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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Research Article

    A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

    Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts ar...

    Luis U. Aguilera, Christoph Zimmer and Ursula Kummer

    BMC Systems Biology 2017 11:26

    Published on: 20 February 2017

  12. Research Article

    Making life difficult for Clostridium difficile: augmenting the pathogen’s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

    Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better under...

    Sara Saheb Kashaf, Claudio Angione and Pietro Lió

    BMC Systems Biology 2017 11:25

    Published on: 16 February 2017

  13. Research

    Gene regulatory network underlying the immortalization of epithelial cells

    Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell–state tran...

    Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García and Elena R. Alvarez-Buylla

    BMC Systems Biology 2017 11:24

    Published on: 16 February 2017

  14. Methodology Article

    A combined model reduction algorithm for controlled biochemical systems

    Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approache...

    Thomas J. Snowden, Piet H. van der Graaf and Marcus J. Tindall

    BMC Systems Biology 2017 11:17

    Published on: 13 February 2017

  15. Research article

    Markov State Models of gene regulatory networks

    Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understan...

    Brian K. Chu, Margaret J. Tse, Royce R. Sato and Elizabeth L. Read

    BMC Systems Biology 2017 11:14

    Published on: 6 February 2017

  16. Research

    Theoretical model of mitotic spindle microtubule growth for FRAP curve interpretation

    Spindle FRAP curves depend on the kinetic parameters of microtubule polymerization and depolymerization. The empirical FRAP curve proposed earlier permits determination of only one such dynamic parameter, comm...

    Leonid V. Omelyanchuk and Alina F. Munzarova

    BMC Systems Biology 2017 11(Suppl 1):378

    Published on: 24 February 2017

    This article is part of a Supplement: Volume 11 Supplement 1

  17. Research

    Understanding key features of bacterial restriction-modification systems through quantitative modeling

    Restriction-modification (R-M) systems are rudimentary bacterial immune systems. The main components include restriction enzyme (R), which cuts specific unmethylated DNA sequences, and the methyltransferase (M...

    Andjela Rodic, Bojana Blagojevic, Evgeny Zdobnov, Magdalena Djordjevic and Marko Djordjevic

    BMC Systems Biology 2017 11(Suppl 1):377

    Published on: 24 February 2017

    This article is part of a Supplement: Volume 11 Supplement 1

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