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. Research Article

    An Integrative multi-lineage model of variation in leukopoiesis and acute myelogenous leukemia

    Acute myelogenous leukemia (AML) progresses uniquely in each patient. However, patients are typically treated with the same types of chemotherapy, despite biological differences that lead to differential respo...

    Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara L. Kinzer-Ursem, David M. Umulis and Ann E. Rundell

    BMC Systems Biology 2017 11:78

    Published on: 25 August 2017

  2. Research Article

    Cooperative binding mitigates the high-dose hook effect

    The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker prot...

    Ranjita Dutta Roy, Christian Rosenmund and Melanie I. Stefan

    BMC Systems Biology 2017 11:74

    Published on: 14 August 2017

  3. Research Article

    An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia

    Triple-negative breast cancer lacks estrogen, progesterone, and HER2 receptors and is thus not possible to treat with targeted therapies for these receptors. Therefore, a greater understanding of triple-negati...

    Kerri-Ann Norton, Travis Wallace, Niranjan B. Pandey and Aleksander S. Popel

    BMC Systems Biology 2017 11:68

    Published on: 11 July 2017

  4. Research Article

    Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

    α2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that...

    Anna Huhtinen, Vesa Hongisto, Asta Laiho, Eliisa Löyttyniemi, Dirk Pijnenburg and Mika Scheinin

    BMC Systems Biology 2017 11:65

    Published on: 28 June 2017

  5. Research article

    Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes

    Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is ...

    Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof and Rafael J. Najmanovich

    BMC Systems Biology 2017 11:60

    Published on: 12 June 2017

  6. Research Article

    A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

    The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens...

    Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan

    BMC Systems Biology 2017 11:51

    Published on: 26 April 2017

  7. Research article

    Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

    Although renal fibrosis and inflammation have shown to be involved in the pathophysiology of obstructive nephropathies, molecular mechanisms underlying evolution of these processes remain undetermined. In an a...

    Theofilos Papadopoulos, Audrey Casemayou, Eric Neau, Benjamin Breuil, Cécile Caubet, Denis Calise, Barbara A. Thornhill, Magdalena Bachvarova, Julie Belliere, Robert L. Chevalier, Panagiotis Moulos, Dimcho Bachvarov, Benedicte Buffin-Meyer, Stéphane Decramer, Françoise Conte Auriol, Jean-Loup Bascands…

    BMC Systems Biology 2017 11:31

    Published on: 1 March 2017

  8. Research article

    Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

    We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis...

    Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J. Waardenberg, Kentu Lassiter and Nicholas J. Hudson

    BMC Systems Biology 2017 11:29

    Published on: 24 February 2017

  9. Research Article

    Making life difficult for Clostridium difficile: augmenting the pathogen’s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

    Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better under...

    Sara Saheb Kashaf, Claudio Angione and Pietro Lió

    BMC Systems Biology 2017 11:25

    Published on: 16 February 2017

  10. Research Article

    Mathematical model on Alzheimer’s disease

    Alzheimer disease (AD) is a progressive neurodegenerative disease that destroys memory and cognitive skills. AD is characterized by the presence of two types of neuropathological hallmarks: extracellular plaqu...

    Wenrui Hao and Avner Friedman

    BMC Systems Biology 2016 10:108

    Published on: 18 November 2016

  11. Research article

    Vascular endothelial growth factor A as predictive marker for mTOR inhibition in relapsing high-grade serous ovarian cancer

    Development of resistance against first line drug therapy including cisplatin and paclitaxel in high-grade serous ovarian cancer (HGSOC) presents a major challenge. Identifying drug candidates breaking resista...

    Peter Andorfer, Alexander Heuwieser, Andreas Heinzel, Arno Lukas, Bernd Mayer and Paul Perco

    BMC Systems Biology 2016 10:33

    Published on: 18 April 2016

  12. Research article

    Systems biology of the structural proteome

    The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis...

    Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O’Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne and Bernhard O. Palsson

    BMC Systems Biology 2016 10:26

    Published on: 11 March 2016

  13. Research article

    Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway

    As in many cancer types, the G1/S restriction point (RP) is deregulated in Acute Lymphoblastic Leukemia (ALL). Hyper-phosphorylated retinoblastoma protein (hyper-pRb) is found in high levels in ALL cells. Neve...

    Eleftherios Ouzounoglou, Dimitra Dionysiou and Georgios S. Stamatakos

    BMC Systems Biology 2016 10:23

    Published on: 1 March 2016

  14. Research article

    Quantitative analysis of insulin-like growth factor 2 receptor and insulin-like growth factor binding proteins to identify control mechanisms for insulin-like growth factor 1 receptor phosphorylation

    The insulin-like growth factor (IGF) system impacts cellular development by regulating proliferation, differentiation, and apoptosis, and is an attractive therapeutic target in cancer. The IGF system is comple...

    Dan Tian, Isaiah Mitchell and Pamela K. Kreeger

    BMC Systems Biology 2016 10:15

    Published on: 9 February 2016

  15. Research article

    In silico evaluation and exploration of antibiotic tuberculosis treatment regimens

    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 ...

    Elsje Pienaar, Véronique Dartois, Jennifer J. Linderman and Denise E. Kirschner

    BMC Systems Biology 2015 9:79

    Published on: 14 November 2015

  16. Research article

    Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo

    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...

    Sarah L. Field, Tathagata Dasgupta, Michele Cummings, Richard S. Savage, Julius Adebayo, Hema McSara, Jeremy Gunawardena and Nicolas M. Orsi

    BMC Systems Biology 2015 9:76

    Published on: 9 November 2015

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