ge...

    Authors: Ashish Misra and Ganesh Sriram

    Citation: BMC Systems Biology 2013 7:126

    Content type: Research article

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  11. Network inference from gene expression data is a typical approach to reconstruct gene regulatory networks. During chondrogenic differentiation of human mesenchymal stem cells (hMSCs), a complex transcriptional...

    Authors: Michael Weber, Ana M Sotoca, Peter Kupfer, Reinhard Guthke and Everardus J van Zoelen

    Citation: BMC Systems Biology 2013 7:124

    Content type: Research article

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  12. Organisms of the genus Clostridium are Gram-positive endospore formers of great importance to the carbon cycle, human normo- and pathophysiology, but also in biofuel and biorefinery applications. Exposure of Clos...

    Authors: Qinghua Wang, Keerthi Prasad Venkataramanan, Hongzhan Huang, Eleftherios T Papoutsakis and Cathy H Wu

    Citation: BMC Systems Biology 2013 7:120

    Content type: Research article

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  13. Function and efficiency of a transcription factor (TF) are often modulated by interactions with other proteins or TFs to achieve finely tuned regulation of target genes. However, complex TF interactions are of...

    Authors: Prashant K Srivastava, Richard P Hull, Jacques Behmoaras, Enrico Petretto and Timothy J Aitman

    Citation: BMC Systems Biology 2013 7:93

    Content type: Research article

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  15. The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how h...

    Authors: Juliana Velasco Oliveira, Anderson Fernandes de Brito, Carla Torres Braconi, Caio César de Melo Freire, Atila Iamarino and Paolo Marinho de Andrade Zanotto

    Citation: BMC Systems Biology 2013 7:87

    Content type: Research article

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  16. Cassava is a well-known starchy root crop utilized for food, feed and biofuel production. However, the comprehension underlying the process of starch production in cassava is not yet available.

    Authors: Treenut Saithong, Oratai Rongsirikul, Saowalak Kalapanulak, Porntip Chiewchankaset, Wanatsanan Siriwat, Supatcharee Netrphan, Malinee Suksangpanomrung, Asawin Meechai and Supapon Cheevadhanarak

    Citation: BMC Systems Biology 2013 7:75

    Content type: Research article

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  18. Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators – and the relative contributions of each toward vir...

    Authors: Nicolas Tchitchek, Amie J Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, Lisa E Gralinski, Christophe Bécavin, Susan C Tilton, Bobbie-Jo Webb-Robertson, Martin T Ferris, Allison L Totura, Chengjun Li, Gabriele Neumann, Thomas O Metz, Richard D Smith, Katrina M Waters, Ralph Baric…

    Citation: BMC Systems Biology 2013 7:69

    Content type: Research article

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    The Related Article to this article has been published in Scientific Data 2014 1:140033

  20. Interferon-beta (IFN-beta) activates the immune response through the type I IFN signaling pathway. IFN-beta is important in the response to pathogen infections and is used as a therapy for Multiple Sclerosis. ...

    Authors: Inna Pertsovskaya, Elena Abad, Núria Domedel-Puig, Jordi Garcia-Ojalvo and Pablo Villoslada

    Citation: BMC Systems Biology 2013 7:59

    Content type: Research article

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  21. Most quantitative measures of phenotypic traits represent macroscopic contributions of large numbers of cells. Yet, cells of a tissue do not behave similarly, and molecular studies on several organisms have sh...

    Authors: Gaël Yvert, Shinsuke Ohnuki, Satoru Nogami, Yasutaka Imanaga, Steffen Fehrmann, Joseph Schacherer and Yoshikazu Ohya

    Citation: BMC Systems Biology 2013 7:54

    Content type: Research article

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  22. Genes for the production of a broad range of fungal secondary metabolites are frequently colinear. The prevalence of such gene clusters was systematically examined across the genome of the cereal pathogen Fusariu...

    Authors: Katherine Lawler, Kim Hammond-Kosack, Alvis Brazma and Richard MR Coulson

    Citation: BMC Systems Biology 2013 7:52

    Content type: Research article

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  23. The establishment of the mid-hindbrain region in vertebrates is mediated by theisthmic organizer, an embryonic secondary organizer characterized by awell-defined pattern of locally restricted gene expression d...

    Authors: Sabrina Hock, Yen-Kar Ng, Jan Hasenauer, Dominik Wittmann, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash and Fabian J Theis

    Citation: BMC Systems Biology 2013 7:48

    Content type: Research article

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  24. Bacterial growth as a function of nutrients has been studied for decades, but is still not fully understood. In particular, the growth laws under dynamically changing environments have been difficult to explor...

    Authors: Anat Bren, Yuval Hart, Erez Dekel, Daniel Koster and Uri Alon

    Citation: BMC Systems Biology 2013 7:27

    Content type: Research article

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  25. The genome of living organisms is constantly exposed to several damaging agents that induce different types of DNA lesions, leading to cellular malfunctioning and onset of many diseases. To maintain genome sta...

    Authors: Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Muzi Falconi, Daniela Besozzi and Paolo Plevani

    Citation: BMC Systems Biology 2013 7:24

    Content type: Research article

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  26. Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial tempe...

    Authors: AnaLuisa B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade and Walter M van Gulik

    Citation: BMC Systems Biology 2012 6:151

    Content type: Research article

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  27. Stomata are tiny pores in plant leaves that regulate gas and water exchange between the plant and its environment. Abscisic acid and ethylene are two well-known elicitors of stomatal closure when acting indepe...

    Authors: Mariano Beguerisse-Dıaz, MercedesC Hernández-Gómez, AlessandroM Lizzul, Mauricio Barahona and Radhika Desikan

    Citation: BMC Systems Biology 2012 6:146

    Content type: Research article

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  28. A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction “degree” of each gene, requires quality genome-wide data. Da...

    Authors: Leandra M Brettner and Joanna Masel

    Citation: BMC Systems Biology 2012 6:128

    Content type: Research article

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  29. Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chickens caused by the oncogenic Gallid herpesvirus type 2 (GaHV-2; MDV). Like several human lymphomas the neoplastic MD lymphoma ...

    Authors: Shyamesh Kumar, Dusan Kunec, Joram J Buza, Hsin-I Chiang, Huaijun Zhou, Sugalesini Subramaniam, Ken Pendarvis, Hans H Cheng and Shane C Burgess

    Citation: BMC Systems Biology 2012 6:123

    Content type: Research article

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  30. Cell-to-cell variability in protein expression can be large, and its propagation through signaling networks affects biological outcomes. Here, we apply deterministic and probabilistic models and biochemical me...

    Authors: Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike and Boris N Kholodenko

    Citation: BMC Systems Biology 2012 6:109

    Content type: Research article

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  31. A well known example of oscillatory phenomena is the transient oscillations of glycolytic intermediates in Saccharomyces cerevisiae, their regulation being predominantly investigated by mathematical modeling. To ...

    Authors: Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz and Lubomira Stateva

    Citation: BMC Systems Biology 2012 6:108

    Content type: Research article

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  32. Eosinophil cationic protein is a clinical asthma biomarker that would be released into blood, especially gathered in bronchia. The signal peptide of eosinophil cationic protein (ECPsp) plays an important role ...

    Authors: Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan and Hao-Teng Chang

    Citation: BMC Systems Biology 2012 6:105

    Content type: Research article

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  33. Starch serves as a temporal storage of carbohydrates in plant leaves during day/night cycles. To study transcriptional regulatory modules of this dynamic metabolic process, we conducted gene regulation network...

    Authors: Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi and Supapon Cheevadhanarak

    Citation: BMC Systems Biology 2012 6:100

    Content type: Research article

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  34. Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic...

    Authors: Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu and Jim A Rogers

    Citation: BMC Systems Biology 2012 6:96

    Content type: Software

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  35. Eukaryotic cell proliferation involves DNA replication, a tightly regulated process mediated by a multitude of protein factors. In budding yeast, the initiation of replication is facilitated by the heterohexam...

    Authors: Rohan D Gidvani, Peter Sudmant, Grace Li, Lance F DaSilva, Brendan J McConkey, Bernard P Duncker and Brian P Ingalls

    Citation: BMC Systems Biology 2012 6:78

    Content type: Research article

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  36. Complex gene regulatory networks underlie many cellular and developmental processes. While a variety of experimental approaches can be used to discover how genes interact, few biological systems have been syst...

    Authors: Brandilyn Stigler and Helen M Chamberlin

    Citation: BMC Systems Biology 2012 6:77

    Content type: Research article

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  37. Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modelin...

    Authors: Maria Cristina Bravo, Thomas Orfeo, Kenneth G Mann and Stephen J Everse

    Citation: BMC Systems Biology 2012 6:45

    Content type: Research article

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  38. The i JO1366 reconstruction of the metabolic network of Escherichia coli is one of the most complete and accurate metabolic reconstructions available for any organism. Still, because our knowledge of even well-st...

    Authors: Jeffrey D Orth and BernhardØ Palsson

    Citation: BMC Systems Biology 2012 6:30

    Content type: Research article

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  40. In System Biology, iterations of wet-lab experiments followed by modelling approaches and model-inspired experiments describe a cyclic workflow. This approach is especially useful for the inference of gene reg...

    Authors: Jörg Linde, Peter Hortschansky, Eugen Fazius, Axel A Brakhage, Reinhard Guthke and Hubertus Haas

    Citation: BMC Systems Biology 2012 6:6

    Content type: Research article

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  41. The WHO considers leishmaniasis as one of the six most important tropical diseases worldwide. It is caused by parasites of the genus Leishmania that are passed on to humans and animals by the phlebotomine sandfly...

    Authors: Bettina M Länger, Cristina Pou-Barreto, Carlos González-Alcón, Basilio Valladares, Bettina Wimmer and Néstor V Torres

    Citation: BMC Systems Biology 2012 6:1

    Content type: Research article

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  42. Apoptosis is a form of programmed cell death essential for the maintenance of homeostasis and the removal of potentially damaged cells in multicellular organisms. By binding its cognate membrane receptor, TNF ...

    Authors: Monica Schliemann, Eric Bullinger, Steffen Borchers, Frank Allgöwer, Rolf Findeisen and Peter Scheurich

    Citation: BMC Systems Biology 2011 5:204

    Content type: Research article

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  43. The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon h...

    Authors: Anna-Katharina Göhler, Öznur Kökpinar, Wolfgang Schmidt-Heck, Robert Geffers, Reinhard Guthke, Ursula Rinas, Stefan Schuster, Knut Jahreis and Christoph Kaleta

    Citation: BMC Systems Biology 2011 5:197

    Content type: Research article

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  44. Unicellular cyanobacteria of the genus Cyanothece are recognized for their ability to execute nitrogen (N2)-fixation in the dark and photosynthesis in the light. An understanding of these mechanistic processes in...

    Authors: 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 and Jon M Jacobs

    Citation: BMC Systems Biology 2011 5:194

    Content type: Research article

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  45. 14-3-3 proteins are considered master regulators of many signal transduction cascades in eukaryotes. In plants, 14-3-3 proteins have major roles as regulators of nitrogen and carbon metabolism, conclusions bas...

    Authors: Celine Diaz, Miyako Kusano, Ronan Sulpice, Mitsutaka Araki, Henning Redestig, Kazuki Saito, Mark Stitt and Ryoung Shin

    Citation: BMC Systems Biology 2011 5:192

    Content type: Research article

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  46. The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Although nearly...

    Authors: Rafael Silva-Rocha, Hidde de Jong, Javier Tamames and Víctor de Lorenzo

    Citation: BMC Systems Biology 2011 5:191

    Content type: Research article

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  47. Understanding host response to influenza virus infection will facilitate development of better diagnoses and therapeutic interventions. Several different experimental models have been used as a proxy for human...

    Authors: Jason E McDermott, Harish Shankaran, Amie J Eisfeld, Sarah E Belisle, Gabriele Neuman, Chengjun Li, Shannon McWeeney, Carol Sabourin, Yoshihiro Kawaoka, Michael G Katze and Katrina M Waters

    Citation: BMC Systems Biology 2011 5:190

    Content type: Research article

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  48. Methylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. Significant progress was made in ...

    Authors: Rémi Peyraud, Kathrin Schneider, Patrick Kiefer, Stéphane Massou, Julia A Vorholt and Jean-Charles Portais

    Citation: BMC Systems Biology 2011 5:189

    Content type: Research article

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  49. Increasing awareness of limitations to natural resources has set high expectations for plant science to deliver efficient crops with increased yields, improved stress tolerance, and tailored composition. Colle...

    Authors: Henning Redestig, Miyako Kusano, Kaworu Ebana, Makoto Kobayashi, Akira Oikawa, Yozo Okazaki, Fumio Matsuda, Masanori Arita, Naoko Fujita and Kazuki Saito

    Citation: BMC Systems Biology 2011 5:176

    Content type: Research article

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  50. Stable isotope tracers are used to assess metabolic flux profiles in living cells. The existing methods of measurement average out the isotopic isomer distribution in metabolites throughout the cell, whereas t...

    Authors: Igor Marin de Mas, Vitaly A Selivanov, Silvia Marin, Josep Roca, Matej Orešič, Loranne Agius and Marta Cascante

    Citation: BMC Systems Biology 2011 5:175

    Content type: Methodology article

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BMC Systems Biology

ISSN: 1752-0509

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