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Systems physiology, pharmacology and medicine

Section edited by Christina Chan

This section covers the analysis and modeling of complex systems to better understand humans and animal biology, in particular with regard to human health and disease.

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  1. Improvement in tuberculosis treatment regimens requires selection of antibiotics and dosing schedules from a large design space of possibilities. Incomplete knowledge of antibiotic and host immune dynamics in ...

    Authors: Elsje Pienaar, Véronique Dartois, Jennifer J. Linderman and Denise E. Kirschner
    Citation: BMC Systems Biology 2015 9:79
    Content type: Research article Published on:

  2. Cytokine-hormone network deregulations underpin pathologies ranging from autoimmune disorders to cancer, but our understanding of these networks in physiological/pathophysiological states remains patchy. We em...

    Authors: Sarah L. Field, Tathagata Dasgupta, Michele Cummings, Richard S. Savage, Julius Adebayo, Hema McSara, Jeremy Gunawardena and Nicolas M. Orsi
    Citation: BMC Systems Biology 2015 9:76
    Content type: Research article Published on:

  3. A hallmark of chronic liver disease is the impairment of the liver’s innate regenerative ability. In this work we use a computational approach to unravel the principles underlying control of liver repair follo...

    Authors: Daniel Cook, Babatunde A. Ogunnaike and Rajanikanth Vadigepalli
    Citation: BMC Systems Biology 2015 9:71
    Content type: Research article Published on:

  4. Methyltransferase (MT) reactions, in which methyl groups are attached to substrates, are fundamental to many aspects of cell biology and human physiology. The universal methyl donor for these reactions is S-ad...

    Authors: Michael C. Reed, Mary V. Gamble, Megan N. Hall and H. Frederik Nijhout
    Citation: BMC Systems Biology 2015 9:69
    Content type: Research Article Published on:

  5. The vascular endothelial growth factor (VEGF) family is central to cancer angiogenesis. However, targeting VEGF as an anti-cancer therapeutic approach has shown success for some tumor types but not others. Her...

    Authors: R. Joseph Bender and Feilim Mac Gabhann
    Citation: BMC Systems Biology 2015 9:55
    Content type: Research article Published on:

  6. Given the complex nature of cardiovascular disease (CVD), information derived from a systems-level will allow us to fully interrogate features of CVD to better understand disease pathogenesis and to identify n...

    Authors: Peng Li, Yingxue Fu, Jinlong Ru, Chao Huang, Jiangfeng Du, Chunli Zheng, Xuetong Chen, Pidong Li, Aiping Lu, Ling Yang and Yonghua Wang
    Citation: BMC Systems Biology 2014 8:141
    Content type: Research article Published on:

  7. Although the growth-factor G-CSF is widely used to prevent granulotoxic side effects of cytotoxic chemotherapies, its optimal use is still unknown since treatment outcome depends on many parameters such as dos...

    Authors: Sibylle Schirm, Christoph Engel, Markus Loeffler and Markus Scholz
    Citation: BMC Systems Biology 2014 8:138
    Content type: Research article Published on:

  10. It has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resis...

    Authors: Shirley Guzmán, Silvia Marin, Anibal Miranda, Vitaly A Selivanov, Josep J Centelles, Romain Harmancey, Fatima Smih, Annie Turkieh, Yves Durocher, Antonio Zorzano, Philippe Rouet and Marta Cascante
    Citation: BMC Systems Biology 2014 8:109
    Content type: Research article Published on:

  11. The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expre...

    Authors: Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris H Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami and Raul Rabadan
    Citation: BMC Systems Biology 2014 8:97
    Content type: Software Published on:

  12. Obesity is now a worldwide epidemic disease and poses a major risk for diet related diseases like type 2 diabetes, cardiovascular disease, stroke and fatty liver among others. In the present study we employed ...

    Authors: Neeraj Sinha, Sachin Sharma, Parul Tripathi, Simarjeet Kaur Negi, Kamiya Tikoo, Dhiraj Kumar, Kanury VS Rao and Samrat Chatterjee
    Citation: BMC Systems Biology 2014 8:104
    Content type: Research article Published on:

  15. Non-coding RNAs (ncRNAs) are emerging as key regulators of many cellular processes in both physiological and pathological states. Moreover, the constant discovery of new non-coding RNA species suggests that th...

    Authors: Paola Paci, Teresa Colombo and Lorenzo Farina
    Citation: BMC Systems Biology 2014 8:83
    Content type: Research article Published on:

  16. Berberine is a natural alkaloid derived from a traditional Chinese herbal medicine. It is known to modulate microRNA (miRNA) levels, although the mechanism for this action is unknown. Here, we previously demon...

    Authors: Xiaochuang Luo, Jingyi Gu, Rongxuan Zhu, Maoxiao Feng, Xuejiao Zhu, Yumin Li and Jia Fei
    Citation: BMC Systems Biology 2014 8:82
    Content type: Research article Published on:

  18. The investigation of complex disease heterogeneity has been challenging. Here, we introduce a network-based approach, using partial correlations, that analyzes the relationships among multiple disease-related ...

    Authors: Jen-hwa Chu, Craig P Hersh, Peter J Castaldi, Michael H Cho, Benjamin A Raby, Nan Laird, Russell Bowler, Stephen Rennard, Joseph Loscalzo, John Quackenbush and Edwin K Silverman
    Citation: BMC Systems Biology 2014 8:78
    Content type: Methodology article Published on:

  22. Striking a balance between the degree of model complexity and parameter identifiability, while still producing biologically feasible simulations using modelling is a major challenge in computational biology. W...

    Authors: Kristin Tøndel, Steven A Niederer, Sander Land and Nicolas P Smith
    Citation: BMC Systems Biology 2014 8:59
    Content type: Research article Published on:

  23. Alpha-synuclein (ASYN) is central in Parkinson’s disease (PD) pathogenesis. Converging pieces of evidence suggest that the levels of ASYN expression play a critical role in both familial and sporadic Parkinson...

    Authors: Eleftherios Ouzounoglou, Dimitrios Kalamatianos, Evangelia Emmanouilidou, Maria Xilouri, Leonidas Stefanis, Kostas Vekrellis and Elias S Manolakos
    Citation: BMC Systems Biology 2014 8:54
    Content type: Research article Published on:

  25. The oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments...

    Authors: Edgar D Coelho, Joel P Arrais, Sérgio Matos, Carlos Pereira, Nuno Rosa, Maria José Correia, Marlene Barros and José Luís Oliveira
    Citation: BMC Systems Biology 2014 8:24
    Content type: Research article Published on:

  26. Data-driven studies on the dynamics of reconstructed protein-protein interaction (PPI) networks facilitate investigation and identification of proteins important for particular processes or diseases and reduce...

    Authors: Gabriel N Teku, Csaba Ortutay and Mauno Vihinen
    Citation: BMC Systems Biology 2014 8:17
    Content type: Research article Published on:

  27. The demand for novel molecularly targeted drugs will continue to rise as we move forward toward the goal of personalizing cancer treatment to the molecular signature of individual tumors. However, the identifi...

    Authors: Nadia M Penrod and Jason H Moore
    Citation: BMC Systems Biology 2014 8:12
    Content type: Research article Published on:

  30. High-throughput profiling of human tissues typically yield as results the gene lists comprised of a mix of relevant molecular entities with multiple false positives that obstruct the translation of such result...

    Authors: Anatoly Mayburd and Ancha Baranova
    Citation: BMC Systems Biology 2013 7:121
    Content type: Research article Published on:

  31. Complex diseases are often difficult to diagnose, treat and study due to the multi-factorial nature of the underlying etiology. Large data sets are now widely available that can be used to define novel, mechan...

    Authors: ClarLynda R Williams-DeVane, David M Reif, Elaine Cohen Hubal, Pierre R Bushel, Edward E Hudgens, Jane E Gallagher and Stephen W Edwards
    Citation: BMC Systems Biology 2013 7:119
    Content type: Methodology article Published on:

  32. Hematopoiesis is a complex process involving different cell types and feedback mechanisms mediated by cytokines. This complexity stimulated various models with different scopes and applications. A combination ...

    Authors: Axel Krinner, Ingo Roeder, Markus Loeffler and Markus Scholz
    Citation: BMC Systems Biology 2013 7:117
    Content type: Research article Published on:

  33. Acute kidney injury (AKI) is a frequent condition in hospitalised patients undergoing major surgery or the critically ill and is associated with increased mortality. Based on the volume of the published litera...

    Authors: Holger Husi, Maria Dolores Sanchez-Niño, Christian Delles, William Mullen, Antonia Vlahou, Alberto Ortiz and Harald Mischak
    Citation: BMC Systems Biology 2013 7:110
    Content type: Research article Published on:

  34. Biliary atresia is a fibroinflammatory obstruction of extrahepatic bile duct that leads to end-stage liver disease in children. Despite advances in understanding the pathogenesis of biliary atresia, very littl...

    Authors: Kazuhiko Bessho, Kumar Shanmukhappa, Rachel Sheridan, Pranavkumar Shivakumar, Reena Mourya, Stephanie Walters, Vivek Kaimal, Eric Dilbone, Anil G Jegga and Jorge A Bezerra
    Citation: BMC Systems Biology 2013 7:104
    Content type: Research article Published on:

  36. MicroRNAs (miRNAs) are important post-transcriptional regulators that have been demonstrated to play an important role in human diseases. Elucidating the associations between miRNAs and diseases at the systema...

    Authors: Hongbo Shi, Juan Xu, Guangde Zhang, Liangde Xu, Chunquan Li, Li Wang, Zheng Zhao, Wei Jiang, Zheng Guo and Xia Li
    Citation: BMC Systems Biology 2013 7:101
    Content type: Research article Published on:

  37. Influenza is a common infectious disease caused by influenza viruses. Annual epidemics cause severe illnesses, deaths, and economic loss around the world. To better defend against influenza viral infection, it...

    Authors: Yukiko Matsuoka, Hiromi Matsumae, Manami Katoh, Amie J Eisfeld, Gabriele Neumann, Takeshi Hase, Samik Ghosh, Jason E Shoemaker, Tiago JS Lopes, Tokiko Watanabe, Shinji Watanabe, Satoshi Fukuyama, Hiroaki Kitano and Yoshihiro Kawaoka
    Citation: BMC Systems Biology 2013 7:97
    Content type: Database Published on:

  38. The complexity and multiscale nature of the mammalian immune response provides an excellent test bed for the potential of mathematical modeling and simulation to facilitate mechanistic understanding. Historica...

    Authors: Sirus Palsson, Timothy P Hickling, Erica L Bradshaw-Pierce, Michael Zager, Karin Jooss, Peter J O’Brien, Mary E Spilker, Bernhard O Palsson and Paolo Vicini
    Citation: BMC Systems Biology 2013 7:95
    Content type: Research article Published on:

  39. Gene expression signatures have been commonly used as diagnostic and prognostic markers for cancer subtyping. However, expression signatures frequently include many passengers, which are not directly related to c...

    Authors: Taejeong Bae, Kyoohyoung Rho, Jin Woo Choi, Katsuhisa Horimoto, Wankyu Kim and Sunghoon Kim
    Citation: BMC Systems Biology 2013 7:86
    Content type: Research article Published on:

  40. HMLEs (HMLE-SNAIL and Kras-HMLE, Kras-HMLE-SNAIL pairs) serve as excellent model system to interrogate the effect of SNAIL targeted agents that reverse epithelial-to-mesenchymal transition (EMT). We had earlie...

    Authors: Asfar S Azmi, Aliccia Bollig-Fischer, Bin Bao, Bum-Joon Park, Sun-Hye Lee, Gyu Yong-Song, Gregory Dyson, Chandan K Reddy, Fazlul H Sarkar and Ramzi M Mohammad
    Citation: BMC Systems Biology 2013 7:85
    Content type: Research article Published on:

  41. The tumor suppressor protein p53 plays important roles in DNA damage repair, cell cycle arrest and apoptosis. Due to its critical functions, the level of p53 is tightly regulated by a negative feedback mechani...

    Authors: Yong-Jun Shin, Kai-Yuan Chen, Ali H Sayed, Brandon Hencey and Xiling Shen
    Citation: BMC Systems Biology 2013 7:83
    Content type: Research article Published on:

  42. The aerobic energy metabolism of cardiac muscle cells is of major importance for the contractile function of the heart. Because energy metabolism is very heterogeneously distributed in heart tissue, especially...

    Authors: Hannes Hettling, David J C Alders, Jaap Heringa, Thomas W Binsl, A B Johan Groeneveld and Johannes H G M van Beek
    Citation: BMC Systems Biology 2013 7:82
    Content type: Methodology article Published on:

  44. Post-traumatic stress disorder (PTSD) is a severe anxiety disorder that affects a substantial portion of combat veterans and poses serious consequences to long-term health. Consequently, the identification of ...

    Authors: Ruoting Yang, Bernie J Daigle Jr, Seid Y Muhie, Rasha Hammamieh, Marti Jett, Linda Petzold and Francis J Doyle III
    Citation: BMC Systems Biology 2013 7:80
    Content type: Research article Published on:

  46. The development of ovarian follicles hinges on the timely exposure to the appropriate combination of hormones. Follicle stimulating hormone (FSH) and luteinizing hormone (LH) are both produced in the pituitary...

    Authors: Dagmar Iber and Christian De Geyter
    Citation: BMC Systems Biology 2013 7:60
    Content type: Research article Published on:

  47. Celiac disease (CD) is an autoimmune disorder that occurs in genetically predisposed people and is caused by a reaction to the gluten protein found in wheat, which leads to intestinal villous atrophy. Currentl...

    Authors: Oleg O Demin, Sergey V Smirnov, Victor V Sokolov, Lourdes Cucurull-Sanchez, Cesar Pichardo-Almarza, M Victoria Flores, Neil Benson and Oleg V Demin
    Citation: BMC Systems Biology 2013 7:56
    Content type: Research article Published on:

  48. Alzheimer’s disease is the most prevalent form of dementia. While a number of transcriptomic studies have been performed on the brains of Alzheimer’s specimens, no clear picture has emerged on the basis of neu...

    Authors: Jessica M Winkler and Howard S Fox
    Citation: BMC Systems Biology 2013 7:51
    Content type: Research article Published on:

  50. Multiple Sclerosis (MS) is considered a T-cell-mediated autoimmune disease with a prototypical oscillatory behavior, as evidenced by the presence of clinical relapses. Understanding the dynamics of immune cell...

    Authors: Sara Martinez-Pasamar, Elena Abad, Beatriz Moreno, Nieves Velez de Mendizabal, Ivan Martinez-Forero, Jordi Garcia-Ojalvo and Pablo Villoslada
    Citation: BMC Systems Biology 2013 7:34
    Content type: Research article Published on:

BMC Systems Biology

ISSN: 1752-0509

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