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  1. Ataxia telangiectasia mutated (ATM) is a detector of double-strand breaks (DSBs) and a crucial component of the DNA damage response (DDR) along with p53 and NF- κB transcription factors and Wip1 phosphatase. Desp...

    Authors: Katarzyna Jonak, Monika Kurpas, Katarzyna Szoltysek, Patryk Janus, Agata Abramowicz and Krzysztof Puszynski
    Citation: BMC Systems Biology 2016 10:75

    The Erratum to this article has been published in BMC Systems Biology 2016 10:99

  2. Glioma differentiation therapy is a novel strategy that has been used to induce glioma cells to differentiate into glia-like cells. Although some advances in experimental methods for exploring the molecular me...

    Authors: Xiaoqiang Sun, Jiajun Zhang, Qi Zhao, Xing Chen, Wenbo Zhu, Guangmei Yan and Tianshou Zhou
    Citation: BMC Systems Biology 2016 10:73
  3. Canonical correlation analysis (CCA) is a multivariate statistical method which describes the associations between two sets of variables. The objective is to find linear combinations of the variables in each d...

    Authors: Ines Wilms and Christophe Croux
    Citation: BMC Systems Biology 2016 10:72
  4. It has been found that microRNAs (miRNAs) can function as a regulatory factor across species. For example, food-derived plant miRNAs may pass through the gastrointestinal (GI) tract, enter into the plasma and ...

    Authors: Hao Zhang, Yanpu Li, Yuanning Liu, Haiming Liu, Hongyu Wang, Wen Jin, Yanmei Zhang, Chao Zhang and Dong Xu
    Citation: BMC Systems Biology 2016 10:60
  5. Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. ...

    Authors: Fleur Jeanquartier, Claire Jean-Quartier, David Cemernek and Andreas Holzinger
    Citation: BMC Systems Biology 2016 10:59
  6. The malarial parasite Plasmodium falciparum undergoes a complex life cycle, including an intraerythrocytic developmental cycle, during which it is metabolically dependent on the infected human red blood cell (RBC...

    Authors: Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye and Jaques Reifman
    Citation: BMC Systems Biology 2016 10:58
  7. Gene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far from the gene promoters are often...

    Authors: Seong Gon Kim, Nawanol Theera-Ampornpunt, Chih-Hao Fang, Mrudul Harwani, Ananth Grama and Somali Chaterji
    Citation: BMC Systems Biology 2016 10(Suppl 2):54

    This article is part of a Supplement: Volume 10 Supplement 2

  8. Methods for inferring signaling networks using single gene knockdown RNAi experiments and reference networks have been proposed in recent years. These methods assume that RNAi information is available for all ...

    Authors: Yuanfang Ren, Qiyao Wang, Md Mahmudul Hasan, Ahmet Ay and Tamer Kahveci
    Citation: BMC Systems Biology 2016 10(Suppl 2):53

    This article is part of a Supplement: Volume 10 Supplement 2

  9. Networks provide effective models to study complex biological systems, such as gene and protein interaction networks. With the advent of new sequencing technologies, many life scientists are grasping for user-...

    Authors: Juli Petereit, Sebastian Smith, Frederick C. Harris Jr and Karen A. Schlauch
    Citation: BMC Systems Biology 2016 10(Suppl 2):51

    This article is part of a Supplement: Volume 10 Supplement 2

  10. Unlike traditional detection of a disease state in which there are clear phenomena, it is usually a challenge to identify the pre-disease state during the progression of a complex disease just before the serio...

    Authors: Pei Chen and Yongjun Li
    Citation: BMC Systems Biology 2016 10(Suppl 2):50

    This article is part of a Supplement: Volume 10 Supplement 2

  11. Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. P...

    Authors: Chinwe Ekenna, Shawna Thomas and Nancy M. Amato
    Citation: BMC Systems Biology 2016 10(Suppl 2):49

    This article is part of a Supplement: Volume 10 Supplement 2

  12. Computational modeling is an important tool for the study of complex biochemical processes associated with cell signaling networks. However, it is challenging to simulate processes that involve hundreds of lar...

    Authors: Brittany Hoard, Bruna Jacobson, Kasra Manavi and Lydia Tapia
    Citation: BMC Systems Biology 2016 10(Suppl 2):48

    This article is part of a Supplement: Volume 10 Supplement 2

  13. Various approaches to calling single-nucleotide variants (SNVs) or insertion-or-deletion (indel) mutations have been developed based on next-generation sequencing (NGS). However, most of them are dedicated to ...

    Authors: Yongchao Liu, Martin Loewer, Srinivas Aluru and Bertil Schmidt
    Citation: BMC Systems Biology 2016 10(Suppl 2):47

    This article is part of a Supplement: Volume 10 Supplement 2

  14. Prediction of de novo protein-protein interaction is a critical step toward reconstructing PPI networks, which is a central task in systems biology. Recent computational approaches have shifted from making PPI pr...

    Authors: Lei Huang, Li Liao and Cathy H. Wu
    Citation: BMC Systems Biology 2016 10(Suppl 2):45

    This article is part of a Supplement: Volume 10 Supplement 2

  15. Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway mainly due to its participation in important biological processes, functions, and diseases, i.e., embryonic development, stem-cell m...

    Authors: Losiana Nayak, Nitai P. Bhattacharyya and Rajat K. De
    Citation: BMC Systems Biology 2016 10(Suppl 2):44

    This article is part of a Supplement: Volume 10 Supplement 2

  16. Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computati...

    Authors: Stefano Schivo, Jetse Scholma, Paul E. van der Vet, Marcel Karperien, Janine N. Post, Jaco van de Pol and Rom Langerak
    Citation: BMC Systems Biology 2016 10:56
  17. Calcium signalling relies on the flux of calcium ions across membranes yet how signals in different compartments are related remains unclear. In particular, similar calcium signals on both sides of the nuclear...

    Authors: Teresa Vaz Martins, Matthew J. Evans, Derin B. Wysham and Richard J. Morris
    Citation: BMC Systems Biology 2016 10:55
  18. The concept of reproducibility is a foundation of the scientific method. With the arrival of fast and powerful computers over the last few decades, there has been an explosion of results based on complex compu...

    Authors: Joanna Lewis, Charles E. Breeze, Jane Charlesworth, Oliver J. Maclaren and Jonathan Cooper
    Citation: BMC Systems Biology 2016 10:52
  19. Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, par...

    Authors: Yeimy Morales, Gabriel Bosque, Josep Vehí, Jesús Picó and Francisco Llaneras
    Citation: BMC Systems Biology 2016 10:46
  20. Cellular barcoding is a recently developed biotechnology tool that enables the familial identification of progeny of individual cells in vivo. In immunology, it has been used to track the burst-sizes of multip...

    Authors: Tom S. Weber, Mark Dukes, Denise C. Miles, Stefan P. Glaser, Shalin H. Naik and Ken R. Duffy
    Citation: BMC Systems Biology 2016 10:43
  21. Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or rea...

    Authors: Adrien Rougny, Christine Froidevaux, Laurence Calzone and Loïc Paulevé
    Citation: BMC Systems Biology 2016 10:42
  22. The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often address...

    Authors: Bin Du, Daniel C. Zielinski, Erol S. Kavvas, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla E. Ruggiero, Garri A. Arzumanyan and Bernhard O. Palsson
    Citation: BMC Systems Biology 2016 10:40
  23. Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer geneti...

    Authors: Nikolay Martyushenko, Sigurd Hagen Johansen, Cheol-Min Ghim and Eivind Almaas
    Citation: BMC Systems Biology 2016 10:39
  24. The insulin signalling pathway (ISP) is an important biochemical pathway, which regulates some fundamental biological functions such as glucose and lipid metabolism, protein synthesis, cell proliferation, cell...

    Authors: Barbara Di Camillo, Azzurra Carlon, Federica Eduati and Gianna Maria Toffolo
    Citation: BMC Systems Biology 2016 10:38
  25. Primary sex determination in placental mammals is a very well studied developmental process. Here, we aim to investigate the currently established scenario and to assess its adequacy to fully recover the obser...

    Authors: Lucas Sánchez and Claudine Chaouiya
    Citation: BMC Systems Biology 2016 10:37
  26. Disease similarity study provides new insights into disease taxonomy, pathogenesis, which plays a guiding role in diagnosis and treatment. The early studies were limited to estimate disease similarities based ...

    Authors: Jing Yang, Su-Juan Wu, Shao-You Yang, Jia-Wei Peng, Shi-Nuo Wang, Fu-Yan Wang, Yu-Xing Song, Ting Qi, Yi-Xue Li and Yuan-Yuan Li
    Citation: BMC Systems Biology 2016 10:36
  27. Invasive aspergillosis is a severe infection of immunocompromised hosts, caused by the inhalation of the spores of the ubiquitous environmental molds of the Aspergillus genus. The innate immune response in this i...

    Authors: Matthew Oremland, Kathryn R. Michels, Alexandra M. Bettina, Chris Lawrence, Borna Mehrad and Reinhard Laubenbacher
    Citation: BMC Systems Biology 2016 10:34
  28. Development of resistance against first line drug therapy including cisplatin and paclitaxel in high-grade serous ovarian cancer (HGSOC) presents a major challenge. Identifying drug candidates breaking resista...

    Authors: Peter Andorfer, Alexander Heuwieser, Andreas Heinzel, Arno Lukas, Bernd Mayer and Paul Perco
    Citation: BMC Systems Biology 2016 10:33
  29. Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in ...

    Authors: Diana V. Salakhieva, Ildar I. Sadreev, Michael Z. Q. Chen, Yoshinori Umezawa, Aleksandr I. Evstifeev, Gavin I. Welsh and Nikolay V. Kotov
    Citation: BMC Systems Biology 2016 10:32
  30. Anaerobic rather than aerobic fermentation is preferred for conversion of biomass derived sugars to high value redox-neutral and reduced commodities. This will likely result in a higher yield of substrate to p...

    Authors: Andrew Iverson, Erin Garza, Ryan Manow, Jinhua Wang, Yuanyuan Gao, Scott Grayburn and Shengde Zhou
    Citation: BMC Systems Biology 2016 10:31
  31. The editors of BMC Systems Biology would like to thank all our reviewers who have contributed to the journal in Volume 9 (2015).

    Authors: Timothy R. Sands
    Citation: BMC Systems Biology 2016 10:29
  32. Systems Biology has motivated dynamic models of important intracellular processes at the pathway level, for example, in signal transduction and cell cycle control. To answer important biomedical questions, how...

    Authors: Katrin Kolczyk and Carsten Conradi
    Citation: BMC Systems Biology 2016 10:28
  33. Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key...

    Authors: Yadira Boada, Gilberto Reynoso-Meza, Jesús Picó and Alejandro Vignoni
    Citation: BMC Systems Biology 2016 10:27
  34. The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis...

    Authors: Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O’Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne and Bernhard O. Palsson
    Citation: BMC Systems Biology 2016 10:26
  35. Recent advances in large datasets analysis offer new insights to modern biology allowing system-level investigation of pathologies. Here we describe a novel computational method that exploits the ever-growing ...

    Authors: Alberto Calderone, Matteo Formenti, Federica Aprea, Michele Papa, Lilia Alberghina, Anna Maria Colangelo and Paola Bertolazzi
    Citation: BMC Systems Biology 2016 10:25
  36. As in many cancer types, the G1/S restriction point (RP) is deregulated in Acute Lymphoblastic Leukemia (ALL). Hyper-phosphorylated retinoblastoma protein (hyper-pRb) is found in high levels in ALL cells. Neve...

    Authors: Eleftherios Ouzounoglou, Dimitra Dionysiou and Georgios S. Stamatakos
    Citation: BMC Systems Biology 2016 10:23
  37. Auxin is a major phytohormone involved in many developmental processes by controlling gene expression through a network of transcriptional regulators. In Arabidopsis thaliana, the auxin signalling network is made...

    Authors: Jonathan Legrand, Jean-Benoist Léger, Stéphane Robin, Teva Vernoux and Yann Guédon
    Citation: BMC Systems Biology 2016 10:22
  38. Microbial systems in which the extracellular environment varies both spatially and temporally are very common in nature and in engineering applications. While the use of genome-scale metabolic reconstructions ...

    Authors: Jin Chen, Jose A. Gomez, Kai Höffner, Poonam Phalak, Paul I. Barton and Michael A. Henson
    Citation: BMC Systems Biology 2016 10:21
  39. The fungal pathogen Candida albicans colonizes the gastrointestinal (GI) tract of mammalian hosts as a benign commensal. However, in an immunocompromised host, the fungus is capable of causing life-threatening in...

    Authors: Katarzyna M. Tyc, Sanna E. Herwald, Jennifer A. Hogan, Jessica V. Pierce, Edda Klipp and Carol A. Kumamoto
    Citation: BMC Systems Biology 2016 10:20
  40. Epigenetics has been investigated in cancer initiation, and development, especially, since the appearance of epigenomics. Epigenetics may be defined as the mechanisms that lead to heritable changes in gene fun...

    Authors: Bor-Sen Chen and Cheng-Wei Li
    Citation: BMC Systems Biology 2016 10:18
  41. In planarian flatworms, the mechanisms underlying the activity of collectively pluripotent adult stem cells (neoblasts) and their descendants can now be studied from the level of the individual gene to the ent...

    Authors: Marc Mangel, Michael B. Bonsall and Aziz Aboobaker
    Citation: BMC Systems Biology 2016 10:17
  42. High throughput technologies have been used to profile genes in multiple different dimensions, such as genetic variation, copy number, gene and protein expression, epigenetics, metabolomics. Computational anal...

    Authors: Ana B. Pavel, Dmitriy Sonkin and Anupama Reddy
    Citation: BMC Systems Biology 2016 10:16
  43. The insulin-like growth factor (IGF) system impacts cellular development by regulating proliferation, differentiation, and apoptosis, and is an attractive therapeutic target in cancer. The IGF system is comple...

    Authors: Dan Tian, Isaiah Mitchell and Pamela K. Kreeger
    Citation: BMC Systems Biology 2016 10:15