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Networks and information flow

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  1. Content type: Research article

    The immune system is a key biological system present in vertebrates. Exposure to pathogens elicits various defensive immune mechanisms that protect the host from potential threats and harmful substances derive...

    Authors: Che Lin, Chin-Nan Lin, Yu-Chao Wang, Fang-Yu Liu, Yung-Jen Chuang, Chung-Yu Lan, Wen-Ping Hsieh and Bor-Sen Chen

    Citation: BMC Systems Biology 2014 8:116

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  2. Content type: Research article

    Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infect...

    Authors: Mathieu Larocque, Thierry Chénard and Rafael Najmanovich

    Citation: BMC Systems Biology 2014 8:117

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  3. Content type: Research

    The maintenance of stem cell pluripotency is controlled by a core cluster of transcription factors, NANOG, OCT4 and SOX2 – genes that jointly regulate each other's expression. The expression of some of these g...

    Authors: Dora Lakatos, Emily D Travis, Kelsey E Pierson, Jay L Vivian and Andras Czirok

    Citation: BMC Systems Biology 2014 8:112

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  4. Content type: Research article

    Recent findings suggest that in pancreatic acinar cells stimulated with bile acid, a pro-apoptotic effect of reactive oxygen species (ROS) dominates their effect on necrosis and spreading of inflammation. The ...

    Authors: Johannes Wollbold, Robert Jaster, Sarah Müller, Katja Rateitschak and Olaf Wolkenhauer

    Citation: BMC Systems Biology 2014 8:101

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  5. Content type: Research article

    Membranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of cellular ultra-str...

    Authors: Joanne K Liu, Edward J O’Brien, Joshua A Lerman, Karsten Zengler, Bernhard O Palsson and Adam M Feist

    Citation: BMC Systems Biology 2014 8:110

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  6. Content type: Research Article

    An algebraic method for information fusion based on nonadditive set functions is used to assess the joint contribution of Boolean network attributes to the sensitivity of the network to individual node mutatio...

    Authors: Naomi Kochi, Tomáš Helikar, Laura Allen, Jim A Rogers, Zhenyuan Wang and Mihaela T Matache

    Citation: BMC Systems Biology 2014 8:92

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  7. Content type: Research article

    Constraint-based models of Escherichia coli metabolic flux have played a key role in computational studies of cellular metabolism at the genome scale. We sought to develop a next-generation constraint-based E. co...

    Authors: Daniel S Weaver, Ingrid M Keseler, Amanda Mackie, Ian T Paulsen and Peter D Karp

    Citation: BMC Systems Biology 2014 8:79

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  8. Content type: Research article

    High-throughput methods for biological measurements generate vast amounts of quantitative data, which necessitate the development of advanced approaches to data analysis to help understand the underlying mecha...

    Authors: Farzaneh Farhangmehr, Mano Ram Maurya, Daniel M Tartakovsky and Shankar Subramaniam

    Citation: BMC Systems Biology 2014 8:77

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  9. Content type: Research article

    Despite promising progress in targeted breast cancer therapy, drug resistance remains challenging. The monoclonal antibody drugs trastuzumab and pertuzumab as well as the small molecule inhibitor erlotinib wer...

    Authors: Silvia Von der Heyde, Christian Bender, Frauke Henjes, Johanna Sonntag, Ulrike Korf and Tim Beißbarth

    Citation: BMC Systems Biology 2014 8:75

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  10. Content type: Research article

    We have recently shown by formally modelling human protein interaction networks (PINs) as metric spaces and classified proteins into zones based on their distance from the topological centre that hub proteins ...

    Authors: Emad Fadhal, Eric C Mwambene and Junaid Gamieldien

    Citation: BMC Systems Biology 2014 8:68

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  11. Content type: Research article

    Metabolic responses are essential for the adaptation of microorganisms to changing environmental conditions. The repertoire of flux responses that the metabolic network can display in different external condit...

    Authors: Magdalena San Román, Héctor Cancela and Luis Acerenza

    Citation: BMC Systems Biology 2014 8:67

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  12. Content type: Research article

    Latent phenotypes are non-adaptive byproducts of adaptive phenotypes. They exist in biological systems as different as promiscuous enzymes and genome-scale metabolic reaction networks, and can give rise to evo...

    Authors: Joshua L Payne and Andreas Wagner

    Citation: BMC Systems Biology 2014 8:64

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  13. Content type: Research article

    A metabolism can evolve through changes in its biochemical reactions that are caused by processes such as horizontal gene transfer and gene deletion. While such changes need to preserve an organism’s viability...

    Authors: Aditya Barve, Sayed-Rzgar Hosseini, Olivier C Martin and Andreas Wagner

    Citation: BMC Systems Biology 2014 8:48

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  14. Content type: Research article

    Although respiratory diseases exhibit in a wide array of clinical manifestations, certain respiratory diseases may share related genetic mechanisms or may be influenced by similar chemical stimuli. Here we exp...

    Authors: Benjamin Garcia, Gargi Datta, Gregory P Cosgrove and Michael Strong

    Citation: BMC Systems Biology 2014 8:34

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  15. Content type: Research article

    Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial...

    Authors: Wai Kit Ong, Trang T Vu, Klaus N Lovendahl, Jenna M Llull, Margrethe H Serres, Margaret F Romine and Jennifer L Reed

    Citation: BMC Systems Biology 2014 8:31

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  16. Content type: Research article

    An important aspect of molecular interactions is the dynamics associated with growth conditions. Intuitively, not all possible interactions take place together all the time in a cell as only a subset of genes ...

    Authors: Shubhada R Hegde, Khushbu Pal and Shekhar C Mande

    Citation: BMC Systems Biology 2014 8:26

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  17. Content type: Research article

    Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and hori...

    Authors: Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan

    Citation: BMC Systems Biology 2014 8:21

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  18. Content type: Methodology article

    Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level....

    Authors: Erno Lindfors, Paula Jouhten, Merja Oja, Eija Rintala, Matej Orešič and Merja Penttilä

    Citation: BMC Systems Biology 2014 8:16

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  19. Content type: Research article

    Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for ac...

    Authors: Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M Sauro, Gustavo Stolovitzky and Julio Saez-Rodriguez

    Citation: BMC Systems Biology 2014 8:13

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  20. Content type: Research article

    Robert Rosen’s Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has...

    Authors: Derek Gatherer and Vashti Galpin

    Citation: BMC Systems Biology 2013 7:128

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  21. Content type: Research article

    The regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transc...

    Authors: Julio A Freyre-González, Alejandra M Manjarrez-Casas, Enrique Merino, Mario Martinez-Nuñez, Ernesto Perez-Rueda and Rosa-María Gutiérrez-Ríos

    Citation: BMC Systems Biology 2013 7:127

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  22. Content type: Research article

    Lung cancer, especially non-small cell lung cancer, is a leading cause of malignant tumor death worldwide. Understanding the mechanisms employed by the main regulators, such as microRNAs (miRNAs) and transcrip...

    Authors: Kening Li, Zihui Li, Ning Zhao, Yaoqun Xu, Yongjing Liu, Yuanshuai Zhou, Desi Shang, Fujun Qiu, Rui Zhang, Zhiqiang Chang and Yan Xu

    Citation: BMC Systems Biology 2013 7:122

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  23. Content type: Research article

    Recovering the network topology and associated kinetic parameter values from time-series data are central topics in systems biology. Nevertheless, methods that simultaneously do both are few and lack generality.

    Authors: Gonzalo Guillén-Gosálbez, Antoni Miró, Rui Alves, Albert Sorribas and Laureano Jiménez

    Citation: BMC Systems Biology 2013 7:113

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  24. Content type: Research article

    Transcription factors (TFs) and miRNAs are essential for the regulation of gene expression; however, the global view of human gene regulatory networks remains poorly understood. For example, how is the express...

    Authors: Pengping Li, Xu Hua, Zhen Zhang, Jie Li and Jin Wang

    Citation: BMC Systems Biology 2013 7:112

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  25. Content type: Methodology article

    Metabolomics has become increasingly popular in the study of disease phenotypes and molecular pathophysiology. One branch of metabolomics that encompasses the high-throughput screening of cellular metabolism i...

    Authors: Helen L Kotze, Emily G Armitage, Kieran J Sharkey, James W Allwood, Warwick B Dunn, Kaye J Williams and Royston Goodacre

    Citation: BMC Systems Biology 2013 7:107

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  26. Content type: Research article

    Influenza A virus (IAV) infection-induced inflammatory regulatory networks (IRNs) are extremely complex and dynamic. Specific biological experiments for investigating the interactions between individual inflam...

    Authors: Suoqin Jin and Xiufen Zou

    Citation: BMC Systems Biology 2013 7:105

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  27. Content type: Research article

    The energetics of cerebral activity critically relies on the functional and metabolic interactions between neurons and astrocytes. Important open questions include the relation between neuronal versus astrocyt...

    Authors: Francesco A Massucci, Mauro DiNuzzo, Federico Giove, Bruno Maraviglia, Isaac Perez Castillo, Enzo Marinari and Andrea De Martino

    Citation: BMC Systems Biology 2013 7:103

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  28. Content type: Research article

    Understanding the topology and dynamics of the human protein-protein interaction (PPI) network will significantly contribute to biomedical research, therefore its systematic reconstruction is required. Several...

    Authors: Maria I Klapa, Kalliopi Tsafou, Evangelos Theodoridis, Athanasios Tsakalidis and Nicholas K Moschonas

    Citation: BMC Systems Biology 2013 7:96

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  29. Content type: Research article

    Cell-to-cell variability in mRNA and proteins has been observed in many biological systems, including the human innate immune response to viral infection. Most of these studies have focused on variability that...

    Authors: Omar P Tabbaa, German Nudelman, Stuart C Sealfon, Fernand Hayot and Ciriyam Jayaprakash

    Citation: BMC Systems Biology 2013 7:94

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  30. Content type: Review

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have...

    Authors: Wynand Winterbach, Piet Van Mieghem, Marcel Reinders, Huijuan Wang and Dick de Ridder

    Citation: BMC Systems Biology 2013 7:90

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  31. Content type: Methodology article

    Microarray experiments can simultaneously identify thousands of genes that show significant perturbation in expression between two experimental conditions. Response networks, computed through the integration o...

    Authors: Christopher D Lasher, Padmavathy Rajagopalan and T M Murali

    Citation: BMC Systems Biology 2013 7:68

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  32. Content type: Research article

    Apoptosis is a tightly regulated process: cellular survive-or-die decisions cannot be accidental and must be unambiguous. Since the suicide program may be initiated in response to numerous stress stimuli, sign...

    Authors: Marta N Bogdał, Beata Hat, Marek Kochańczyk and Tomasz Lipniacki

    Citation: BMC Systems Biology 2013 7:67

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  33. Content type: Research article

    Construction of a reliable network remains the bottleneck for network-based protein function prediction. We built an artificial network model called protein overlap network (PON) for the entire genome of yeast...

    Authors: Shide Liang, Dandan Zheng, Daron M Standley, Huarong Guo and Chi Zhang

    Citation: BMC Systems Biology 2013 7:61

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  34. Content type: Research article

    Intracellular signalling systems are highly complex, rendering mathematical modelling of large signalling networks infeasible or impractical. Boolean modelling provides one feasible approach to whole-network m...

    Authors: Max Flöttmann, Falko Krause, Edda Klipp and Marcus Krantz

    Citation: BMC Systems Biology 2013 7:58

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  35. Content type: Research article

    Gene expression profiles and protein dynamics in single cells have a large cell-to-cell variability due to intracellular noise. Intracellular fluctuations originate from two sources: intrinsic noise due to the pr...

    Authors: Jaewook Joo, Steven J Plimpton and Jean-Loup Faulon

    Citation: BMC Systems Biology 2013 7:45

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  36. Content type: Methodology article

    In genomics, highly relevant gene interaction (co-expression) networks have been constructed by finding significant pair-wise correlations between genes in expression datasets. These networks are then mined to...

    Authors: F Alex Feltus, Stephen P Ficklin, Scott M Gibson and Melissa C Smith

    Citation: BMC Systems Biology 2013 7:44

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  37. Content type: Methodology article

    In Saccharomyces cerevisiæ, structural bistability generates a bimodal expression of the galactose uptake genes (GAL) when exposed to low and high glucose concentrations. This indicates that yeast cells can decid...

    Authors: Luca Salerno, Carlo Cosentino, Alessio Merola, Declan G Bates and Francesco Amato

    Citation: BMC Systems Biology 2013 7:39

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  38. Content type: Research article

    The cyclic AMP-Protein Kinase A (cAMP-PKA) pathway is an evolutionarily conserved signal transduction mechanism that regulates cellular growth and differentiation in animals and fungi. We present a mathematica...

    Authors: Kevin Gonzales, Ömür Kayıkçı, David G Schaeffer and Paul M Magwene

    Citation: BMC Systems Biology 2013 7:40

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  39. Content type: Research article

    Hematopoietic ontogeny is characterized by overlapping waves of primitive, fetal definitive, and adult definitive erythroid lineages. Our aim is to identify differences in the transcriptional control of these ...

    Authors: Emily Greenfest-Allen, Jeffrey Malik, James Palis and Christian J Stoeckert Jr

    Citation: BMC Systems Biology 2013 7:38

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2017 Journal Metrics

  • Citation Impact
    2.05 - 2-year Impact Factor
    2.505 - 5-year Impact Factor
    0.689 - Source Normalized Impact per Paper (SNIP)
    1.109 - SCImago Journal Rank (SJR)


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