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  1. Content type: Methodology Article

    Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tiss...

    Authors: Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah J. Anderson, Jonathan Gorky, Prasad Dhurjati and Deni S. Galileo

    Citation: BMC Systems Biology 2017 11:124

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  2. Content type: Methodology Article

    State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell...

    Authors: Roland Prielhofer, Juan J. Barrero, Stefanie Steuer, Thomas Gassler, Richard Zahrl, Kristin Baumann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser and Hans Marx

    Citation: BMC Systems Biology 2017 11:123

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  3. Content type: Research Article

    Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean mo...

    Authors: Parul Maheshwari and Réka Albert

    Citation: BMC Systems Biology 2017 11:122

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  4. Content type: Research Article

    Polygenic diseases are usually caused by the dysfunction of multiple genes. Unravelling such disease genes is crucial to fully understand the genetic landscape of diseases on molecular level. With the advent o...

    Authors: Limei Lin, Tinghong Yang, Ling Fang, Jian Yang, Fan Yang and Jing Zhao

    Citation: BMC Systems Biology 2017 11:121

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  6. Content type: Research Article

    In favorable conditions bacterial doubling time is less than 20 min, shorter than DNA replication time. In E. coli a single round of genome replication lasts about 40 min and it must be accomplished about 20 min ...

    Authors: Joanna Jaruszewicz-Błońska and Tomasz Lipniacki

    Citation: BMC Systems Biology 2017 11:117

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  8. Content type: Research Article

    Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite ...

    Authors: Kenneth A. Barr, Carlos Martinez, Jennifer R. Moran, Ah-Ram Kim, Alexandre F. Ramos and John Reinitz

    Citation: BMC Systems Biology 2017 11:116

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  9. Content type: Research Article

    The complexity of metabolic networks can make the origin and impact of changes in central metabolism occurring during diseases difficult to understand. Computer simulations can help unravel this complexity, an...

    Authors: Anthony C. Smith, Filmon Eyassu, Jean-Pierre Mazat and Alan J. Robinson

    Citation: BMC Systems Biology 2017 11:114

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  10. Content type: Research Article

    Particle size is a key parameter for drug-delivery nanoparticle design. It is believed that the size of a nanoparticle may have important effects on its ability to overcome the transport barriers in biological...

    Authors: Mohammad Aminul Islam, Sutapa Barua and Dipak Barua

    Citation: BMC Systems Biology 2017 11:113

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  11. Content type: Research Article

    The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even wi...

    Authors: S. Cardinale and G. Cambray

    Citation: BMC Systems Biology 2017 11:112

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  13. Content type: Research Article

    Helicobacter Pylori (HP) is the most common risk factor for gastric cancer. Nearly half the world’s population is infected with HP, but only a small percentage of those develop significant pathology. The bacte...

    Authors: Richard Ballweg, Frederick Schozer, Kelsey Elliott, Alexander Kuhn, Logan Spotts, Eitaro Aihara and Tongli Zhang

    Citation: BMC Systems Biology 2017 11:111

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  15. Content type: Research Article

    The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, infer...

    Authors: Ulysse Herbach, Arnaud Bonnaffoux, Thibault Espinasse and Olivier Gandrillon

    Citation: BMC Systems Biology 2017 11:105

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  16. Content type: Research Article

    Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, ke...

    Authors: Víctor A. López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F. Barrera and Rigoberto Ríos-Estepa

    Citation: BMC Systems Biology 2017 11:107

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  17. Content type: Research Article

    Drug resistance mediated by P-glycoprotein (P-gp) renders many cancer therapies ineffective. One P-gp substrate is the widely used chemotherapy drug paclitaxel. Co-administration of paclitaxel and another drug...

    Authors: Joe Bender, Jianwen Fang and Richard Simon

    Citation: BMC Systems Biology 2017 11:108

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  18. Content type: Research Article

    Vitiligo is a long-term skin disease characterized by the loss of pigment in the skin. The current therapeutic approaches are limited. Although the anti-vitiligo mechanisms of Vernonia anthelmintica (L.) remain a...

    Authors: Ji Ye Wang, Hong Chen, Yin Yin Wang, Xiao Qin Wang, Han Ying Chen, Mei Zhang, Yun Tang and Bo Zhang

    Citation: BMC Systems Biology 2017 11:103

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  19. Content type: Research Article

    One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this e...

    Authors: Cihan Oguz, Shurjo K. Sen, Adam R. Davis, Yi-Ping Fu, Christopher J. O’Donnell and Gary H. Gibbons

    Citation: BMC Systems Biology 2017 11:99

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  20. Content type: Research Article

    Cells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organi...

    Authors: Niklas Hartung, Uwe Benary, Jana Wolf and Bente Kofahl

    Citation: BMC Systems Biology 2017 11:98

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  22. Content type: Research Article

    Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Authors: Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph

    Citation: BMC Systems Biology 2017 11:96

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  23. Content type: Research Article

    Biochemical oscillations play an important role in maintaining physiological and cellular homeostasis in biological systems. The frequency and amplitude of oscillations are regulated to properly adapt to envir...

    Authors: Jun Hyuk Kang and Kwang-Hyun Cho

    Citation: BMC Systems Biology 2017 11:95

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  24. Content type: Research

    Molecular mechanisms of the functional alteration of hematopoietic stem cells (HSCs) in leukemic environment attract intensive research interests. As known in previous researches, Maff and Egr3 are two important ...

    Authors: Rudong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu and Lei Liu

    Citation: BMC Systems Biology 2017 11(Suppl 5):91

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    This article is part of a Supplement: Volume 11 Supplement 5

  25. Content type: Research

    The discovery of novel anticancer drugs is critical for the pharmaceutical research and development, and patient treatment. Repurposing existing drugs that may have unanticipated effects as potential candidate...

    Authors: Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu and Hua Xu

    Citation: BMC Systems Biology 2017 11(Suppl 5):87

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    This article is part of a Supplement: Volume 11 Supplement 5

  26. Content type: Research

    Previous studies suggested that cancer cells possess traits reminiscent of the biological mechanisms ascribed to normal embryonic stem cells (ESCs) regulated by MYC and Polycomb repressive complex 2 (PRC2). Se...

    Authors: Xinan Holly Yang, Fangming Tang, Jisu Shin and John M. Cunningham

    Citation: BMC Systems Biology 2017 11(Suppl 5):92

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    This article is part of a Supplement: Volume 11 Supplement 5

  28. Content type: Research

    Adult hippocampal neurogenesis, the process of formation of new neurons, occurs throughout life in the hippocampus. New neurons have been associated with learning and memory as well as mood control, and impair...

    Authors: Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel and Mirjana Maletic-Savatic

    Citation: BMC Systems Biology 2017 11(Suppl 5):90

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    This article is part of a Supplement: Volume 11 Supplement 5

  29. Content type: Research

    The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain prote...

    Authors: Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang and Yunlong Liu

    Citation: BMC Systems Biology 2017 11(Suppl 5):89

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    This article is part of a Supplement: Volume 11 Supplement 5

  30. Content type: Introduction

    Between December 8–10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, on...

    Authors: W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao and Zhangdong Liu

    Citation: BMC Systems Biology 2017 11(Suppl 5):88

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    This article is part of a Supplement: Volume 11 Supplement 5

  31. Content type: Research

    Due to advances in next generation sequencing technologies and corresponding reductions in cost, it is now attainable to investigate genome-wide gene expression and variants at a patient-level, so as to better...

    Authors: Haoyang Wu, Elise Miller, Denethi Wijegunawardana, Kelly Regan, Philip R.O. Payne and Fuhai Li

    Citation: BMC Systems Biology 2017 11(Suppl 5):86

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    This article is part of a Supplement: Volume 11 Supplement 5

  32. Content type: Research

    The boundary formation in the Drosophila large intestine is widely studied as an important biological problem. It has been shown that the Delta-Notch signaling pathway plays an essential role in the formation of ...

    Authors: Fei Liu, Deshun Sun, Ryutaro Murakami and Hiroshi Matsuno

    Citation: BMC Systems Biology 2017 11(Suppl 4):80

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    This article is part of a Supplement: Volume 11 Supplement 4

  33. Content type: Research

    The human phenome has been widely used with a variety of genomic data sources in the inference of disease genes. However, most existing methods thus far derive phenotype similarity based on the analysis of bio...

    Authors: Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang and Rui Jiang

    Citation: BMC Systems Biology 2017 11(Suppl 4):76

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    This article is part of a Supplement: Volume 11 Supplement 4

  34. Content type: Research

    The Notch family of proteins plays a vital role in determining cell fates, such as proliferation, differentiation, and apoptosis. It has been shown that Notch1 and its ligands, Dll1 and Jag1, are overexpressed...

    Authors: Xiaofei Shi and Ruiqi Wang

    Citation: BMC Systems Biology 2017 11(Suppl 4):84

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    This article is part of a Supplement: Volume 11 Supplement 4

  35. Content type: Research

    Predicting protein structure from amino acid sequence is a prominent problem in computational biology. The long range interactions (or non-local interactions) are known as the main source of complexity for pro...

    Authors: Yuzhen Guo, Fengying Tao, Zikai Wu and Yong Wang

    Citation: BMC Systems Biology 2017 11(Suppl 4):93

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    This article is part of a Supplement: Volume 11 Supplement 4

  36. Content type: Research

    High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as different...

    Authors: Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang and Ling-Yun Wu

    Citation: BMC Systems Biology 2017 11(Suppl 4):75

    Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  37. Content type: Research

    The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) represents one of the most effective tools to reconstruct gene regulatory networks from large-scale molecular profile datasets. Howev...

    Authors: Jing He, Zhou Zhou, Michael Reed and Andrea Califano

    Citation: BMC Systems Biology 2017 11(Suppl 4):83

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    This article is part of a Supplement: Volume 11 Supplement 4

  38. Content type: Research

    Influenza A virus is prone to mutation and susceptible to human beings and spread in the crowds when affected by the external environment or other factors. It is very necessary to forecast influenza A pandemic...

    Authors: Jie Gao, Kang Wang, Tao Ding and Shanshan Zhu

    Citation: BMC Systems Biology 2017 11(Suppl 4):85

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    This article is part of a Supplement: Volume 11 Supplement 4

  39. Content type: Research

    Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally ref...

    Authors: Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang and Fei Guo

    Citation: BMC Systems Biology 2017 11(Suppl 4):79

    Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  40. Content type: Research

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despit...

    Authors: Changhe Fu, Su Deng, Guangxu Jin, Xinxin Wang and Zu-Guo Yu

    Citation: BMC Systems Biology 2017 11(Suppl 4):81

    Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  42. Content type: Research

    Affinity purification-mass spectrometry (AP-MS) has been widely used for generating bait-prey data sets so as to identify underlying protein-protein interactions and protein complexes. However, the AP-MS data ...

    Authors: Bo Tian, Can Zhao, Feiyang Gu and Zengyou He

    Citation: BMC Systems Biology 2017 11(Suppl 4):82

    Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  43. Content type: Research Article

    Acute myelogenous leukemia (AML) progresses uniquely in each patient. However, patients are typically treated with the same types of chemotherapy, despite biological differences that lead to differential respo...

    Authors: Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara L. Kinzer-Ursem, David M. Umulis and Ann E. Rundell

    Citation: BMC Systems Biology 2017 11:78

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  44. Content type: Research Article

    The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker prot...

    Authors: Ranjita Dutta Roy, Christian Rosenmund and Melanie I. Stefan

    Citation: BMC Systems Biology 2017 11:74

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  45. Content type: Methodology Article

    High-throughput assays are widely used in biological research to select potential targets. One single high-throughput experiment can efficiently study a large number of candidates simultaneously, but is subjec...

    Authors: Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu and Yuefeng Lu

    Citation: BMC Systems Biology 2017 11:73

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  46. Content type: Methodology Article

    Signal transduction pathways are important cellular processes to maintain the cell’s integrity. Their imbalance can cause severe pathologies. As signal transduction pathways feature complex regulations, they f...

    Authors: Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic and Ina Koch

    Citation: BMC Systems Biology 2017 11:72

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  49. Content type: Research Article

    A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to th...

    Authors: Anna Doloman, Honey Varghese, Charles D. Miller and Nicholas S. Flann

    Citation: BMC Systems Biology 2017 11:69

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  50. Content type: Research Article

    Triple-negative breast cancer lacks estrogen, progesterone, and HER2 receptors and is thus not possible to treat with targeted therapies for these receptors. Therefore, a greater understanding of triple-negati...

    Authors: Kerri-Ann Norton, Travis Wallace, Niranjan B. Pandey and Aleksander S. Popel

    Citation: BMC Systems Biology 2017 11:68

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