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  1. Content type: Research article

    Omics data provide deep insights into overall biological processes of organisms. However, integration of data from different molecular levels such as transcriptomics and proteomics, still remains challenging. ...

    Authors: T. Conrad, O. Kniemeyer, S. G. Henkel, T. Krüger, D. J. Mattern, V. Valiante, R. Guthke, I. D. Jacobsen, A. A. Brakhage, S. Vlaic and J. Linde

    Citation: BMC Systems Biology 2018 12:88

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  2. Content type: Methodology article

    Mathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Paramete...

    Authors: Adithya Sagar, Rachel LeCover, Christine Shoemaker and Jeffrey Varner

    Citation: BMC Systems Biology 2018 12:87

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  3. Content type: Research article

    Recent results from single cell gene and protein regulation studies are starting to uncover the previously underappreciated fact that individual cells within a population exhibit high variability in the expres...

    Authors: Daniel Cook, Sirisha Achanta, Jan B. Hoek, Babatunde A. Ogunnaike and Rajanikanth Vadigepalli

    Citation: BMC Systems Biology 2018 12:86

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  4. Content type: Research article

    Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent ce...

    Authors: Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres and Karmella A. Haynes

    Citation: BMC Systems Biology 2018 12:83

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  5. Content type: Research article

    Carbon catabolite repression (CCR) controls the order in which different carbon sources are metabolised. Although this system is one of the paradigms of regulation in bacteria, the underlying mechanisms remain...

    Authors: Andreas Kremling, Johannes Geiselmann, Delphine Ropers and Hidde de Jong

    Citation: BMC Systems Biology 2018 12:82

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  6. Content type: Research article

    A challenge of in vitro to in vivo extrapolation (IVIVE) is to predict the physical state of organisms exposed to chemicals in the environment from in vitro exposure assay data. Although toxicokinetic modeling...

    Authors: Michael A. Rowland, Hannah Wear, Karen H. Watanabe, Kurt A. Gust and Michael L. Mayo

    Citation: BMC Systems Biology 2018 12:81

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  7. Content type: Research article

    Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measu...

    Authors: Minoo Ashtiani, Ali Salehzadeh-Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie and Mohieddin Jafari

    Citation: BMC Systems Biology 2018 12:80

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  8. Content type: Methodology article

    The dynamics of biochemical networks can be modelled by systems of ordinary differential equations. However, these networks are typically large and contain many parameters. Therefore model reduction procedures...

    Authors: Håvard G. Frøysa, Shirin Fallahi and Nello Blaser

    Citation: BMC Systems Biology 2018 12:79

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  9. Content type: Research article

    The yeast-like fungi Pneumocystis, resides in lung alveoli and can cause a lethal infection known as Pneumocystis pneumonia (PCP) in hosts with impaired immune systems. Current therapies for PCP, such as trimetho...

    Authors: Guan-Sheng Liu, Richard Ballweg, Alan Ashbaugh, Yin Zhang, Joseph Facciolo, Melanie T. Cushion and Tongli Zhang

    Citation: BMC Systems Biology 2018 12:77

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  10. Content type: Research article

    The hypothalamic-pituitary-adrenal (HPA) axis is a central regulator of stress response and its dysfunction has been associated with a broad range of complex illnesses including Gulf War Illness (GWI) and Chro...

    Authors: Hooman Sedghamiz, Matthew Morris, Travis J. A. Craddock, Darrell Whitley and Gordon Broderick

    Citation: BMC Systems Biology 2018 12:76

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  11. Content type: Research article

    The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements kno...

    Authors: Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin, Alex Nguyen Ba and Alan M. Moses

    Citation: BMC Systems Biology 2018 12:75

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  12. Content type: Research article

    Reaction gap filling is a computational technique for proposing the addition of reactions to genome-scale metabolic models to permit those models to run correctly. Gap filling completes what are otherwise inco...

    Authors: Peter D. Karp, Daniel Weaver and Mario Latendresse

    Citation: BMC Systems Biology 2018 12:73

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  13. Content type: Software

    One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental ...

    Authors: Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic and Mingyang Lu

    Citation: BMC Systems Biology 2018 12:74

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  14. Content type: Software

    Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic syste...

    Authors: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos and Christian Fleck

    Citation: BMC Systems Biology 2018 12:72

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  15. Content type: Research article

    Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between...

    Authors: Rosa D. Hernansaiz-Ballesteros, Luca Cardelli and Attila Csikász-Nagy

    Citation: BMC Systems Biology 2018 12:70

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  16. Content type: Methodology article

    A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the ti...

    Authors: Abel Folch-Fortuny, Bas Teusink, Huub C.J. Hoefsloot, Age K. Smilde and Alberto Ferrer

    Citation: BMC Systems Biology 2018 12:71

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  17. Content type: Methodology article

    Understanding the dynamical behaviour of biological systems is challenged by their large number of components and interactions. While efforts have been made in this direction to reduce model complexity, they o...

    Authors: Stefano Casagranda, Suzanne Touzeau, Delphine Ropers and Jean-Luc Gouzé

    Citation: BMC Systems Biology 2018 12:68

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  18. Content type: Research article

    Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad compara...

    Authors: Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand V. Sastry, Erol Kavvas, Yara Seif, Larry Smarr and Bernhard O. Palsson

    Citation: BMC Systems Biology 2018 12:66

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  19. Content type: Methodology article

    Certain biological processes, such as the development of cancer and immune activation, can be controlled by rare cellular events that are difficult to capture computationally through simulations of individual ...

    Authors: Brian C. Ross, Mayla Boguslav, Holly Weeks and James C. Costello

    Citation: BMC Systems Biology 2018 12:64

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  20. 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

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  21. Content type: Research article

    Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess ...

    Authors: Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha and Sónia Carneiro

    Citation: BMC Systems Biology 2018 12:61

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  22. Content type: Regular article

    Atrial fibrillation is a cardiac disease driven by numerous idiopathic etiologies. NUP155 is a nuclear pore complex protein that has been identified as a clinical driver of atrial fibrillation, yet the precise...

    Authors: Claudia C. Preston, Saranya P. Wyles, Santiago Reyes, Emily C. Storm, Bruce W. Eckloff and Randolph S. Faustino

    Citation: BMC Systems Biology 2018 12:62

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  23. 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

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  24. 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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  25. 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

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  26. 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

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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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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  41. 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

  42. 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

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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