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  1. Bistable behaviors are prevalent in cell signaling and can be modeled by ordinary differential equations (ODEs) with kinetic parameters. A bistable switch has recently been found to regulate the activation of ...

    Authors: Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob K. White, Hanry Yu and Lisa Tucker-Kellogg
    Citation: BMC Systems Biology 2017 11(Suppl 7):136
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  2. Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of protein...

    Authors: Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi and Tzong-Yi Lee
    Citation: BMC Systems Biology 2017 11(Suppl 7):132
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  3. Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12–100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacte...

    Authors: Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee
    Citation: BMC Systems Biology 2017 11(Suppl 7):131
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  4. Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. H...

    Authors: Qingping Liu, Jiahao Wang, Yan Zhu and Yongqun He
    Citation: BMC Systems Biology 2017 11(Suppl 7):130
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 7

  5. 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:

  6. 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:

  8. Traditional drug identification methods follow the “one drug-one target” thought. But those methods ignore the natural characters of human diseases. To overcome this limitation, many identification methods of ...

    Authors: Jin-Xing Liu, Dong-Qin Wang, Chun-Hou Zheng, Ying-Lian Gao, Sha-Sha Wu and Jun-Liang Shang
    Citation: BMC Systems Biology 2017 11(Suppl 6):119
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  9. Positive semi-definiteness is a critical property in kernel methods for Support Vector Machine (SVM) by which efficient solutions can be guaranteed through convex quadratic programming. However, a lot of simil...

    Authors: Hao Jiang, Wai-Ki Ching, Yushan Qiu and Xiao-Qing Cheng
    Citation: BMC Systems Biology 2017 11(Suppl 6):115
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  10. Mining frequent gene regulation sequential patterns in time course microarray datasets is an important mining task in bioinformatics. Although finding such patterns are of paramount important for studying a di...

    Authors: Morteza Zihayat, Heidar Davoudi and Aijun An
    Citation: BMC Systems Biology 2017 11(Suppl 6):109
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  11. Probabilistic Boolean networks (PBNs) have been proposed for analyzing external control in gene regulatory networks with incorporation of uncertainty. A context-sensitive PBN with perturbation (CS-PBNp), exten...

    Authors: Ou Wei, Zonghao Guo, Yun Niu and Wenyuan Liao
    Citation: BMC Systems Biology 2017 11(Suppl 6):104
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  13. Drug side effects are one of main concerns in the drug discovery, which gains wide attentions. Investigating drug side effects is of great importance, and the computational prediction can help to guide wet exp...

    Authors: Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu and Xining Zhang
    Citation: BMC Systems Biology 2017 11(Suppl 6):101
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  14. Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment ...

    Authors: Quan Zou, Shixiang Wan, Xiangxiang Zeng and Zhanshan Sam Ma
    Citation: BMC Systems Biology 2017 11(Suppl 6):100
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  15. Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple e...

    Authors: Daniel Schlauch, Kimberly Glass, Craig P. Hersh, Edwin K. Silverman and John Quackenbush
    Citation: BMC Systems Biology 2017 11:139
    Content type: Research Article Published on:

  16. Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tiss...

    Authors: Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah J. Anderson, Jonathan Gorky, Prasad Dhurjati and Deni S. Galileo
    Citation: BMC Systems Biology 2017 11:124
    Content type: Methodology Article Published on:

  17. State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell...

    Authors: Roland Prielhofer, Juan J. Barrero, Stefanie Steuer, Thomas Gassler, Richard Zahrl, Kristin Baumann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser and Hans Marx
    Citation: BMC Systems Biology 2017 11:123
    Content type: Methodology Article Published on:

  18. Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean mo...

    Authors: Parul Maheshwari and Réka Albert
    Citation: BMC Systems Biology 2017 11:122
    Content type: Research Article Published on:

  19. 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:

  22. In favorable conditions bacterial doubling time is less than 20 min, shorter than DNA replication time. In E. coli a single round of genome replication lasts about 40 min and it must be accomplished about 20 min ...

    Authors: Joanna Jaruszewicz-Błońska and Tomasz Lipniacki
    Citation: BMC Systems Biology 2017 11:117
    Content type: Research Article Published on:

  23. Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite ...

    Authors: Kenneth A. Barr, Carlos Martinez, Jennifer R. Moran, Ah-Ram Kim, Alexandre F. Ramos and John Reinitz
    Citation: BMC Systems Biology 2017 11:116
    Content type: Research Article Published on:

  24. The complexity of metabolic networks can make the origin and impact of changes in central metabolism occurring during diseases difficult to understand. Computer simulations can help unravel this complexity, an...

    Authors: Anthony C. Smith, Filmon Eyassu, Jean-Pierre Mazat and Alan J. Robinson
    Citation: BMC Systems Biology 2017 11:114
    Content type: Research Article Published on:

  25. 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:

  26. The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even wi...

    Authors: S. Cardinale and G. Cambray
    Citation: BMC Systems Biology 2017 11:112
    Content type: Research Article Published on:

  27. 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:

  32. The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, infer...

    Authors: Ulysse Herbach, Arnaud Bonnaffoux, Thibault Espinasse and Olivier Gandrillon
    Citation: BMC Systems Biology 2017 11:105
    Content type: Research Article Published on:

  33. 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:

  34. 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:

  35. 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:

  37. Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Authors: Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph
    Citation: BMC Systems Biology 2017 11:96
    Content type: Research Article Published on:

  38. Biochemical oscillations play an important role in maintaining physiological and cellular homeostasis in biological systems. The frequency and amplitude of oscillations are regulated to properly adapt to envir...

    Authors: Jun Hyuk Kang and Kwang-Hyun Cho
    Citation: BMC Systems Biology 2017 11:95
    Content type: Research Article Published on:

  40. Previous studies suggested that cancer cells possess traits reminiscent of the biological mechanisms ascribed to normal embryonic stem cells (ESCs) regulated by MYC and Polycomb repressive complex 2 (PRC2). Se...

    Authors: Xinan Holly Yang, Fangming Tang, Jisu Shin and John M. Cunningham
    Citation: BMC Systems Biology 2017 11(Suppl 5):92
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  41. Molecular mechanisms of the functional alteration of hematopoietic stem cells (HSCs) in leukemic environment attract intensive research interests. As known in previous researches, Maff and Egr3 are two important ...

    Authors: Rudong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu and Lei Liu
    Citation: BMC Systems Biology 2017 11(Suppl 5):91
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  42. Adult hippocampal neurogenesis, the process of formation of new neurons, occurs throughout life in the hippocampus. New neurons have been associated with learning and memory as well as mood control, and impair...

    Authors: Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel and Mirjana Maletic-Savatic
    Citation: BMC Systems Biology 2017 11(Suppl 5):90
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  43. The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain prote...

    Authors: Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang and Yunlong Liu
    Citation: BMC Systems Biology 2017 11(Suppl 5):89
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  44. Between December 8–10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, on...

    Authors: W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao and Zhangdong Liu
    Citation: BMC Systems Biology 2017 11(Suppl 5):88
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  45. The discovery of novel anticancer drugs is critical for the pharmaceutical research and development, and patient treatment. Repurposing existing drugs that may have unanticipated effects as potential candidate...

    Authors: Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu and Hua Xu
    Citation: BMC Systems Biology 2017 11(Suppl 5):87
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  46. Due to advances in next generation sequencing technologies and corresponding reductions in cost, it is now attainable to investigate genome-wide gene expression and variants at a patient-level, so as to better...

    Authors: Haoyang Wu, Elise Miller, Denethi Wijegunawardana, Kelly Regan, Philip R.O. Payne and Fuhai Li
    Citation: BMC Systems Biology 2017 11(Suppl 5):86
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  47. Affinity purification-mass spectrometry (AP-MS) has been widely used for generating bait-prey data sets so as to identify underlying protein-protein interactions and protein complexes. However, the AP-MS data ...

    Authors: Bo Tian, Can Zhao, Feiyang Gu and Zengyou He
    Citation: BMC Systems Biology 2017 11(Suppl 4):82
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  48. Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despit...

    Authors: Changhe Fu, Su Deng, Guangxu Jin, Xinxin Wang and Zu-Guo Yu
    Citation: BMC Systems Biology 2017 11(Suppl 4):81
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  49. Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally ref...

    Authors: Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang and Fei Guo
    Citation: BMC Systems Biology 2017 11(Suppl 4):79
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

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