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  1. Infections with Salmonella cause significant morbidity and mortality worldwide. Replication of Salmonella typhimurium inside its host cell is a model system for studying the pathogenesis of intracellular bacteria...

    Authors: Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson and Simon Daefler
    Citation: BMC Systems Biology 2009 3:38
  2. The identification of key target nodes within complex molecular networks remains a common objective in scientific research. The results of pathway analyses are usually sets of fairly complex networks or functi...

    Authors: Zoltán Dezső, Yuri Nikolsky, Tatiana Nikolskaya, Jeremy Miller, David Cherba, Craig Webb and Andrej Bugrim
    Citation: BMC Systems Biology 2009 3:36
  3. Computational modelling has become an important tool in understanding biological systems such as signalling pathways. With an increase in size complexity of models comes a need for techniques to manage model v...

    Authors: Peter Saffrey and Richard Orton
    Citation: BMC Systems Biology 2009 3:34
  4. Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were...

    Authors: Seongwon Seo and Harris A Lewin
    Citation: BMC Systems Biology 2009 3:33
  5. Human cells of various tissue types differ greatly in morphology despite having the same set of genetic information. Some genes are expressed in all cell types to perform house-keeping functions, while some ar...

    Authors: Wen-hsien Lin, Wei-chung Liu and Ming-jing Hwang
    Citation: BMC Systems Biology 2009 3:32
  6. Calorie restriction (CR) produces a number of health benefits and ameliorates diseases of aging such as type 2 diabetes. The components of the pathways downstream of CR may provide intervention points for deve...

    Authors: Jesse J Smith, Renée Deehan Kenney, David J Gagne, Brian P Frushour, William Ladd, Heidi L Galonek, Kristine Israelian, Jeffrey Song, Giedre Razvadauskaite, Amy V Lynch, David P Carney, Robin J Johnson, Siva Lavu, Andre Iffland, Peter J Elliott, Philip D Lambert…
    Citation: BMC Systems Biology 2009 3:31
  7. Metabolism and its regulation constitute a large fraction of the molecular activity within cells. The control of cellular metabolic state is mediated by numerous molecular mechanisms, which in effect position ...

    Authors: Christian L Barrett, Markus J Herrgard and Bernhard Palsson
    Citation: BMC Systems Biology 2009 3:30
  8. Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and ...

    Authors: Chang Jin Shin, Simon Wong, Melissa J Davis and Mark A Ragan
    Citation: BMC Systems Biology 2009 3:28
  9. Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems bio...

    Authors: Laurence Loewe
    Citation: BMC Systems Biology 2009 3:27
  10. Determining the interaction topology of biological systems is a topic that currently attracts significant research interest. Typical models for such systems take the form of differential equations that involve...

    Authors: Elias August and Antonis Papachristodoulou
    Citation: BMC Systems Biology 2009 3:25
  11. In silico analyses provide valuable insight into the biology of obligately intracellular pathogens and symbionts with small genomes. There is a particular opportunity to apply systems-level tools developed for th...

    Authors: Gavin H Thomas, Jeremy Zucker, Sandy J Macdonald, Anatoly Sorokin, Igor Goryanin and Angela E Douglas
    Citation: BMC Systems Biology 2009 3:24
  12. Duplicate genes are considered to have evolved through the partitioning of ancestral functions among duplicates (subfunctionalization) and/or the acquisition of novel functions from a beneficial mutation (neof...

    Authors: Yukuto Sato, Yasuyuki Hashiguchi and Mutsumi Nishida
    Citation: BMC Systems Biology 2009 3:23
  13. The architectural structure of cellular networks provides a framework for innovations as well as constraints for protein evolution. This issue has previously been studied extensively by analyzing protein inter...

    Authors: Qinghua Cui, Enrico O Purisima and Edwin Wang
    Citation: BMC Systems Biology 2009 3:21
  14. The process of cellular differentiation is governed by complex dynamical biomolecular networks consisting of a multitude of genes and their products acting in concert to determine a particular cell fate. Thus,...

    Authors: Albert C Huang, Limei Hu, Stuart A Kauffman, Wei Zhang and Ilya Shmulevich
    Citation: BMC Systems Biology 2009 3:20
  15. The identification of novel genes by high-throughput studies of complex diseases is complicated by the large number of potential genes. However, since disease-associated genes tend to interact, one solution is...

    Authors: Reza Mobini, Bengt A Andersson, Jonas Erjefält, Mirjana Hahn-Zoric, Michael A Langston, Andy D Perkins, Lars Olaf Cardell and Mikael Benson
    Citation: BMC Systems Biology 2009 3:19
  16. A comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol. 2008;2:1

    Authors: Reiner A Veitia
    Citation: BMC Systems Biology 2009 3:16
  17. Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurre...

    Authors: Jun Sun, Bahareh Sayyar, Jessica E Butler, Priti Pharkya, Tom R Fahland, Iman Famili, Christophe H Schilling, Derek R Lovley and Radhakrishnan Mahadevan
    Citation: BMC Systems Biology 2009 3:15
  18. Rodent kindling induced by PTZ is a widely used model of epileptogenesis and AED testing. Overlapping pathophysiological mechanisms may underlie epileptogenesis and other neuropsychiatric conditions. Besides e...

    Authors: Farhan Mohammad, Priyanka Singh and Abhay Sharma
    Citation: BMC Systems Biology 2009 3:11
  19. Studies of cellular signaling indicate that signal transduction pathways combine to form large networks of interactions. Viewing protein-protein and ligand-protein interactions as graphs (networks), where biom...

    Authors: Avi Ma'ayan, Sherry L Jenkins, Ryan L Webb, Seth I Berger, Sudarshan P Purushothaman, Noura S Abul-Husn, Jeremy M Posner, Tony Flores and Ravi Iyengar
    Citation: BMC Systems Biology 2009 3:10
  20. Intra-cellular information exchange, propelled by cascades of interacting signalling proteins, is essential for the proper functioning and survival of cells. Now that the interactome of several organisms is be...

    Authors: Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz and Frederic Rousseau
    Citation: BMC Systems Biology 2009 3:9
  21. In the yeast Saccharomyces cerevisiae, the presence of high levels of glucose leads to an array of down-regulatory effects known as glucose repression. This process is complex due to the presence of feedback loop...

    Authors: Tobias S Christensen, Ana Paula Oliveira and Jens Nielsen
    Citation: BMC Systems Biology 2009 3:7
  22. To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws ...

    Authors: Andreas Dräger, Marcel Kronfeld, Michael J Ziller, Jochen Supper, Hannes Planatscher, Jørgen B Magnus, Marco Oldiges, Oliver Kohlbacher and Andreas Zell
    Citation: BMC Systems Biology 2009 3:5
  23. Cell function necessitates the assemblage of proteins into complexes, a process which requires further regulation on top of the fairly understood mechanisms used to control the transcription and translation of...

    Authors: Shai Carmi, Erez Y Levanon and Eli Eisenberg
    Citation: BMC Systems Biology 2009 3:3
  24. The oxidation of fatty acids in mitochondria plays an important role in energy metabolism and genetic disorders of this pathway may cause metabolic diseases. Enzyme deficiencies can block the metabolism at def...

    Authors: Robert Modre-Osprian, Ingrid Osprian, Bernhard Tilg, Günter Schreier, Klaus M Weinberger and Armin Graber
    Citation: BMC Systems Biology 2009 3:2
  25. In breast cancer, overexpression of the transmembrane tyrosine kinase ERBB2 is an adverse prognostic marker, and occurs in almost 30% of the patients. For therapeutic intervention, ERBB2 is targeted by monoclo...

    Authors: Özgür Sahin, Holger Fröhlich, Christian Löbke, Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth and Dorit Arlt
    Citation: BMC Systems Biology 2009 3:1
  26. Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. ...

    Authors: Yunlei Li, Dick de Ridder, Marco JL de Groot and Marcel JT Reinders
    Citation: BMC Systems Biology 2008 2:111
  27. Our objective was to discover in silico axioms that are plausible representations of the operating principles realized during characteristic growth of EMT6/Ro mouse mammary tumor spheroids in culture. To reach...

    Authors: Jesse A Engelberg, Glen EP Ropella and C Anthony Hunt
    Citation: BMC Systems Biology 2008 2:110
  28. Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are ...

    Authors: Karthik Raman, Kalidas Yeturu and Nagasuma Chandra
    Citation: BMC Systems Biology 2008 2:109
  29. When purified phagosomes are incubated in the presence of actin under appropriate conditions, microfilaments start growing from the membrane in a process that is affected by ATP and the lipid composition of th...

    Authors: Mark Kühnel, Luis S Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths and Jens Reich
    Citation: BMC Systems Biology 2008 2:107
  30. Prostate cancer is a leading cause of death in the male population, therefore, a comprehensive study about the genes and the molecular networks involved in the tumoral prostate process becomes necessary. In or...

    Authors: André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos Eduardo Thomaz, Mari Cleide Sogayar and Satoru Miyano
    Citation: BMC Systems Biology 2008 2:106
  31. Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visua...

    Authors: Georgios A Pavlopoulos, Seán I O'Donoghue, Venkata P Satagopam, Theodoros G Soldatos, Evangelos Pafilis and Reinhard Schneider
    Citation: BMC Systems Biology 2008 2:104
  32. In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermo...

    Authors: Christopher R Bauer, Andrew M Epstein, Sarah J Sweeney, Daniela C Zarnescu and Giovanni Bosco
    Citation: BMC Systems Biology 2008 2:101