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  1. Content type: Research article

    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

    Published on:

  2. Content type: Research article

    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

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  3. Content type: Research

    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

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

  4. Content type: Research

    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

    Published on:

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

  5. Content type: Research

    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

    Published on:

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

  6. Content type: Research

    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

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

  7. Content type: Research

    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

    Published on:

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

  8. Content type: Research

    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

    Published on:

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

  9. Content type: Research

    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

    Published on:

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

  10. Content type: Research

    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

    Published on:

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

  11. Content type: Research

    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

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

  12. Content type: Methodology

    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

    Published on:

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

  13. Content type: Research

    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

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

  14. Content type: Research

    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

    Published on:

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

  15. Content type: Research

    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

    Published on:

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

  16. Content type: Research

    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

    Published on:

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

  17. Content type: Research

    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

    Published on:

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

  18. Content type: Research

    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

    Published on:

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

  19. Content type: Research

    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

    Published on:

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

  20. Content type: Software

    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

    Published on:

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

  21. Content type: Research

    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

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

  22. Content type: Research

    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

    Published on:

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

  23. Content type: Research

    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

    Published on:

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

  24. Content type: Research

    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

    Published on:

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

  25. Content type: Research

    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

    Published on:

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

  26. Content type: Research

    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

    Published on:

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

  27. Content type: Research

    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

    Published on:

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

  28. Content type: Database

    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

    Published on:

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

  29. Content type: Research

    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

    Published on:

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

  30. Content type: Retraction Note

    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

    Published on:

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

  31. Content type: Research article

    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

    Published on:

  32. Content type: Research article

    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

    Published on:

  33. Content type: Research article

    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

    Published on:

  34. 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

    Published on:

  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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

    Published on:

  46. 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

    Published on:

  47. 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

    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 
    852,052 downloads


    Social Media Impact
    523 mentions

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