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  1. Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using ...

    Authors: Shila Ghazanfar, Adam J. Bisogni, John T. Ormerod, David M. Lin and Jean Y. H. Yang
    Citation: BMC Systems Biology 2016 10(Suppl 5):127
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  2. MicroRNAs (miRNAs) play important regulatory roles in the wide range of biological processes by inducing target mRNA degradation or translational repression. Based on the correlation between expression profile...

    Authors: Minsu Lee and HyungJune Lee
    Citation: BMC Systems Biology 2016 10(Suppl 5):125
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  3. Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is seg...

    Authors: Binh P. Nguyen, Hans Heemskerk, Peter T. C. So and Lisa Tucker-Kellogg
    Citation: BMC Systems Biology 2016 10(Suppl 5):124
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  4. As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resou...

    Authors: Jesse R. Walsh, Mary L. Schaeffer, Peifen Zhang, Seung Y. Rhee, Julie A. Dickerson and Taner Z. Sen
    Citation: BMC Systems Biology 2016 10:129
    Content type: Research Article Published on:

  5. Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. ...

    Authors: Robert W. Smith, Britta Helwig, Adrie H. Westphal, Eran Pel, Maximilian Hörner, Hannes M. Beyer, Sophia L. Samodelov, Wilfried Weber, Matias D. Zurbriggen, Jan Willem Borst and Christian Fleck
    Citation: BMC Systems Biology 2016 10:110
    Content type: Methodology Article Published on:

  6. Despite the increasing availability of high performance computing capabilities, analysis and characterization of stochastic biochemical systems remain a computational challenge. To address this challenge, the ...

    Authors: Min K. Roh and Bernie J. Daigle Jr.
    Citation: BMC Systems Biology 2016 10:109
    Content type: Research Article Published on:

  7. Alzheimer disease (AD) is a progressive neurodegenerative disease that destroys memory and cognitive skills. AD is characterized by the presence of two types of neuropathological hallmarks: extracellular plaqu...

    Authors: Wenrui Hao and Avner Friedman
    Citation: BMC Systems Biology 2016 10:108
    Content type: Research Article Published on:

  9. Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the d...

    Authors: Andrew T. McKenzie, Igor Katsyv, Won-Min Song, Minghui Wang and Bin Zhang
    Citation: BMC Systems Biology 2016 10:106
    Content type: Research article Published on:

  10. Individuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in th...

    Authors: Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng and Herbert M. Lachman
    Citation: BMC Systems Biology 2016 10:105
    Content type: Research Article Published on:

  11. Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousand...

    Authors: Zrinka Raguz Nakic, Gerhard Seisenbacher, Francesc Posas and Uwe Sauer
    Citation: BMC Systems Biology 2016 10:104
    Content type: Research article Published on:

  12. Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis,...

    Authors: Edson Luiz Folador, Paulo Vinícius Sanches Daltro de Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo and Richard Röttger
    Citation: BMC Systems Biology 2016 10:103
    Content type: Research article Published on:

  13. During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understandin...

    Authors: Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver Ernst Bläsing, Regine Fuchs, Thomas Ehrhardt and Christoph Wittmann
    Citation: BMC Systems Biology 2016 10:102
    Content type: Research article Published on:

  14. Macrophages are essential to innate immunity against many pathogens, but some pathogens also target macrophages as routes to infection. The Porcine Reproductive and Respiratory Syndrome virus (PRRSV) is an RNA...

    Authors: Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan Archibald and Tahar Ait-Ali
    Citation: BMC Systems Biology 2016 10:101
    Content type: Research article Published on:

  19. Colorectal cancer arises from the accumulation of genetic mutations that induce dysfunction of intracellular signaling. However, the underlying mechanism of colorectal tumorigenesis driven by genetic mutations...

    Authors: Sung-Hwan Cho, Sang-Min Park, Ho-Sung Lee, Hwang-Yeol Lee and Kwang-Hyun Cho
    Citation: BMC Systems Biology 2016 10:96
    Content type: Research article Published on:

  21. Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biologica...

    Authors: David Murrugarra, Alan Veliz-Cuba, Boris Aguilar and Reinhard Laubenbacher
    Citation: BMC Systems Biology 2016 10:94
    Content type: Research Article Published on:

  22. The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ anti-immune strategies to facilitate their replicatio...

    Authors: Jason E. McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead III, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Li, Shufang Fan, Shannon McWeeney, Ralph S. Baric, Michael G. Katze and Katrina M. Waters
    Citation: BMC Systems Biology 2016 10:93
    Content type: Research article Published on:

  23. The increased availability of high-throughput datasets has revealed a need for reproducible and accessible analyses which can quantitatively relate molecular changes to phenotypic behavior. Existing tools for ...

    Authors: Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler and Paul Macklin
    Citation: BMC Systems Biology 2016 10:92
    Content type: Software Published on:

  24. The estimation of intracellular flux through traditional metabolic flux analysis (MFA) using an overdetermined system of equations is a well established practice in metabolic engineering. Despite the continued...

    Authors: Stanislav Sokolenko, Marco Quattrociocchi and Marc G. Aucoin
    Citation: BMC Systems Biology 2016 10:91
    Content type: Methodology Article Published on:

  25. Chronic wounds are often colonized by consortia comprised of different bacterial species growing as biofilms on a complex mixture of wound exudate. Bacteria growing in biofilms exhibit phenotypes distinct from...

    Authors: Poonam Phalak, Jin Chen, Ross P. Carlson and Michael A. Henson
    Citation: BMC Systems Biology 2016 10:90
    Content type: Research article Published on:

  27. Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis....

    Authors: Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed and Volkhard Helms
    Citation: BMC Systems Biology 2016 10:88
    Content type: Research Article Published on:

  28. Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a ...

    Authors: Xun Yue, Xing Guo Li, Xin-Qi Gao, Xiang Yu Zhao, Yu Xiu Dong and Chao Zhou
    Citation: BMC Systems Biology 2016 10:87
    Content type: Research article Published on:

  30. A complex network of gene interactions controls gene regulation throughout development and the life of the organisms. Insights can be made into these processes by studying the functional interactions (or “moti...

    Authors: Ashley A. Jermusyk, Nicholas P. Murphy and Gregory T. Reeves
    Citation: BMC Systems Biology 2016 10:85
    Content type: Research article Published on:

  31. Glioma is the most common brain tumor and it has very high mortality rate due to its infiltration and heterogeneity. Precise classification of glioma subtype is essential for proper therapeutic treatment and b...

    Authors: Sujuan Wu, Junyi Li, Mushui Cao, Jing Yang, Yi-Xue Li and Yuan-Yuan Li
    Citation: BMC Systems Biology 2016 10(Suppl 3):71
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  32. Driving Boolean networks to desired states is of paramount significance toward our ultimate goal of controlling the progression of biological pathways and regulatory networks. Despite recent computational deve...

    Authors: Rongjie Liu, Chunjiang Qian, Shuqian Liu and Yu-Fang Jin
    Citation: BMC Systems Biology 2016 10(Suppl 3):70
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  33. Technological advances in medicine have led to a rapid proliferation of high-throughput “omics” data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understa...

    Authors: Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson and Zhandong Liu
    Citation: BMC Systems Biology 2016 10(Suppl 3):69
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  34. Recently, structured sparse canonical correlation analysis (SCCA) has received increased attention in brain imaging genetics studies. It can identify bi-multivariate imaging genetic associations as well as sel...

    Authors: Lei Du, Heng Huang, Jingwen Yan, Sungeun Kim, Shannon Risacher, Mark Inlow, Jason Moore, Andrew Saykin and Li Shen
    Citation: BMC Systems Biology 2016 10(Suppl 3):68
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  35. Information about drug–drug interactions (DDIs) supported by scientific evidence is crucial for establishing computational knowledge bases for applications like pharmacovigilance. Since new reports of DDIs are...

    Authors: Yaoyun Zhang, Heng-Yi Wu, Jun Xu, Jingqi Wang, Ergin Soysal, Lang Li and Hua Xu
    Citation: BMC Systems Biology 2016 10(Suppl 3):67
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  36. The advance in targeted therapy has greatly increased the effectiveness of clinical cancer therapy and reduced the cytotoxicity of treatments to normal cells. However, patients still suffer from cancer relapse...

    Authors: Yu-Ching Hsu, Yu-Chiao Chiu, Yidong Chen, Tzu-Hung Hsiao and Eric Y. Chuang
    Citation: BMC Systems Biology 2016 10(Suppl 3):66
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  37. Cancer is increasingly recognized as a cellular system phenomenon that is attributed to the accumulation of genetic or epigenetic alterations leading to the perturbation of the molecular network architecture. ...

    Authors: Feixiong Cheng, Chuang Liu, Bairong Shen and Zhongming Zhao
    Citation: BMC Systems Biology 2016 10(Suppl 3):65
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  38. Computer-aided, interdisciplinary researches for biomedicine have valuable prospects, as digitalization of experimental subjects provide opportunities for saving the economic costs of researches, as well as pr...

    Authors: Rudong Li, Hui Cheng, Tao Cheng and Lei Liu
    Citation: BMC Systems Biology 2016 10(Suppl 3):64
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  39. Alzheimer’s disease (AD) is complex, with genetic, epigenetic, and environmental factors contributing to disease susceptibility and progression. While significant progress has been made in understanding geneti...

    Authors: Rong Xu and QuanQiu Wang
    Citation: BMC Systems Biology 2016 10(Suppl 3):63
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  40. The high degree of heterogeneity observed in breast cancers makes it very difficult to classify the cancer patients into distinct clinical subgroups and consequently limits the ability to devise effective ther...

    Authors: Suleyman Vural, Xiaosheng Wang and Chittibabu Guda
    Citation: BMC Systems Biology 2016 10(Suppl 3):62
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  41. The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13–15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial ...

    Authors: Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang and Jianhua Ruan
    Citation: BMC Systems Biology 2016 10(Suppl 3):61
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  42. Signal transduction is the process through which cells communicate with the external environment, interpret stimuli and respond to them. This mechanism is controlled by signaling cascades, which play the role ...

    Authors: Simona Catozzi, Juan Pablo Di-Bella, Alejandra C. Ventura and Jacques-Alexandre Sepulchre
    Citation: BMC Systems Biology 2016 10:84
    Content type: Research Article Published on:

  45. Gene expression is known to be an intrinsically stochastic process which can involve single-digit numbers of mRNA molecules in a cell at any given time. The modelling of such processes calls for the use of exa...

    Authors: Oleg Lenive, Paul D. W. Kirk and Michael P. H. Stumpf
    Citation: BMC Systems Biology 2016 10:81
    Content type: Research Article Published on:

  46. Ordinary differential equation (ODE) models are widely used to describe (bio-)chemical and biological processes. To enhance the predictive power of these models, their unknown parameters are estimated from exp...

    Authors: Anna Fiedler, Sebastian Raeth, Fabian J. Theis, Angelika Hausser and Jan Hasenauer
    Citation: BMC Systems Biology 2016 10:80
    Content type: Methodology Article Published on:

  47. Progesterone promotes uterine relaxation and is essential for the maintenance of pregnancy. Withdrawal of progesterone activity and increased inflammation within the uterine tissues are key triggers for partur...

    Authors: Douglas Brubaker, Alethea Barbaro, Mark R. Chance and Sam Mesiano
    Citation: BMC Systems Biology 2016 10:79
    Content type: Research Article Published on:

  49. The CD8+ T cell immune response fights acute infections by intracellular pathogens and, by generating an immune memory, enables immune responses against secondary infections. Activation of the CD8+ T cell immune ...

    Authors: Xuefeng Gao, Christophe Arpin, Jacqueline Marvel, Sotiris A. Prokopiou, Olivier Gandrillon and Fabien Crauste
    Citation: BMC Systems Biology 2016 10:77
    Content type: Research article Published on:

  50. Many large data compendia on context-specific high-throughput genomic and regulatory data have been made available by international research consortia such as ENCODE, TCGA, and Epigenomics Roadmap. The use of ...

    Authors: Robert Pesch and Ralf Zimmer
    Citation: BMC Systems Biology 2016 10:76
    Content type: Software Published on:

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