Skip to main content

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 3 of 3

  1. The mitochondrial inner membrane contains five large complexes that are essential for oxidative phosphorylation. Although the structure and the catalytic mechanisms of the respiratory complexes have been progr...

    Authors: Annie Glatigny, Lise Mathieu, Christopher J Herbert, Geneviève Dujardin, Brigitte Meunier and Marie-Hélène Mucchielli-Giorgi

    Citation: BMC Systems Biology 2011 5:173

    Content type: Research article

    Published on:

  2. Vascular homeostasis and response to injury are dependent on the coordinated activity of growth factors such as vascular endothelial growth factor-A (VEGF). VEGF signaling is mediated by VEGF receptors 1 (VEGF...

    Authors: Kimberly Forsten-Williams, Elma Kurtagic and Matthew A Nugent

    Citation: BMC Systems Biology 2011 5:170

    Content type: Research article

    Published on:

  3. Cellular interaction networks can be used to analyze the effects on cell signaling and other functional consequences of perturbations to cellular physiology. Thus, several methods have been used to reconstitut...

    Authors: Glauber C Brito and David W Andrews

    Citation: BMC Systems Biology 2011 5:169

    Content type: Research article

    Published on:

  4. Cellular clearance of reactive oxygen species is dependent on a network of tightly coupled redox enzymes; this network rapidly adapts to oxidative conditions such as aging, viral entry, or inflammation. Curren...

    Authors: Linda E Kippner, Nnenna A Finn, Shreya Shukla and Melissa L Kemp

    Citation: BMC Systems Biology 2011 5:164

    Content type: Research article

    Published on:

  5. Neuro-glial interactions are important for normal functioning of the brain as well as brain energy metabolism. There are two major working models - in the classical view, both neurons and astrocytes can utiliz...

    Authors: Seda Genc, Isil A Kurnaz and Mustafa Ozilgen

    Citation: BMC Systems Biology 2011 5:162

    Content type: Research article

    Published on:

  6. A myriad of new chemicals has been introduced into our environment and exposure to these agents can damage cells and induce cytotoxicity through different mechanisms, including damaging DNA directly. Analysis ...

    Authors: J Peter Svensson, Laia Quirós Pesudo, Rebecca C Fry, Yeyejide A Adeleye, Paul Carmichael and Leona D Samson

    Citation: BMC Systems Biology 2011 5:157

    Content type: Research article

    Published on:

  7. One of the puzzles in bacterial quorum sensing is understanding how an organism integrates the information gained from multiple input signals. The marine bacterium Vibrio fischeri regulates its bioluminescence th...

    Authors: Pablo D Pérez, Joel T Weiss and Stephen J Hagen

    Citation: BMC Systems Biology 2011 5:153

    Content type: Research article

    Published on:

  8. In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-li...

    Authors: Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja and Andre S Ribeiro

    Citation: BMC Systems Biology 2011 5:149

    Content type: Research article

    Published on:

  9. A microorganism is able to adapt to changes in its physicochemical or nutritional environment and this is crucial for its survival. The yeast, Saccharomyces cerevisiae, has developed mechanisms to respond to such...

    Authors: Duygu Dikicioglu, Erkan Karabekmez, Bharat Rash, Pınar Pir, Betul Kirdar and Stephen G Oliver

    Citation: BMC Systems Biology 2011 5:148

    Content type: Research article

    Published on:

  10. Immunotherapies, including vaccines, represent a potent tool to prevent or contain disease with high morbidity or mortality such as infections and cancer. However, despite their widespread use, we still have a...

    Authors: Luigi Buonaguro, Ena Wang, Maria Lina Tornesello, Franco M Buonaguro and Francesco M Marincola

    Citation: BMC Systems Biology 2011 5:146

    Content type: Review

    Published on:

  11. The integration of different 'omics' technologies has already been shown in several in vivo studies to offer a complementary insight into cellular responses to toxic challenges. Being interested in developing in ...

    Authors: Danyel Jennen, Ainhoa Ruiz-Aracama, Christina Magkoufopoulou, Ad Peijnenburg, Arjen Lommen, Joost van Delft and Jos Kleinjans

    Citation: BMC Systems Biology 2011 5:139

    Content type: Research article

    Published on:

  12. In animals, microRNAs (miRNAs) regulate the protein synthesis of their target messenger RNAs (mRNAs) by either translational repression or deadenylation. miRNAs are frequently found to be co-expressed in diffe...

    Authors: Steffen Sass, Sabine Dietmann, Ulrike C Burk, Simone Brabletz, Dominik Lutter, Andreas Kowarsch, Klaus F Mayer, Thomas Brabletz, Andreas Ruepp, Fabian J Theis and Yu Wang

    Citation: BMC Systems Biology 2011 5:136

    Content type: Research article

    Published on:

  13. How transcriptionally regulated gene expression evolves under natural selection is an open question. The cost and benefit of gene expression are the driving factors. While the former can be determined by gratu...

    Authors: Frank J Poelwijk, Philip D Heyning, Marjon GJ de Vos, Daniel J Kiviet and Sander J Tans

    Citation: BMC Systems Biology 2011 5:128

    Content type: Research article

    Published on:

  14. Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogen...

    Authors: Osbaldo Resendis-Antonio, Magdalena Hernández, Emmanuel Salazar, Sandra Contreras, Gabriel Martínez Batallar, Yolanda Mora and Sergio Encarnación

    Citation: BMC Systems Biology 2011 5:120

    Content type: Research article

    Published on:

  15. Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related fac...

    Authors: Saheed Imam, Safak Yilmaz, Ugur Sohmen, Alexander S Gorzalski, Jennifer L Reed, Daniel R Noguera and Timothy J Donohue

    Citation: BMC Systems Biology 2011 5:116

    Content type: Research article

    Published on:

  17. The development of high-throughput technologies capable of whole cell measurements of genes, proteins, and metabolites has led to the emergence of systems biology. Integrated analysis of the resulting omic dat...

    Authors: Aarash Bordbar, Neema Jamshidi and Bernhard O Palsson

    Citation: BMC Systems Biology 2011 5:110

    Content type: Research article

    Published on:

  18. Signalling pathways are the cornerstone on understanding cell function and predicting cell behavior. Recently, logical models of canonical pathways have been optimised with high-throughput phosphoproteomic dat...

    Authors: Ioannis N Melas, Alexander Mitsos, Dimitris E Messinis, Thomas S Weiss and Leonidas G Alexopoulos

    Citation: BMC Systems Biology 2011 5:107

    Content type: Research article

    Published on:

  19. Growth substrates, aerobic/anaerobic conditions, specific growth rate (μ) etc. strongly influence Escherichia coli cell physiology in terms of cell size, biomass composition, gene and protein expression. To under...

    Authors: Kaspar Valgepea, Kaarel Adamberg and Raivo Vilu

    Citation: BMC Systems Biology 2011 5:106

    Content type: Research article

    Published on:

  20. Systemic bacterial infections are highly regulated and complex processes that are orchestrated by numerous virulence factors. Genes that are coordinately controlled by the set of regulators required for system...

    Authors: Hyunjin Yoon, Charles Ansong, Jason E McDermott, Marina Gritsenko, Richard D Smith, Fred Heffron and Joshua N Adkins

    Citation: BMC Systems Biology 2011 5:100

    Content type: Research article

    Published on:

  21. 13C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explor....

    Authors: Marie Beurton-Aimar, Bertrand Beauvoit, Antoine Monier, François Vallée, Martine Dieuaide-Noubhani and Sophie Colombié

    Citation: BMC Systems Biology 2011 5:95

    Content type: Research article

    Published on:

  22. Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel...

    Authors: Kristin Tøndel, Ulf G Indahl, Arne B Gjuvsland, Jon Olav Vik, Peter Hunter, Stig W Omholt and Harald Martens

    Citation: BMC Systems Biology 2011 5:90

    Content type: Research article

    Published on:

  23. Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in tre...

    Authors: Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn MC Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor AP Martins dos Santos and Jing Wang

    Citation: BMC Systems Biology 2011 5:83

    Content type: Research article

    Published on:

  24. The carotenoids are pure isoprenoids that are essential components of the photosynthetic apparatus and are coordinately synthesized with chlorophylls in chloroplasts. However, little is known about the mechani...

    Authors: Stuart Meier, Oren Tzfadia, Ratnakar Vallabhaneni, Chris Gehring and Eleanore T Wurtzel

    Citation: BMC Systems Biology 2011 5:77

    Content type: Research article

    Published on:

  25. Synthetic lethal genetic interactions among proteins have been widely used to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interac...

    Authors: Bo Li, Weiguo Cao, Jizhong Zhou and Feng Luo

    Citation: BMC Systems Biology 2011 5:73

    Content type: Research article

    Published on:

  26. In this paper we apply a novel agent-based simulation method in order to model intracellular reactions in detail. The simulations are performed within a virtual cytoskeleton enriched with further crowding elem...

    Authors: Michael T Klann, Alexei Lapin and Matthias Reuss

    Citation: BMC Systems Biology 2011 5:71

    Content type: Research article

    Published on:

  27. Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the so...

    Authors: Peter E Larsen, Avinash Sreedasyam, Geetika Trivedi, Gopi K Podila, Leland J Cseke and Frank R Collart

    Citation: BMC Systems Biology 2011 5:70

    Content type: Research article

    Published on:

  28. Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source o...

    Authors: Ian M Overton, Shirley Graham, Katherine A Gould, Jason Hinds, Catherine H Botting, Sally Shirran, Geoffrey J Barton and Peter J Coote

    Citation: BMC Systems Biology 2011 5:68

    Content type: Research article

    Published on:

  29. Large-scale RNAi-based screens are playing a critical role in defining sets of genes that regulate specific cellular processes. Numerous screens have been completed and in some cases more than one screen has e...

    Authors: Stephen T Guest, Jingkai Yu, Dongmei Liu, Julie A Hines, Maria A Kashat and Russell L Finley Jr

    Citation: BMC Systems Biology 2011 5:65

    Content type: Research article

    Published on:

  30. Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental ...

    Authors: Taewoo Ryu, Charalampos Harris Mavromatis, Till Bayer, Christian R Voolstra and Timothy Ravasi

    Citation: BMC Systems Biology 2011 5:58

    Content type: Research article

    Published on:

  31. Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern ...

    Authors: Antonio Gómez, Juan Cedano, Isaac Amela, Antoni Planas, Jaume Piñol and Enrique Querol

    Citation: BMC Systems Biology 2011 5:49

    Content type: Research article

    Published on:

  32. Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to anal...

    Authors: Christopher C Park, Greg D Gale, Simone de Jong, Anatole Ghazalpour, Brian J Bennett, Charles R Farber, Peter Langfelder, Andy Lin, Arshad H Khan, Eleazar Eskin, Steve Horvath, Aldons J Lusis, Roel A Ophoff and Desmond J Smith

    Citation: BMC Systems Biology 2011 5:43

    Content type: Research article

    Published on:

BMC Systems Biology

ISSN: 1752-0509

Contact us