Networks and information flow

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  1. Methodology Article

    Manatee invariants reveal functional pathways in signaling networks

    Signal transduction pathways are important cellular processes to maintain the cell’s integrity. Their imbalance can cause severe pathologies. As signal transduction pathways feature complex regulations, they f...

    Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic and Ina Koch

    BMC Systems Biology 2017 11:72

    Published on: 28 July 2017

  2. Database

    SSER: Species specific essential reactions database

    Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction i...

    Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang and Feng-Biao Guo

    BMC Systems Biology 2017 11:50

    Published on: 19 April 2017

  3. Research article

    Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data

    Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biolo...

    Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen and Mikael Rørdam Andersen

    BMC Systems Biology 2017 11:37

    Published on: 15 March 2017

  4. Research article

    Network topology of NaV1.7 mutations in sodium channel-related painful disorders

    Gain-of-function mutations in SCN9A gene that encodes the voltage-gated sodium channel NaV1.7 have been associated with a wide spectrum of painful syndromes in humans including inherited erythromelalgia, paroxysm...

    Dimos Kapetis, Jenny Sassone, Yang Yang, Barbara Galbardi, Markos N. Xenakis, Ronald L. Westra, Radek Szklarczyk, Patrick Lindsey, Catharina G. Faber, Monique Gerrits, Ingemar S. J. Merkies, Sulayman D. Dib-Hajj, Massimo Mantegazza, Stephen G. Waxman and Giuseppe Lauria

    BMC Systems Biology 2017 11:28

    Published on: 24 February 2017

  5. Research article

    The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

    Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we ...

    Joseph J. Gardner and Nanette R. Boyle

    BMC Systems Biology 2017 11:4

    Published on: 19 January 2017

  6. Research Article

    The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize

    As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resou...

    Jesse R. Walsh, Mary L. Schaeffer, Peifen Zhang, Seung Y. Rhee, Julie A. Dickerson and Taner Z. Sen

    BMC Systems Biology 2016 10:129

    Published on: 29 November 2016

  7. Research article

    In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

    Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis,...

    Edson Luiz Folador, Paulo Vinícius Sanches Daltro de Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo and Richard Röttger

    BMC Systems Biology 2016 10:103

    Published on: 4 November 2016

  8. Research article

    In silico metabolic network analysis of Arabidopsis leaves

    During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understandin...

    Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver Ernst Bläsing, Regine Fuchs, Thomas Ehrhardt and Christoph Wittmann

    BMC Systems Biology 2016 10:102

    Published on: 29 October 2016

  9. Research article

    The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

    The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ anti-immune strategies to facilitate their replicatio...

    Jason E. McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead III, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Li, Shufang Fan, Shannon McWeeney, Ralph S. Baric, Michael G. Katze and Katrina M. Waters

    BMC Systems Biology 2016 10:93

    Published on: 23 September 2016

  10. Research Article

    Identification of key player genes in gene regulatory networks

    Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis....

    Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed and Volkhard Helms

    BMC Systems Biology 2016 10:88

    Published on: 6 September 2016

  11. Research article

    The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes

    Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a ...

    Xun Yue, Xing Guo Li, Xin-Qi Gao, Xiang Yu Zhao, Yu Xiu Dong and Chao Zhou

    BMC Systems Biology 2016 10:87

    Published on: 2 September 2016

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