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  1. Time course measurement of single molecules on a cell surface provides detailed information about the dynamics of the molecules that would otherwise be inaccessible. To extract the quantitative information, si...

    Authors: Shunsuke Teraguchi and Yutaro Kumagai
    Citation: BMC Systems Biology 2018 12(Suppl 1):15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  2. Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires...

    Authors: Hui Yu, Kui-Tao Mao, Jian-Yu Shi, Hua Huang, Zhi Chen, Kai Dong and Siu-Ming Yiu
    Citation: BMC Systems Biology 2018 12(Suppl 1):14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  3. Alzheimer’s disease (AD) is a progressive neurological disorder, recognized as the most common cause of dementia affecting people aged 65 and above. AD is characterized by an increase in amyloid metabolism, an...

    Authors: Bobby Ranjan, Ket Hing Chong and Jie Zheng
    Citation: BMC Systems Biology 2018 12(Suppl 1):10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  4. Signaling pathways can be reconstructed by identifying ‘effect types’ (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of ‘directions’ (i.e. upstream/downstream) a...

    Authors: Soorin Yim, Hasun Yu, Dongjin Jang and Doheon Lee
    Citation: BMC Systems Biology 2018 12(Suppl 1):9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  5. Breast cancer and ovarian cancer are hormone driven and are known to have some predisposition genes in common such as the two well known cancer genes BRCA1 and BRCA2. The objective of this study is to compare ...

    Authors: Shuqin Zhang
    Citation: BMC Systems Biology 2018 12(Suppl 1):8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  6. Traditional drug discovery methods focused on the efficacy of drugs rather than their toxicity. However, toxicity and/or lack of efficacy are produced when unintended targets are affected in metabolic networks...

    Authors: Yushan Qiu, Hao Jiang, Wai-Ki Ching and Xiaoqing Cheng
    Citation: BMC Systems Biology 2018 12(Suppl 1):7
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  7. A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding moti...

    Authors: Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher and Tamer Kahveci
    Citation: BMC Systems Biology 2018 12(Suppl 1):6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  8. 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:

  9. Controlling complex molecular regulatory networks is getting a growing attention as it can provide a systematic way of driving any cellular state to a desired cell phenotypic state. A number of recent studies ...

    Authors: Sang-Mok Choo, Byunghyun Ban, Jae Il Joo and Kwang-Hyun Cho
    Citation: BMC Systems Biology 2018 12:49
    Content type: Research article Published on:

  10. Kinase inhibition in the mitogen activated protein kinase (MAPK) pathway is a standard therapy for cancer patients with activating BRAF mutations. However, the anti-tumorigenic effect and clinical benefit are ...

    Authors: Helma Zecena, Daniel Tveit, Zi Wang, Ahmed Farhat, Parvita Panchal, Jing Liu, Simar J. Singh, Amandeep Sanghera, Ajay Bainiwal, Shuan Y. Teo, Frank L. Meyskens Jr, Feng Liu-Smith and Fabian V. Filipp
    Citation: BMC Systems Biology 2018 12:33
    Content type: Research Article Published on:

  11. 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:

  12. Existing experimental data have shown hypoxia to be an important factor affecting the proliferation of mesenchymal stromal cells (MSCs), but the contrasting observations made at various hypoxic levels raise th...

    Authors: Bo Zhang, Hua Ye and Aidong Yang
    Citation: BMC Systems Biology 2018 12:35
    Content type: Research article Published on:

  13. Melanoma can be diagnosed by identifying nests of cells on the skin surface. Understanding the processes that drive nest formation is important as these processes could be potential targets for new cancer drug...

    Authors: Parvathi Haridas, Alexander P. Browning, Jacqui A. McGovern, D. L. Sean McElwain and Matthew J. Simpson
    Citation: BMC Systems Biology 2018 12:34
    Content type: Research article Published on:

  14. The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distanc...

    Authors: Bertrand Miannay, Stéphane Minvielle, Florence Magrangeas and Carito Guziolowski
    Citation: BMC Systems Biology 2018 12(Suppl 3):32
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  15. Decomposing a protein-protein interaction network (PPI network) into non-overlapping clusters or communities, sometimes called “network modules,” is an important way to explore functional roles of sets of gene...

    Authors: Sarah Hall-Swan, Jake Crawford, Rebecca Newman and Lenore J. Cowen
    Citation: BMC Systems Biology 2018 12(Suppl 3):24
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

    The Retraction Note to this article has been published in BMC Systems Biology 2018 12:113

  16. Expression-based phenotype classification using either microarray or RNA-Seq measurements suffers from a lack of specificity because pathway timing is not revealed and expressions are averaged across groups of...

    Authors: Alireza Karbalayghareh, Ulisses Braga-Neto and Edward R. Dougherty
    Citation: BMC Systems Biology 2018 12(Suppl 3):23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  17. 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
    Content type: Software Published on:

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

  18. Regeneration is an important biological process for the restoration of organ mass, structure, and function after damage, and involves complex bio-physiological mechanisms including cell differentiation and imm...

    Authors: Fang-Yu Liu, Te-Cheng Hsu, Patrick Choong, Min-Hsuan Lin, Yung-Jen Chuang, Bor-Sen Chen and Che Lin
    Citation: BMC Systems Biology 2018 12(Suppl 2):29
    Content type: Research Published on:

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

  19. 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
    Content type: Research Published on:

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

  20. Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Pan...

    Authors: Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim and Woosuk Jung
    Citation: BMC Systems Biology 2018 12(Suppl 2):27
    Content type: Research Published on:

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

  21. Identifying gene regulatory networks is an important task for understanding biological systems. Time-course measurement data became a valuable resource for inferring gene regulatory networks. Various methods h...

    Authors: Sungjoon Park, Jung Min Kim, Wonho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik-Soon Jang and Jaewoo Kang
    Citation: BMC Systems Biology 2018 12(Suppl 2):20
    Content type: Research Published on:

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

  22. With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it...

    Authors: Minseok Kwon, Sangseob Leem, Joon Yoon and Taesung Park
    Citation: BMC Systems Biology 2018 12(Suppl 2):19
    Content type: Research Published on:

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

  23. Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple...

    Authors: Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu and Xuequn Shang
    Citation: BMC Systems Biology 2018 12(Suppl 2):18
    Content type: Research Published on:

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

  24. Cell surface proteins have provided useful targets and biomarkers for advanced cancer therapies. The recent clinical success of antibody-drug conjugates (ADCs) highlights the importance of finding selective su...

    Authors: Yourae Hong, Choa Park, Nayoung Kim, Juyeon Cho, Sung Ung Moon, Jongmin Kim, Euna Jeong and Sukjoon Yoon
    Citation: BMC Systems Biology 2018 12(Suppl 2):17
    Content type: Research Published on:

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

  25. Drug combination therapy, which is considered as an alternative to single drug therapy, can potentially reduce resistance and toxicity, and have synergistic efficacy. As drug combination therapies are widely u...

    Authors: Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee and Jaewoo Kang
    Citation: BMC Systems Biology 2018 12(Suppl 2):16
    Content type: Research Published on:

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

  26. One of the crucial steps toward understanding the associations among molecular interactions, pathways, and diseases in a cell is to investigate detailed atomic protein-protein interactions (PPIs) in the struct...

    Authors: Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yu-Yao Tseng and Jinn-Moon Yang
    Citation: BMC Systems Biology 2018 12(Suppl 2):13
    Content type: Research Published on:

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

  27. Recently, there have been several attempts to produce long-chain dicarboxylic acids (DCAs) in various microbial hosts. Of these, Yarrowia lipolytica has great potential due to its oleaginous characteristics and u...

    Authors: Pranjul Mishra, Na-Rae Lee, Meiyappan Lakshmanan, Minsuk Kim, Byung-Gee Kim and Dong-Yup Lee
    Citation: BMC Systems Biology 2018 12(Suppl 2):12
    Content type: Research Published on:

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

  28. 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:

  29. 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
    Content type: Research Article Published on:

  30. 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
    Content type: Research Article Published on:

  32. 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
    Content type: Correction Published on:

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

  34. 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:

  35. 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

  36. 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
    Content type: Methodology Article Published on:

  37. 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
    Content type: Research Article Published on:

  39. 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:

  40. 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
    Content type: Software Published on:

  41. 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
    Content type: Research Published on:

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

  42. 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
    Content type: Research Published on:

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

  43. 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
    Content type: Research Published on:

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

  44. 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
    Content type: Research Published on:

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

  45. 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
    Content type: Research Published on:

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

  46. 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
    Content type: Research Published on:

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

  47. 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
    Content type: Research Published on:

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

  48. 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
    Content type: Research Published on:

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

  49. 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
    Content type: Research Published on:

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

  50. 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
    Content type: Research Published on:

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

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