Skip to content


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.

Page 2 of 4

  1. Content type: Software

    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

    Published on:

  2. Content type: Research article

    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

    Published on:

  3. Content type: Research article

    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

    Published on:

  4. Content type: Research article

    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

    Published on:

  5. Content type: Methodology article

    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

    Published on:

  6. Content type: Research article

    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

    Published on:

  7. Content type: Research article

    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

    Published on:

  8. Content type: Research article

    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

    Published on:

  9. Content type: Research article

    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

    Published on:

  10. Content type: Research article

    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

    Published on:

  11. Content type: Research article

    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

    Published on:

  12. Content type: Methodology article

    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

    Published on:

  13. Content type: Research article

    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

    Published on:

  14. Content type: Research article

    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

    Published on:

  15. Content type: Research article

    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

    Published on:

  16. Content type: Research article

    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

    Published on:

  17. Content type: Database

    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

    Published on:

  18. Content type: Research article

    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

    Published on:

  19. Content type: Research article

    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

    Published on:

  20. Content type: Research article

    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

    Published on:

  21. Content type: Research article

    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

    Published on:

  22. Content type: Methodology article

    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

    Published on:

  23. Content type: Research article

    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

    Published on:

  24. Content type: Research article

    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

    Published on:

  25. Content type: Research article

    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

    Published on:

  26. Content type: Research article

    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

    Published on:

  27. Content type: Research article

    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

    Published on:

  28. Content type: Research article

    Abnormal synchronization of brain oscillations is found to be associated with various core symptoms of schizophrenia. However, the underlying mechanism of this association remains yet to be elucidated.

    Authors: Kyungchul Noh, Kyung Soon Shin, Dongkwan Shin, Jae Yeon Hwang, June Sic Kim, Joon Hwan Jang, Chun Kee Chung, Jun Soo Kwon and Kwang-Hyun Cho

    Citation: BMC Systems Biology 2013 7:30

    Published on:

  29. Content type: Research article

    Cancer is a complex disease where molecular mechanism remains elusive. A systems approach is needed to integrate diverse biological information for the prognosis and therapy risk assessment using mechanistic a...

    Authors: Gaurav Kumar, Edmond J Breen and Shoba Ranganathan

    Citation: BMC Systems Biology 2013 7:12

    Published on:

  30. Content type: Research article

    Palmitic acid, the most common saturated free fatty acid, has been implicated in ER (endoplasmic reticulum) stress-mediated apoptosis. This lipoapotosis is dependent, in part, on the upregulation of the activa...

    Authors: Hyunju Cho, Ming Wu, Linxia Zhang, Ryan Thompson, Aritro Nath and Christina Chan

    Citation: BMC Systems Biology 2013 7:9

    Published on:

  31. Content type: Methodology article

    When mathematical modelling is applied to many different application areas, a common task is the estimation of states and parameters based on measurements. With this kind of inference making, uncertainties in ...

    Authors: Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels and Mats Jirstrand

    Citation: BMC Systems Biology 2013 7:8

    Published on:

  32. Content type: Research article

    Lineage specific differentiation of human embryonic stem cells (hESCs) is largely mediated by specific growth factors and extracellular matrix molecules. Growth factors initiate a cascade of signals which cont...

    Authors: Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Ang Zhang, Alejandro Soto-Gutiérrez and Ipsita Banerjee

    Citation: BMC Systems Biology 2012 6:154

    Published on:

  33. Content type: Research article

    Torcetrapib, a cholesteryl ester transfer protein (CETP) inhibitor which raises high-density lipoprotein (HDL) cholesterol and reduces low-density lipoprotein (LDL) cholesterol level, has been documented to in...

    Authors: Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan and Xuejun Li

    Citation: BMC Systems Biology 2012 6:152

    Published on:

  34. Content type: Research article

    5-lipoxygenase (5-LO) is a key enzyme in the synthesis of leukotrienes and 5-Oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid (oxoETE). These inflammatory signaling molecules play a role in the pathology of asthma and ...

    Authors: Tatiana A Karelina, Kirill V Zhudenkov, Oleg O Demin, Dmitry V Svetlichny, Balaji Agoram, David Fairman and Oleg V Demin

    Citation: BMC Systems Biology 2012 6:141

    Published on:

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)


    Social Media Impact
    523 mentions