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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Research

    Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics

    Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion sy...

    Minghan Chen, Fei Li, Shuo Wang and Young Cao

    BMC Systems Biology 2017 11(Suppl 3):21

    Published on: 14 March 2017

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

  9. Research

    SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance

    Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular comp...

    Hyundoo Jeong and Byung-Jun Yoon

    BMC Systems Biology 2017 11(Suppl 3):20

    Published on: 14 March 2017

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

  10. Research

    PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI

    Identifying perturbed pathways in a given condition is crucial in understanding biological phenomena. In addition to identifying perturbed pathways individually, pathway analysis should consider interactions a...

    Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo and Sun Kim

    BMC Systems Biology 2017 11(Suppl 2):15

    Published on: 14 March 2017

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

  11. Research article

    Mathematical modelling and a systems science approach to describe the role of cytokines in the evolution of severe dengue

    Dengue causes considerable morbidity and mortality in Sri Lanka. Inflammatory mediators such as cytokines, contribute to its evolution from an asymptotic infection to severe forms of dengue. The majority of pr...

    S. D. Pavithra Jayasundara, S. S. N. Perera, Gathsaurie Neelika Malavige and Saroj Jayasinghe

    BMC Systems Biology 2017 11:34

    Published on: 11 March 2017

  12. Research article

    Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

    Although renal fibrosis and inflammation have shown to be involved in the pathophysiology of obstructive nephropathies, molecular mechanisms underlying evolution of these processes remain undetermined. In an a...

    Theofilos Papadopoulos, Audrey Casemayou, Eric Neau, Benjamin Breuil, Cécile Caubet, Denis Calise, Barbara A. Thornhill, Magdalena Bachvarova, Julie Belliere, Robert L. Chevalier, Panagiotis Moulos, Dimcho Bachvarov, Benedicte Buffin-Meyer, Stéphane Decramer, Françoise Conte Auriol, Jean-Loup Bascands…

    BMC Systems Biology 2017 11:31

    Published on: 1 March 2017

  13. Research article

    Network topology of NaV1.7 mutations in sodium channel-related painful disorders

    Gain-of-function mutations in SCN9A gene that encodes the voltage-gated sodium channel NaV1.7 have been associated with a wide spectrum of painful syndromes in humans including inherited erythromelalgia, paroxysm...

    Dimos Kapetis, Jenny Sassone, Yang Yang, Barbara Galbardi, Markos N. Xenakis, Ronald L. Westra, Radek Szklarczyk, Patrick Lindsey, Catharina G. Faber, Monique Gerrits, Ingemar S. J. Merkies, Sulayman D. Dib-Hajj, Massimo Mantegazza, Stephen G. Waxman and Giuseppe Lauria

    BMC Systems Biology 2017 11:28

    Published on: 24 February 2017

  14. Research article

    Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

    We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis...

    Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J. Waardenberg, Kentu Lassiter and Nicholas J. Hudson

    BMC Systems Biology 2017 11:29

    Published on: 24 February 2017

  15. Research article

    Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris

    Pichia pastoris shows physiological advantages in producing recombinant proteins, compared to other commonly used cell factories. This yeast is mostly grown in dynamic cultivation syst...

    Francisco Saitua, Paulina Torres, José Ricardo Pérez-Correa and Eduardo Agosin

    BMC Systems Biology 2017 11:27

    Published on: 21 February 2017

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