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  1. Many mathematical and statistical models and algorithms have been proposed to do biomarker identification in recent years. However, the biomarkers inferred from different datasets suffer a lack of reproducibil...

    Authors: Ke Zhang, Wei Geng and Shuqin Zhang
    Citation: BMC Systems Biology 2018 12(Suppl 9):135
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  2. With the rapid accumulation of genomic data, it has become a challenge issue to annotate and interpret these data. As a representative, Gene set enrichment analysis has been widely used to interpret large mole...

    Authors: Dong Wang, Jie Li, Rui Liu and Yadong Wang
    Citation: BMC Systems Biology 2018 12(Suppl 9):133
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  3. Biological Regulatory Networks (BRNs) are responsible for developmental and maintenance related functions in organisms. These functions are implemented by the dynamics of BRNs and are sensitive to regulations ...

    Authors: Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach, Josch Pauling, Aamir Shafi, Rehan Zafar Paracha, Asad Hayat and Amjad Ali
    Citation: BMC Systems Biology 2018 12:146
    Content type: Software Published on:

  5. Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists’ capability to discover functional relevance of their ...

    Authors: Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang and Yidong Chen
    Citation: BMC Systems Biology 2018 12(Suppl 8):142
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  6. Chromatin interactions medicated by genomic elements located throughout the genome play important roles in gene regulation and can be identified with the technologies such as high-throughput chromosome conform...

    Authors: Yulin Dai, Chao Li, Guangsheng Pei, Xiao Dong, Guohui Ding, Zhongming Zhao, Yixue Li and Peilin Jia
    Citation: BMC Systems Biology 2018 12(Suppl 8):140
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  7. A fundamental problem for translational genomics is to find optimal therapies based on gene regulatory intervention. Dynamic intervention involves a control policy that optimally reduces a cost function based ...

    Authors: Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani and Edward R. Dougherty
    Citation: BMC Systems Biology 2018 12(Suppl 8):137
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  8. Traumatic brain injury (TBI) represents a critical health problem of which timely diagnosis and treatment remain challenging. TBI is a result of an external force damaging brain tissue, accompanied by delayed ...

    Authors: F. Anthony San Lucas, John Redell, Dash Pramod and Yin Liu
    Citation: BMC Systems Biology 2018 12(Suppl 8):131
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  9. As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics st...

    Authors: Jie Ren, Bo Wang and Jing Li
    Citation: BMC Systems Biology 2018 12(Suppl 8):130
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  10. Self-interacting Proteins (SIPs) plays a critical role in a series of life function in most living cells. Researches on SIPs are important part of molecular biology. Although numerous SIPs data be provided, tr...

    Authors: Yan-Bin Wang, Zhu-Hong You, Xiao Li, Tong-Hai Jiang, Li Cheng and Zhan-Heng Chen
    Citation: BMC Systems Biology 2018 12(Suppl 8):129
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  11. Circular RNAs (circRNAs) have recently been found to be expressed in human brain tissue, and many lines ofevidence indicate that circRNAs play regulatory roles in neurodevelopment. Proliferation and differenti...

    Authors: Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song and Ping Han
    Citation: BMC Systems Biology 2018 12(Suppl 8):128
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

    The Correction to this article has been published in BMC Systems Biology 2019 13:14

  12. The mammalian brain is organized into regions with specific biological functions and properties. These regions have distinct transcriptomes, but little is known whether they may also differ in their metabolome...

    Authors: William T. Choi, Mehmet Tosun, Hyun-Hwan Jeong, Cemal Karakas, Fatih Semerci, Zhandong Liu and Mirjana Maletić-Savatić
    Citation: BMC Systems Biology 2018 12(Suppl 8):127
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  13. Gene signatures are important to represent the molecular changes in the disease genomes or the cells in specific conditions, and have been often used to separate samples into different groups for better resear...

    Authors: Saurav Mallik and Zhongming Zhao
    Citation: BMC Systems Biology 2018 12(Suppl 8):126
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  14. Between June 10–12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials,...

    Authors: Kai Wang, Xiaoming Liu, Yan Guo, Zhijin Wu, Degui Zhi, Jianhua Ruan and Zhongming Zhao
    Citation: BMC Systems Biology 2018 12(Suppl 8):125
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  15. Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of the tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed...

    Authors: Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen and Yu-Hsuan Joni Shao
    Citation: BMC Systems Biology 2018 12(Suppl 8):124
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  16. Gut microbiota interacts with the human gut in multiple ways. Microbiota composition is altered in inflamed gut conditions. Likewise, certain microbial fermentation products as well as the lipopolysaccharides ...

    Authors: Gunter Neumann, Rebecca Wall, Ignacio Rangel, Tatiana M. Marques and Dirk Repsilber
    Citation: BMC Systems Biology 2018 12:144
    Content type: Research article Published on:

  17. Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive...

    Authors: Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard O. Palsson and Adam M. Feist
    Citation: BMC Systems Biology 2018 12:143
    Content type: Research article Published on:

  18. Accumulation of amyloid β-peptide (Aβ) is implicated in the pathogenesis and development of Alzheimer’s disease (AD). Neuron-enriched miRNA was aberrantly regulated and may be associated with the pathogenesis ...

    Authors: Ling Hu, Rong Zhang, Qiong Yuan, Yinping Gao, Mary Q. Yang, Chunxiang Zhang, Jiankun Huang, Yufei Sun, William Yang, Jack Y. Yang, Zhen-li Min, Jing Cheng, Youping Deng and Xiamin Hu
    Citation: BMC Systems Biology 2018 12(Suppl 7):119
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  19. Bladder cancer (BC) is the most common cancer of the urinary bladder and upper tract, in which the clinical management is limited. AURKA (aurora kinase A) has been identified as an oncogene in cancer developme...

    Authors: Mengjie Guo, Sicheng Lu, Hongming Huang, Yaohui Wang, Mary Q. Yang, Ye Yang, Zhimin Fan, Bin Jiang and Youping Deng
    Citation: BMC Systems Biology 2018 12(Suppl 7):118
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  20. Adenocarcinoma in situ (AIS) is a pre-invasive lesion in the lung and a subtype of lung adenocarcinoma. The patients with AIS can be cured by resecting the lesion completely. In contrast, the patients with inv...

    Authors: Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera and Mary Qu Yang
    Citation: BMC Systems Biology 2018 12(Suppl 7):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  21. Nowadays, because of the huge economic burden on society causing by obesity and diabetes, they turn into the most serious public health challenges in the world. To reveal the close and complex relationships be...

    Authors: Guannan He, Yanchun Liang, Yan Chen, William Yang, Jun S. Liu, Mary Qu Yang and Renchu Guan
    Citation: BMC Systems Biology 2018 12(Suppl 7):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  22. Reconstruction of gene regulatory networks (GRNs), also known as reverse engineering of GRNs, aims to infer the potential regulation relationships between genes. With the development of biotechnology, such as ...

    Authors: Bei Yang, Yaohui Xu, Andrew Maxwell, Wonryull Koh, Ping Gong and Chaoyang Zhang
    Citation: BMC Systems Biology 2018 12(Suppl 7):115
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  23. Single-cell RNA sequencing (scRNA-seq) technology provides an effective way to study cell heterogeneity. However, due to the low capture efficiency and stochastic gene expression, scRNA-seq data often contains...

    Authors: Mary Qu Yang, Sherman M. Weissman, William Yang, Jialing Zhang, Allon Canaann and Renchu Guan
    Citation: BMC Systems Biology 2018 12(Suppl 7):114
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

    The Correction to this article has been published in BMC Systems Biology 2019 13:13

  24. Ecotoxicological studies on the insensitive munitions formulation IMX-101 and its components 2,4-dinitroanisole (DNAN), nitroguanidine (NQ) and nitrotriazolone (NTO) in various organisms showed that DNAN was t...

    Authors: Ping Gong, Keri B. Donohue, Anne M. Mayo, Yuping Wang, Huixiao Hong, Mitchell S. Wilbanks, Natalie D. Barker, Xin Guan and Kurt A. Gust
    Citation: BMC Systems Biology 2018 12(Suppl 7):92
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  25. Autism Spectrum Disorder (ASD) is the umbrella term for a group of neurodevelopmental disorders convergent on behavioral phenotypes. While many genes have been implicated in the disorder, the predominant focus...

    Authors: Steven B. Cogill, Anand K. Srivastava, Mary Qu Yang and Liangjiang Wang
    Citation: BMC Systems Biology 2018 12(Suppl 7):91
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 7

  26. Recent research has found that abnormal functioning of Microtubules (MTs) could be linked to fatal diseases such as Alzheimer’s. Hence, there is an imminent need to understand the implications of MTs for disea...

    Authors: Vineetha Menon, Shantia Yarahmadian and Vahid Rezania
    Citation: BMC Systems Biology 2018 12(Suppl 6):112
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  27. While there are a large number of bioinformatics datasets for clustering, many of them are incomplete, i.e., missing attribute values in some data samples needed by clustering algorithms. A variety of clusteri...

    Authors: Longlong Liao, Kenli Li, Keqin Li, Canqun Yang and Qi Tian
    Citation: BMC Systems Biology 2018 12(Suppl 6):111
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  28. Cancer is one of the leading causes for the morbidity and mortality worldwide. Although substantial studies have been conducted theoretically and experimentally in recent years, it is still a challenge to expl...

    Authors: Shuhao Sun, Fima Klebaner, Xinan Zhang and Tianhai Tian
    Citation: BMC Systems Biology 2018 12(Suppl 6):110
    Content type: Software Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  29. Ubiquitination, which is also called “lysine ubiquitination”, occurs when an ubiquitin is attached to lysine (K) residues in targeting proteins. As one of the most important post translational modifications (P...

    Authors: Fei He, Rui Wang, Jiagen Li, Lingling Bao, Dong Xu and Xiaowei Zhao
    Citation: BMC Systems Biology 2018 12(Suppl 6):109
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  30. The unregulated use of antibiotics not only in clinical practice but also in farm animals breeding is causing a unprecedented growth of antibiotic resistant bacterial strains. This problem can be analyzed at d...

    Authors: Roberta Bardini, Stefano Di Carlo, Gianfranco Politano and Alfredo Benso
    Citation: BMC Systems Biology 2018 12(Suppl 6):108
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  31. Epilepsy is a neurological disease characterized by unprovoked seizures in the brain. The recent advances in sensor technologies allow researchers to analyze the collected biological records to improve the tre...

    Authors: Ye Yuan, Guangxu Xun, Kebin Jia and Aidong Zhang
    Citation: BMC Systems Biology 2018 12(Suppl 6):107
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  32. Microbe plays a crucial role in the functional mechanism of an ecosystem. Identification of the interactions among microbes is an important step towards understand the structure and function of microbial commu...

    Authors: Xiaoyan Wang, Yichuan Li, Tingting He, Xingpeng Jiang and Xiaohua Hu
    Citation: BMC Systems Biology 2018 12(Suppl 6):106
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  33. Osteoarthritis (OA) is the most common disease of arthritis. Analgesics are widely used in the treat of arthritis, which may increase the risk of cardiovascular diseases by 20% to 50% overall.There are few stu...

    Authors: Liangliang Liu, Ying Yu, Zhihui Fei, Min Li, Fang-Xiang Wu, Hong-Dong Li, Yi Pan and Jianxin Wang
    Citation: BMC Systems Biology 2018 12(Suppl 6):105
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  34. Although substance use disorders (SUDs) are heritable, few genetic risk factors for them have been identified, in part due to the small sample sizes of study populations. To address this limitation, researcher...

    Authors: Jin Lu, Jiangwen Sun, Xinyu Wang, Henry Kranzler, Joel Gelernter and Jinbo Bi
    Citation: BMC Systems Biology 2018 12(Suppl 6):104
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  35. Ordinary differential equations (ODEs) are often used to understand biological processes. Since ODE-based models usually contain many unknown parameters, parameter estimation is an important step toward deeper...

    Authors: Jenny E. Jeong and Peng Qiu
    Citation: BMC Systems Biology 2018 12(Suppl 6):103
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 12 Supplement 6

  36. Although cellular metabolism has been widely studied, its fully comprehension is still a challenge. A main tool for this study is the analysis of meaningful pieces of knowledge called modes and, in particular,...

    Authors: José F. Hidalgo, Jose A. Egea, Francisco Guil and José M. García
    Citation: BMC Systems Biology 2018 12(Suppl 5):101
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  37. To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more acc...

    Authors: Christophe Guyeux, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot and Michel Salomon
    Citation: BMC Systems Biology 2018 12(Suppl 5):100
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  38. Spatial localization of natural products or proteins during microbial interactions can help to identify new antimicrobials both as offensive or defensive agents. Visible spatial interactions have been used for...

    Authors: Víctor González-Menéndez, Germán Martínez, Rachel Serrano, Francisca Muñoz, Jesús Martín, Olga Genilloud and José R. Tormo
    Citation: BMC Systems Biology 2018 12(Suppl 5):99
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  39. Several online databases provide a large amount of biomedical data of different biological entities. These resources are typically stored in systems implementing their own data model, user interface and query ...

    Authors: Antonio Messina, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa and Alfonso Urso
    Citation: BMC Systems Biology 2018 12(Suppl 5):98
    Content type: Database Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  40. During the last decade, the interest to apply machine learning algorithms to genomic data has increased in many bioinformatics applications. Analyzing this type of data entails difficulties for managing high-d...

    Authors: María Gabriela Valdés, Iván Galván-Femenía, Vicent Ribas Ripoll, Xavier Duran, Jun Yokota, Ricard Gavaldà, Xavier Rafael-Palou and Rafael de Cid
    Citation: BMC Systems Biology 2018 12(Suppl 5):97
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  41. The Smith-Waterman (SW) algorithm is the best choice for searching similar regions between two DNA or protein sequences. However, it may become impracticable in some contexts due to its high computational dema...

    Authors: Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf and Manuel Prieto-Matias
    Citation: BMC Systems Biology 2018 12(Suppl 5):96
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  42. Systems biology aims to analyse regulation mechanisms into the cell. By mapping interactions observed in different situations, differential network analysis has shown its power to reveal specific cellular resp...

    Authors: Marc Legeay, Sébastien Aubourg, Jean-Pierre Renou and Béatrice Duval
    Citation: BMC Systems Biology 2018 12(Suppl 5):95
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  43. In RNA-Seq gene expression analysis, a genetic signature or biomarker is defined as a subset of genes that is probably involved in a given complex human trait and usually provide predictive capabilities for th...

    Authors: Daniel Urda, Francisco Aragón, Rocío Bautista, Leonardo Franco, Francisco J. Veredas, Manuel Gonzalo Claros and José Manuel Jerez
    Citation: BMC Systems Biology 2018 12(Suppl 5):94
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  44. Photosynthetic microalgae have been in the spotlight of biotechnological production (biofuels, lipids, etc), however, current barriers in mass cultivation of microalgae are limiting its successful industrializ...

    Authors: Stepan Papacek, Jiri Jablonsky and Karel Petera
    Citation: BMC Systems Biology 2018 12(Suppl 5):93
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 5

  45. The authors have retracted this article [1]. After publication they discovered a technical error in the Louvain algorithm with bounded cluster sizes. Correction of this error substantially changed the results ...

    Authors: Sarah Hall-Swan, Jake Crawford, Rebecca Newman and Lenore J. Cowen
    Citation: BMC Systems Biology 2018 12:113
    Content type: Retraction Note Published on:

    The original article was published in BMC Systems Biology 2018 12:24

  46. Classic metabolic engineering strategies often induce significant flux imbalances to microbial metabolism, causing undesirable outcomes such as suboptimal conversion of substrates to products. Several mathemat...

    Authors: Juan A. Martínez, Alberto Rodriguez, Fabian Moreno, Noemí Flores, Alvaro R. Lara, Octavio T. Ramírez, Guillermo Gosset and Francisco Bolivar
    Citation: BMC Systems Biology 2018 12:102
    Content type: Research article Published on:

  47. Cancer is the second most common cause of death globally. The anticancer effects of Tanshinone IIA (Tan IIA) has been confirmed by numerous researches. However, the underlying mechanism remained to be integrated ...

    Authors: Yan-feng Cao, Shi-feng Wang, Xi Li, Yan-ling Zhang and Yan-jiang Qiao
    Citation: BMC Systems Biology 2018 12:90
    Content type: Research article Published on:

  48. There are large differences between men and women of child-bearing age in the expression level of 5 key enzymes in one-carbon metabolism almost certainly caused by the sex hormones. These male-female differenc...

    Authors: Farrah Sadre-Marandi, Thabat Dahdoul, Michael C. Reed and H. Frederik Nijhout
    Citation: BMC Systems Biology 2018 12:89
    Content type: Research article Published on:

  49. 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
    Content type: Research article Published on:

  50. 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
    Content type: Methodology article Published on:

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