Special Issue "Modeling and Analysis of Signal Transduction Networks"

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A special issue of Processes (ISSN 2227-9717).

Deadline for manuscript submissions: closed (31 July 2014)

Special Issue Editor

Guest Editor
Prof. Juergen Hahn
Department of Biomedical Engineering, Department of Chemical & Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, New York 12180, USA
Website: http://homepages.rpi.edu/~hahnj/
E-Mail: hahnj@rpi.edu
Phone: +1 518 276 2138
Fax: +1 518 276 3035

Special Issue Information

Dear Colleagues,

Signal transduction pathways play a key role in systems biology. These pathways are responsible for relaying cellular information and are also involved in regulating cellular responses. An understanding of signal transduction mechanisms may enable the improvement of treatment options for diseases that are affected by signal transduction mechanisms. One approach for elucidating the dynamics of signal transduction pathways is the derivation of models describing said pathways. However, deriving an accurate signal transduction pathway is difficult. The mechanisms tend to involve many components and there is cross-talk among different pathways. Also, measurements of signal transduction pathway components tend to be sparse and noisy such that the system will have a large degree of uncertainty with respect to both its structure and parameter values. Consequently, validating and refining signal transduction pathway models is crucial.

This Special Issue solicits contributions concerning the modeling and analysis of signal transduction pathways. Contributions involving the modeling and simulation of pathways are of interest. Also welcome are papers concerning methodologies used for modeling and analyzing pathways (e.g., sensitivity analysis, experimental design, parameter estimation, inverse problems or experimental techniques).

Professor Juergen Hahn
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • signal transduction
  • modeling
  • sensitivity analysis
  • parameter estimation
  • experimental design
  • cross-talk

Published Papers (3 papers)

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Displaying article 1-3
p. 867-900
by , , ,  and
Processes 2014, 2(4), 867-900; doi:10.3390/pr2040867
Received: 29 September 2014; in revised form: 10 November 2014 / Accepted: 13 November 2014 / Published: 25 November 2014
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(This article belongs to the Special Issue Modeling and Analysis of Signal Transduction Networks)
p. 773-794
by ,  and
Processes 2014, 2(4), 773-794; doi:10.3390/pr2040773
Received: 29 August 2014; in revised form: 26 September 2014 / Accepted: 8 October 2014 / Published: 17 October 2014
Show/Hide Abstract | PDF Full-text (1750 KB) | HTML Full-text | XML Full-text | Supplementary Files
(This article belongs to the Special Issue Modeling and Analysis of Signal Transduction Networks)
abstract graphic
p. 570-595
by ,  and
Processes 2014, 2(3), 570-595; doi:10.3390/pr2030570
Received: 6 June 2014; in revised form: 15 July 2014 / Accepted: 21 July 2014 / Published: 4 August 2014
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(This article belongs to the Special Issue Modeling and Analysis of Signal Transduction Networks)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Mathematical modeling and analysis of cross talk between the MAPK pathway and Smad-dependent TGF-β signal transduction
Authors: Ji Liu and Juergen Hahn
Affiliation: Rensselaer Polytechnic Institute
Abstract: Broad evidence exists for cross talk between the MAPK pathway and Smad-dependent TGF-β signal transduction. A variety of studies, oftentimes involving different cell types, have identified different potential mechanisms for the cross talk. However, there is no clear consensus on the actual mechanism(s) responsible for the cross talk. This work develops a model of the pathway, including several hypothesized cross talk mechanisms, and uses sensitivity analysis to determine which of the potential mechanisms can appropriately describe observed behaviors. Simulation results show a good agreement of the findings with results reported in the literature.

 

Title: A Computational Study of the Effects of Syk Activity on B Cell Receptor Signaling Dynamics
Author: Ann E Rundell
Affiliation: Weldon School of Biomedical Engineering, Purdue University
Abstract: The kinase Syk is intricately involved in early signaling events in B cells and is required for proper response when antigens bind to B cell receptors (BCRs). Experiments using analog-sensitive versions of Syk (Syk-AQL) have better elucidated its role, but have not completely characterized its behavior. We present a computational model for BCR signaling, using dynamical systems, which incorporates both wild-type Syk and Syk-AQL. We investigate how manipulation of Syk-AQL can be used to modulate the downstream response associated with BCR stimulation.

 

Title: Resolving early signaling events in T cell activation leading to differentiation
Author: Ann E Rundell
Affiliation: Weldon School of Biomedical Engineering, Purdue University
Abstract: Proliferation and differentiation of CD4+ T cells into effector or regulatory phenotypes are initiated and mediated by the recognition of foreign antigenic peptides on professional antigen-presenting cells. The stimulation intensity of the T cell receptor (TCR) and its various co-receptors is known to be a major determinant for the signaling profile of numerous transcriptional regulators of differentiation, but the exact nature of these relationships remains in question. We present a computational model to help investigate the complex intracellular signaling networks connecting the TCR and co-receptors to their respective transcription factors and how to manipulate these networks to elicit alternative phenotypes.

Last update: 14 April 2014

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