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  1. Content type: Software

    The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary r...

    Authors: Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada and Ken Kurokawa

    Citation: BMC Systems Biology 2018 12(Suppl 2):30

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  2. Content type: Research

    Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental con...

    Authors: Abha Belorkar, Rajanikanth Vadigepalli and Limsoon Wong

    Citation: BMC Systems Biology 2018 12(Suppl 2):28

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  3. Content type: Review Article

    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

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  4. Content type: Research Article

    Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we presen...

    Authors: Jinmyung Jung, Mijin Kwon, Sunghwa Bae, Soorin Yim and Doheon Lee

    Citation: BMC Systems Biology 2018 12:26

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  5. Content type: Research Article

    The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environ...

    Authors: Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson and Jonathan M. Monk

    Citation: BMC Systems Biology 2018 12:25

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  6. Content type: Correction

    After publication of the article [1], it has been brought to our attention that an author’s name was spelt incorrectly in the original published article. Yonghua Wang was previously spelt “Yonghua Wan”. This h...

    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 12:21

    Published on:

    The original article was published in BMC Systems Biology 2018 12:2

  7. Content type: Research article

    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

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  8. Content type: Research Article

    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

    Published on:

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

  9. Content type: Methodology Article

    Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substanti...

    Authors: Ian Vernon, Junli Liu, Michael Goldstein, James Rowe, Jen Topping and Keith Lindsey

    Citation: BMC Systems Biology 2018 12:1

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  10. Content type: Research Article

    Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate ...

    Authors: Rakesh Pandey, Judith P. Armitage and George H. Wadhams

    Citation: BMC Systems Biology 2017 11:146

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  11. Content type: Research article

    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

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  12. Content type: Research

    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

    Published on:

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

  13. Content type: Research

    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

    Published on:

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

  14. Content type: Research

    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

    Published on:

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

  15. Content type: Research

    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

    Published on:

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

  16. Content type: Software

    We propose OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets, based on a consensus approach. The method generates consensus hypotheses for metabolic engineering applications by combining severa...

    Authors: András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie-France Sagot, Jan Marienhagen and Susana Vinga

    Citation: BMC Systems Biology 2017 11:143

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  17. Content type: Research

    Biological networks consisting of molecular components and interactions are represented by a graph model. There have been some studies based on that model to analyze a relationship between structural character...

    Authors: Cong-Doan Truong and Yung-Keun Kwon

    Citation: BMC Systems Biology 2017 11(Suppl 7):125

    Published on:

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

  18. Content type: Research

    Cell fate regulation directly affects tissue homeostasis and human health. Research on cell fate decision sheds light on key regulators, facilitates understanding the mechanisms, and suggests novel strategies ...

    Authors: Lichun Ma and Jie Zheng

    Citation: BMC Systems Biology 2017 11(Suppl 7):126

    Published on:

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

  19. Content type: Research

    Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signat...

    Authors: Hao Jiang, Wai-Ki Ching, Wai-Shun Cheung, Wenpin Hou and Hong Yin

    Citation: BMC Systems Biology 2017 11(Suppl 7):138

    Published on:

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

  20. Content type: Research

    Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is r...

    Authors: Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang and Tzong-Yi Lee

    Citation: BMC Systems Biology 2017 11(Suppl 7):137

    Published on:

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

  21. Content type: Research

    Identification of novel gene-gene relations is a crucial issue to understand system-level biological phenomena. To this end, many methods based on a correlation analysis of gene expressions or structural analy...

    Authors: Maulida Mazaya, Hung-Cuong Trinh and Yung-Keun Kwon

    Citation: BMC Systems Biology 2017 11(Suppl 7):133

    Published on:

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

  22. Content type: Research

    Effectively predicting protein complexes not only helps to understand the structures and functions of proteins and their complexes, but also is useful for diagnosing disease and developing new drugs. Up to now...

    Authors: Ying Xu, Jiaogen Zhou, Shuigeng Zhou and Jihong Guan

    Citation: BMC Systems Biology 2017 11(Suppl 7):135

    Published on:

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

  23. Content type: Research

    In recent years, the integration of ‘omics’ technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the ...

    Authors: Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng and Lei Shi

    Citation: BMC Systems Biology 2017 11(Suppl 7):127

    Published on:

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

  24. Content type: Research

    Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and co...

    Authors: Shun Asami, Daisuke Kiga and Akihiko Konagaya

    Citation: BMC Systems Biology 2017 11(Suppl 7):129

    Published on:

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

  25. Content type: Research

    Detecting causality for short time-series data such as gene regulation data is quite important but it is usually very difficult. This can be used in many fields especially in biological systems. Recently, seve...

    Authors: Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu and Luonan Chen

    Citation: BMC Systems Biology 2017 11(Suppl 7):128

    Published on:

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

  26. Content type: Research

    Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is...

    Authors: Daniel Trejo Banos, Pauline Trébulle and Mohamed Elati

    Citation: BMC Systems Biology 2017 11(Suppl 7):134

    Published on:

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

  27. Content type: Review

    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

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  28. Content type: Research Article

    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

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  29. Content type: Methodology

    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

    Published on:

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

  30. Content type: Research

    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

    Published on:

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

  31. Content type: Research

    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

    Published on:

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

  32. Content type: Research

    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

    Published on:

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

  33. Content type: Methodology

    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

    Published on:

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

  34. Content type: Research

    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

    Published on:

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

  35. Content type: Research Article

    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

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  36. Content type: Methodology Article

    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

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  37. Content type: Methodology Article

    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

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  38. Content type: Research Article

    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

    Published on:

  39. Content type: Research Article

    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

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  40. Content type: Research Article

    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

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  41. Content type: Research Article

    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

    Published on:

  42. Content type: Research Article

    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

    Published on:

  43. Content type: Research Article

    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

    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)

    Usage 
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    Social Media Impact
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