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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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  2. A positive energy balance is considered to be the primary cause of the development of obesity-related diseases. Treatment often consists of a combination of reducing energy intake and increasing energy expendi...

    Authors: Yvonne J. W. Rozendaal, Yanan Wang, Peter A. J. Hilbers and Natal A. W. van Riel
    Citation: BMC Systems Biology 2019 13:24
    Content type: Research article Published on:

  3. Clinical integration of systems biology approaches is gaining in importance in the course of digital revolution in modern medicine. We present our results of the analysis of an extended mathematical model desc...

    Authors: Jan Christoph Banck and Dennis Görlich
    Citation: BMC Systems Biology 2019 13:18
    Content type: Research article Published on:

  4. Understanding what determines the between-host variability in infection dynamics is a key issue to better control the infection spread. In particular, pathogen clearance is desirable over rebounds for the heal...

    Authors: Natacha Go, Suzanne Touzeau, Zeenath Islam, Catherine Belloc and Andrea Doeschl-Wilson
    Citation: BMC Systems Biology 2019 13:15
    Content type: Research article Published on:

  5. Cholesterylester transfer protein (CETP) modulates the composition of various lipoproteins associated with cardiovascular disease. Despite its central role in lipoprotein metabolism, its mode of action is stil...

    Authors: Martin Jansen, Gerhard Puetz, Michael M. Hoffmann and Karl Winkler
    Citation: BMC Systems Biology 2019 13:12
    Content type: Research article Published on:

  6. Parkinson’s disease (PD) is the second most common neurodegenerative disease, and it is a multifactorial disease with no definite diagnostic index. The aim of this study is to construct a molecular network to ...

    Authors: Xiaoting Liu, Jinhu Chen, Tianyuan Guan, Hui Yao, Wenpei Zhang, Zhenlong Guan and Yanqin Wang
    Citation: BMC Systems Biology 2019 13:10
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Systems Biology 2019 13:20

  7. Liver has the unique ability to regenerate following injury, with a wide range of variability of the regenerative response across individuals. Existing computational models of the liver regeneration are largel...

    Authors: Babita K. Verma, Pushpavanam Subramaniam and Rajanikanth Vadigepalli
    Citation: BMC Systems Biology 2019 13:9
    Content type: Research article Published on:

  8. The Notch signaling pathway is involved in cell fate decision and developmental patterning in diverse organisms. A receptor molecule, Notch (N), and a ligand molecule (in this case Delta or Dl) are the central...

    Authors: Elaine R. Reynolds, Ryan Himmelwright, Christopher Sanginiti and Jeffrey O. Pfaffmann
    Citation: BMC Systems Biology 2019 13:7
    Content type: Research article Published on:

  9. Cancer is the second most common cause of death globally. The anticancer effects of Tanshinone IIA (Tan IIA) has been confirmed by numerous researches. However, the underlying mechanism remained to be integrated ...

    Authors: Yan-feng Cao, Shi-feng Wang, Xi Li, Yan-ling Zhang and Yan-jiang Qiao
    Citation: BMC Systems Biology 2018 12:90
    Content type: Research article Published on:

  10. There are large differences between men and women of child-bearing age in the expression level of 5 key enzymes in one-carbon metabolism almost certainly caused by the sex hormones. These male-female differenc...

    Authors: Farrah Sadre-Marandi, Thabat Dahdoul, Michael C. Reed and H. Frederik Nijhout
    Citation: BMC Systems Biology 2018 12:89
    Content type: Research article Published on:

  11. Recent results from single cell gene and protein regulation studies are starting to uncover the previously underappreciated fact that individual cells within a population exhibit high variability in the expres...

    Authors: Daniel Cook, Sirisha Achanta, Jan B. Hoek, Babatunde A. Ogunnaike and Rajanikanth Vadigepalli
    Citation: BMC Systems Biology 2018 12:86
    Content type: Research article Published on:

  12. A challenge of in vitro to in vivo extrapolation (IVIVE) is to predict the physical state of organisms exposed to chemicals in the environment from in vitro exposure assay data. Although toxicokinetic modeling...

    Authors: Michael A. Rowland, Hannah Wear, Karen H. Watanabe, Kurt A. Gust and Michael L. Mayo
    Citation: BMC Systems Biology 2018 12:81
    Content type: Research article Published on:

  13. The yeast-like fungi Pneumocystis, resides in lung alveoli and can cause a lethal infection known as Pneumocystis pneumonia (PCP) in hosts with impaired immune systems. Current therapies for PCP, such as trimetho...

    Authors: Guan-Sheng Liu, Richard Ballweg, Alan Ashbaugh, Yin Zhang, Joseph Facciolo, Melanie T. Cushion and Tongli Zhang
    Citation: BMC Systems Biology 2018 12:77
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Systems Biology 2019 13:40

  14. Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad compara...

    Authors: Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand V. Sastry, Erol Kavvas, Yara Seif, Larry Smarr and Bernhard O. Palsson
    Citation: BMC Systems Biology 2018 12:66
    Content type: Research article Published on:

  15. Cardiovascular diseases (CVD) represent one of the most important causes of morbidity and mortality worldwide. Innovative approaches to increase the understanding of the underpinnings of CVD promise to enhance...

    Authors: Frank Kramer, Steffen Just and Tanja Zeller
    Citation: BMC Systems Biology 2018 12:57
    Content type: Review Published on:

  16. Cell death as a result of ischemic injury triggers powerful mechanisms regulated by germline-encoded Pattern Recognition Receptors (PRRs) with shared specificity that recognize invading pathogens and endogenou...

    Authors: Elena Dimitrova, Leslie A. Caromile, Reinhard Laubenbacher and Linda H. Shapiro
    Citation: BMC Systems Biology 2018 12:50
    Content type: Research article Published on:

  17. Progesterone plays an essential role in mammalian ovulation. Although much is known about this process, the gene networks involved in ovulation have yet to be established. When analyze the mechanisms of ovulat...

    Authors: Fang Yang, Meng Wang, Baoyun Zhang, Wei Xiang, Ke Zhang, Mingxin Chu and Pingqing Wang
    Citation: BMC Systems Biology 2018 12:36
    Content type: Research article Published on:

  18. Blood transfusions are an important part of modern medicine, delivering approximately 85 million blood units to patients annually. Recently, the field of transfusion medicine has started to benefit from the “o...

    Authors: James T. Yurkovich, Aarash Bordbar, Ólafur E. Sigurjónsson and Bernhard O. Palsson
    Citation: BMC Systems Biology 2018 12:31
    Content type: Review Article Published on:

  20. With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors.

    Authors: Zhang Wang, Seda Arat, Michal Magid-Slav and James R. Brown
    Citation: BMC Systems Biology 2018 12:3
    Content type: Research article Published on:

  21. Dengue virus (DENV) is an increasing global health threat and associated with induction of both a long-lived protective immune response and immune-suppression. So far, the potency of treatment of DENV via anti...

    Authors: Mohamed Shahen, Zihu Guo, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao and Yonghua Wang
    Citation: BMC Systems Biology 2018 12:2
    Content type: Research Article Published on:

    The Correction to this article has been published in BMC Systems Biology 2018 12:21

  23. Osmanthus fragrans has been used as folk medicine for thousands of years. The extracts of Osmanthus fragrans flowers were reported to have various bioactivities including free radical ...

    Authors: Le Wang, Nana Tan, Jiayao Hu, Huan Wang, Dongzhu Duan, Lin Ma, Jian Xiao and Xiaoling Wang
    Citation: BMC Systems Biology 2017 11:144
    Content type: Research article Published on:

  24. Systems healthcare is a holistic approach to health premised on systems biology and medicine. The approach integrates data from molecules, cells, organs, the individual, families, communities, and the natural ...

    Authors: Massimo S. Fiandaca, Mark Mapstone, Elenora Connors, Mireille Jacobson, Edwin S. Monuki, Shaista Malik, Fabio Macciardi and Howard J. Federoff
    Citation: BMC Systems Biology 2017 11:142
    Content type: Review Published on:

  25. Estrogen is a vital hormone that regulates many biological functions within the body. These include roles in the development of the secondary sexual organs in both sexes, plus uterine angiogenesis and prolifer...

    Authors: Joanna H. Sier, Alfred E. Thumser and Nick J. Plant
    Citation: BMC Systems Biology 2017 11:141
    Content type: Research Article Published on:

  26. Polygenic diseases are usually caused by the dysfunction of multiple genes. Unravelling such disease genes is crucial to fully understand the genetic landscape of diseases on molecular level. With the advent o...

    Authors: Limei Lin, Tinghong Yang, Ling Fang, Jian Yang, Fan Yang and Jing Zhao
    Citation: BMC Systems Biology 2017 11:121
    Content type: Research Article Published on:

  27. Particle size is a key parameter for drug-delivery nanoparticle design. It is believed that the size of a nanoparticle may have important effects on its ability to overcome the transport barriers in biological...

    Authors: Mohammad Aminul Islam, Sutapa Barua and Dipak Barua
    Citation: BMC Systems Biology 2017 11:113
    Content type: Research Article Published on:

  28. Helicobacter Pylori (HP) is the most common risk factor for gastric cancer. Nearly half the world’s population is infected with HP, but only a small percentage of those develop significant pathology. The bacte...

    Authors: Richard Ballweg, Frederick Schozer, Kelsey Elliott, Alexander Kuhn, Logan Spotts, Eitaro Aihara and Tongli Zhang
    Citation: BMC Systems Biology 2017 11:111
    Content type: Research Article Published on:

  29. Drug resistance mediated by P-glycoprotein (P-gp) renders many cancer therapies ineffective. One P-gp substrate is the widely used chemotherapy drug paclitaxel. Co-administration of paclitaxel and another drug...

    Authors: Joe Bender, Jianwen Fang and Richard Simon
    Citation: BMC Systems Biology 2017 11:108
    Content type: Research Article Published on:

  30. Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, ke...

    Authors: Víctor A. López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F. Barrera and Rigoberto Ríos-Estepa
    Citation: BMC Systems Biology 2017 11:107
    Content type: Research Article Published on:

  31. Vitiligo is a long-term skin disease characterized by the loss of pigment in the skin. The current therapeutic approaches are limited. Although the anti-vitiligo mechanisms of Vernonia anthelmintica (L.) remain a...

    Authors: Ji Ye Wang, Hong Chen, Yin Yin Wang, Xiao Qin Wang, Han Ying Chen, Mei Zhang, Yun Tang and Bo Zhang
    Citation: BMC Systems Biology 2017 11:103
    Content type: Research Article Published on:

  32. One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this e...

    Authors: Cihan Oguz, Shurjo K. Sen, Adam R. Davis, Yi-Ping Fu, Christopher J. O’Donnell and Gary H. Gibbons
    Citation: BMC Systems Biology 2017 11:99
    Content type: Research Article Published on:

  33. Cells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organi...

    Authors: Niklas Hartung, Uwe Benary, Jana Wolf and Bente Kofahl
    Citation: BMC Systems Biology 2017 11:98
    Content type: Research Article Published on:

  34. 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...

    Authors: Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara L. Kinzer-Ursem, David M. Umulis and Ann E. Rundell
    Citation: BMC Systems Biology 2017 11:78
    Content type: Research Article Published on:

  35. 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...

    Authors: Ranjita Dutta Roy, Christian Rosenmund and Melanie I. Stefan
    Citation: BMC Systems Biology 2017 11:74
    Content type: Research Article Published on:

  36. 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...

    Authors: Kerri-Ann Norton, Travis Wallace, Niranjan B. Pandey and Aleksander S. Popel
    Citation: BMC Systems Biology 2017 11:68
    Content type: Research Article Published on:

  37. 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...

    Authors: Anna Huhtinen, Vesa Hongisto, Asta Laiho, Eliisa Löyttyniemi, Dirk Pijnenburg and Mika Scheinin
    Citation: BMC Systems Biology 2017 11:65
    Content type: Research Article Published on:

  38. 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 ...

    Authors: Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof and Rafael J. Najmanovich
    Citation: BMC Systems Biology 2017 11:60
    Content type: Research article Published on:

  39. 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...

    Authors: Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan
    Citation: BMC Systems Biology 2017 11:51
    Content type: Research Article Published on:

  40. Physiologically-based toxicokinetic (PBTK) models are often developed to facilitate in vitro to in vivo extrapolation (IVIVE) using a top-down, compartmental approach, favoring architectural simplicity over ph...

    Authors: Michael A. Rowland, Edward J. Perkins and Michael L. Mayo
    Citation: BMC Systems Biology 2017 11:35
    Content type: Research article Published on:

  41. 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...

    Authors: 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…
    Citation: BMC Systems Biology 2017 11:31
    Content type: Research article Published on:

  42. 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...

    Authors: Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J. Waardenberg, Kentu Lassiter and Nicholas J. Hudson
    Citation: BMC Systems Biology 2017 11:29
    Content type: Research article Published on:

  43. 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...

    Authors: Sara Saheb Kashaf, Claudio Angione and Pietro Lió
    Citation: BMC Systems Biology 2017 11:25
    Content type: Research Article Published on:

  44. 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...

    Authors: Wenrui Hao and Avner Friedman
    Citation: BMC Systems Biology 2016 10:108
    Content type: Research Article Published on:

  45. Progesterone promotes uterine relaxation and is essential for the maintenance of pregnancy. Withdrawal of progesterone activity and increased inflammation within the uterine tissues are key triggers for partur...

    Authors: Douglas Brubaker, Alethea Barbaro, Mark R. Chance and Sam Mesiano
    Citation: BMC Systems Biology 2016 10:79
    Content type: Research Article Published on:

  46. 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...

    Authors: Peter Andorfer, Alexander Heuwieser, Andreas Heinzel, Arno Lukas, Bernd Mayer and Paul Perco
    Citation: BMC Systems Biology 2016 10:33
    Content type: Research article Published on:

  47. 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...

    Authors: 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
    Citation: BMC Systems Biology 2016 10:26
    Content type: Research article Published on:

  48. 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...

    Authors: Eleftherios Ouzounoglou, Dimitra Dionysiou and Georgios S. Stamatakos
    Citation: BMC Systems Biology 2016 10:23
    Content type: Research article Published on:

  50. 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...

    Authors: Dan Tian, Isaiah Mitchell and Pamela K. Kreeger
    Citation: BMC Systems Biology 2016 10:15
    Content type: Research article Published on:

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