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  1. Content type: Methodology article

    Metabolic reactions are chemical transformations commonly catalyzed by enzymes. In recent years, the explosion of genomic data and individual experimental characterizations have contributed to the construction...

    Authors: Carlos Vazquez-Hernandez, Antonio Loza, Esteban Peguero-Sanchez, Lorenzo Segovia and Rosa-Maria Gutierrez-Rios

    Citation: BMC Systems Biology 2018 12:63

    Published on:

  2. Content type: Research Article

    Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-‘omics datasets on complex diseases are becoming more readily available and there is a need to set s...

    Authors: Bertrand De Meulder, Diane Lefaudeux, Aruna T. Bansal, Alexander Mazein, Amphun Chaiboonchoe, Hassan Ahmed, Irina Balaur, Mansoor Saqi, Johann Pellet, Stéphane Ballereau, Nathanaël Lemonnier, Kai Sun, Ioannis Pandis, Xian Yang, Manohara Batuwitage, Kosmas Kretsos…

    Citation: BMC Systems Biology 2018 12:60

    Published on:

  3. Content type: Software

    Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human C...

    Authors: Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Göttgens and Jasmin Fisher

    Citation: BMC Systems Biology 2018 12:59

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  4. Content type: Review

    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

    Published on:

  5. Content type: Research

    Differential gene expression analysis using RNA-seq data is a popular approach for discovering specific regulation mechanisms under certain environmental settings. Both gene ontology (GO) and KEGG pathway enri...

    Authors: Kuo-Sheng Hung, Chung-Chi Hsiao, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou, Wen-Der Wang and Yet-Ran Chen

    Citation: BMC Systems Biology 2018 12(Suppl 4):45

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  6. Content type: Research

    Essential proteins are necessary for the survival and development of cells. The identification of essential proteins can help to understand the minimal requirements for cellular life and it also plays an impor...

    Authors: Xiujuan Lei, Ming Fang, Fang-Xiang Wu and Luonan Chen

    Citation: BMC Systems Biology 2018 12(Suppl 4):46

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  7. Content type: Research

    WD40 repeat proteins constitute one of the largest families in eukaryotes, and widely participate in various fundamental cellular processes by interacting with other molecules. Based on individual WD40 protein...

    Authors: Xu-Dong Zou, Ke An, Yun-Dong Wu and Zhi-Qiang Ye

    Citation: BMC Systems Biology 2018 12(Suppl 4):41

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  8. Content type: Research

    Promoter is an important sequence regulation element, which is in charge of gene transcription initiation. In prokaryotes, σ70 promoters regulate the transcription of most genes. The promoter recognition has been...

    Authors: Wenying He, Cangzhi Jia, Yucong Duan and Quan Zou

    Citation: BMC Systems Biology 2018 12(Suppl 4):44

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  9. Content type: Research

    Finding potential drug targets is a crucial step in drug discovery and development. Recently, resources such as the Library of Integrated Network-Based Cellular Signatures (LINCS) L1000 database provide gene e...

    Authors: Limin Li, Xiao He and Karsten Borgwardt

    Citation: BMC Systems Biology 2018 12(Suppl 4):55

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  10. Content type: Research

    Diamond-Blackfan anemia (DBA) is a congenital erythroid aplasia that usually presents in infancy. In order to explore the molecular mechanisms of wild and mutated samples from DBA patients were exposed to bioi...

    Authors: Abbas Khan, Arif Ali, Muhammad Junaid, Chang Liu, Aman Chandra Kaushik, William C. S. Cho and Dong-Qing Wei

    Citation: BMC Systems Biology 2018 12(Suppl 4):39

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  11. Content type: Research

    Identifying complexes from PPI networks has become a key problem to elucidate protein functions and identify signal and biological processes in a cell. Proteins binding as complexes are important roles of life...

    Authors: Zehua Zhang, Jian Song, Jijun Tang, Xinying Xu and Fei Guo

    Citation: BMC Systems Biology 2018 12(Suppl 4):40

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  12. Content type: Research

    Rice (Oryza sativa) is one of the most important grain crops, which serves as food source for nearly half of the world population. The study of rice development process as well as related strategies for productio...

    Authors: Fangzhou Shen, Xueting Wu, Luoxi Shi, Hang Zhang, Yangmin Chen, Xiaoquan Qi, Zhuo Wang and Xuan Li

    Citation: BMC Systems Biology 2018 12(Suppl 4):47

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  13. Content type: Research

    One central building block of population genetics is the fixation probability. It is a probabilistic understanding of the eventual fate of new mutations. Moreover, the fixation probability of new beneficial mu...

    Authors: Fangshu Cui and Bo Yuan

    Citation: BMC Systems Biology 2018 12(Suppl 4):48

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  14. Content type: Research

    Uncertainties exist in many biological systems, which can be classified as random uncertainties and fuzzy uncertainties. The former can usually be dealt with using stochastic methods, while the latter have to ...

    Authors: Fei Liu, Siyuan Chen, Monika Heiner and Hengjie Song

    Citation: BMC Systems Biology 2018 12(Suppl 4):42

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  15. Content type: Research

    Gastric Carcinoma is one of the most lethal cancer around the world, and is also the most common cancers in Eastern Asia. A lot of differentially expressed genes have been detected as being associated with Gas...

    Authors: Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li and Yuan-Yuan Li

    Citation: BMC Systems Biology 2018 12(Suppl 4):51

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  16. Content type: Research

    The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent stu...

    Authors: Jialu Hu, Yiqun Gao, Yan Zheng and Xuequn Shang

    Citation: BMC Systems Biology 2018 12(Suppl 4):54

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  17. Content type: Research

    The haematopoietic lineages with leukaemia lineages are considered in this paper. In particular, we mainly consider that haematopoietic lineages are tightly controlled by negative feedback inhibition of end-pr...

    Authors: Jianfeng Jiao, Min Luo and Ruiqi Wang

    Citation: BMC Systems Biology 2018 12(Suppl 4):43

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  18. Content type: Research

    Efficient computational recognition and segmentation of target organ from medical images are foundational in diagnosis and treatment, especially about pancreas cancer. In practice, the diversity in appearance ...

    Authors: Min Fu, Wenming Wu, Xiafei Hong, Qiuhua Liu, Jialin Jiang, Yaobin Ou, Yupei Zhao and Xinqi Gong

    Citation: BMC Systems Biology 2018 12(Suppl 4):56

    Published on:

    This article is part of a Supplement: Volume 12 Supplement 4

  19. Content type: Research Article

    A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even sm...

    Authors: Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer and Dagmar Waltemath

    Citation: BMC Systems Biology 2018 12:53

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  20. Content type: Research

    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

    Published on:

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

  21. Content type: Research

    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

    Published on:

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

  22. Content type: Research

    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

    Published on:

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

  23. Content type: Research

    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

    Published on:

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

  24. Content type: Research

    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

    Published on:

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

  25. Content type: Research

    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

    Published on:

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

  26. Content type: Research article

    For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) with...

    Authors: Alessandra Ordinelli, Nicola Bernabò, Massimiliano Orsini, Mauro Mattioli and Barbara Barboni

    Citation: BMC Systems Biology 2018 12:52

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  27. Content type: Research

    25% of breast cancer patients suffer from aggressive HER2-positive tumours that are characterised by overexpression of the HER2 protein or by its increased tyrosine kinase activity. Herceptin is a major drug u...

    Authors: Petronela Buiga, Ari Elson, Lydia Tabernero and Jean-Marc Schwartz

    Citation: BMC Systems Biology 2018 12(Suppl 1):11

    Published on:

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

  28. Content type: Research

    Current technology has demonstrated that mutation and deregulation of non-coding RNAs (ncRNAs) are associated with diverse human diseases and important biological processes. Therefore, developing a novel compu...

    Authors: Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu and Jose C. Nacher

    Citation: BMC Systems Biology 2018 12(Suppl 1):37

    Published on:

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

  29. Content type: Research

    Microbial abundance profiles are applied widely to understand diseases from the aspect of microbial communities. By investigating the abundance associations of species or genes, we can construct molecular ecol...

    Authors: Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Zhou Fang and Shuaicheng Li

    Citation: BMC Systems Biology 2018 12(Suppl 1):5

    Published on:

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

  30. Content type: Methodology

    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

    Published on:

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

  31. Content type: Research article

    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

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  32. Content type: Research article

    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

    Published on:

  33. Content type: Research Article

    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

    Published on:

  34. Content type: Research article

    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

    Published on:

  35. Content type: Research article

    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

    Published on:

  36. Content type: Research article

    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

    Published on:

  37. Content type: Research

    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

    Published on:

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

  38. Content type: Research

    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

    Published on:

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

  39. Content type: Research

    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

    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

  40. Content type: Research

    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

    Published on:

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

  41. Content type: Research

    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

    Published on:

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

  42. Content type: Research

    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

    Published on:

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

  43. Content type: Research

    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

    Published on:

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

  44. Content type: Research

    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

    Published on:

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

  45. Content type: Research

    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

    Published on:

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

  46. Content type: Research

    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

    Published on:

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

  47. Content type: Research

    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

    Published on:

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

  48. Content type: Research

    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

    Published on:

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

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 
    852,052 downloads


    Social Media Impact
    523 mentions

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