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  1. Research Article

    A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

    The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens...

    Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan

    BMC Systems Biology 2017 11:51

    Published on: 26 April 2017

  2. Methodology Article

    Parameter inference for stochastic single-cell dynamics from lineage tree data

    With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods sui...

    Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash

    BMC Systems Biology 2017 11:52

    Published on: 26 April 2017

  3. Database

    SSER: Species specific essential reactions database

    Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction i...

    Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang and Feng-Biao Guo

    BMC Systems Biology 2017 11:50

    Published on: 19 April 2017

  4. Research article

    Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae

    Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences...

    Hugo F. Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M. Pieterse, Antonius J. A. van Maris, Jean-Marc Daran and S. Aljoscha Wahl

    BMC Systems Biology 2017 11:49

    Published on: 17 April 2017

  5. Research Article

    Mathematical model of TGF-βsignalling: feedback coupling is consistent with signal switching

    Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is as...

    Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton and Antony W. Burgess

    BMC Systems Biology 2017 11:48

    Published on: 13 April 2017

  6. Software

    An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks

    Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of cluste...

    Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten and Michael E. Weale

    BMC Systems Biology 2017 11:47

    Published on: 12 April 2017

  7. Methodology article

    Image analysis driven single-cell analytics for systems microbiology

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited ...

    Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis and Elias S. Manolakos

    BMC Systems Biology 2017 11:43

    Published on: 4 April 2017

  8. Research Article

    Quantifying the roles of random motility and directed motility using advection-diffusion theory for a 3T3 fibroblast cell migration assay stimulated with an electric field

    Directed cell migration can be driven by a range of external stimuli, such as spatial gradients of: chemical signals (chemotaxis); adhesion sites (haptotaxis); or temperature (thermotaxis). Continuum models of...

    Matthew J. Simpson, Kai-Yin Lo and Yung-Shin Sun

    BMC Systems Biology 2017 11:39

    Published on: 17 March 2017

  9. Research article

    Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data

    Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biolo...

    Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen and Mikael Rørdam Andersen

    BMC Systems Biology 2017 11:37

    Published on: 15 March 2017

  10. Research article

    Systematic identification of an integrative network module during senescence from time-series gene expression

    Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological proce...

    Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon and Sang Chul Park

    BMC Systems Biology 2017 11:36

    Published on: 15 March 2017

  11. Research

    DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks

    An orphan disease is any disease that affects a small percentage of the population. Orphan diseases are a great burden to patients and society, and most of them are genetic in origin. Unfortunately, our curren...

    Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons and Zhiyong Lu

    BMC Systems Biology 2017 11(Suppl 3):23

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 11 Supplement 3

  12. Research

    Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

    Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia ...

    Pavithra K. Balasubramanian, Anand Balupuri, Hee-Young Kang and Seung Joo Cho

    BMC Systems Biology 2017 11(Suppl 2):6

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 11 Supplement 2

  13. Research

    Selecting high-quality negative samples for effectively predicting protein-RNA interactions

    The identification of Protein-RNA Interactions (PRIs) is important to understanding cell activities. Recently, several machine learning-based methods have been developed for identifying PRIs. However, the perf...

    Zhanzhan Cheng, Kai Huang, Yang Wang, Hui Liu, Jihong Guan and Shuigeng Zhou

    BMC Systems Biology 2017 11(Suppl 2):9

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 11 Supplement 2

  14. Research

    Predicting protein-binding regions in RNA using nucleotide profiles and compositions

    Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding si...

    Daesik Choi, Byungkyu Park, Hanju Chae, Wook Lee and Kyungsook Han

    BMC Systems Biology 2017 11(Suppl 2):16

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 11 Supplement 2

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