Multiscale modeling of mucosal immune responses

BMC Bioinformatics
Yongguo MeiJosep Bassaganya-Riera

Abstract

Computational techniques are becoming increasingly powerful and modeling tools for biological systems are of greater needs. Biological systems are inherently multiscale, from molecules to tissues and from nano-seconds to a lifespan of several years or decades. ENISI MSM integrates multiple modeling technologies to understand immunological processes from signaling pathways within cells to lesion formation at the tissue level. This paper examines and summarizes the technical details of ENISI, from its initial version to its latest cutting-edge implementation. Object-oriented programming approach is adopted to develop a suite of tools based on ENISI. Multiple modeling technologies are integrated to visualize tissues, cells as well as proteins; furthermore, performance matching between the scales is addressed. We used ENISI MSM for developing predictive multiscale models of the mucosal immune system during gut inflammation. Our modeling predictions dissect the mechanisms by which effector CD4+ T cell responses contribute to tissue damage in the gut mucosa following immune dysregulation.Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological proc...Continue Reading

References

Jan 1, 1983·Annual Review of Biophysics and Bioengineering·C DeLisi
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D B DavisonM S Waterman
Sep 6, 2001·Computers in Biology and Medicine·M Bernaschi, F Castiglione
Oct 6, 2001·Trends in Biotechnology·L M Loew, J C Schaff
Feb 2, 2002·Nature·Erica Klarreich
May 25, 2002·Developmental Biology·C Titus BrownHamid Bolouri
Nov 15, 2002·Nature·Hiroaki Kitano
Sep 30, 2003·Nature Immunology·Arup K ChakrabortyAndrey S Shaw
Nov 15, 2005·Science·Volker GrimmDonald L DeAngelis
Apr 1, 2006·Bioinformatics·Sarah M KeatingMichael Hucka
Oct 13, 2006·Bioinformatics·Stefan HoopsUrsula Kummer
Mar 21, 2007·Immunological Reviews·Stephanie Forrest, Catherine Beauchemin
Mar 21, 2007·Immunological Reviews·James Mata, Melvin Cohn
Mar 31, 2007·Drug Discovery Today·Wayne Materi, David S Wishart
Jun 15, 2007·Artificial Life·Elizabeth Sklar
Sep 29, 2007·Theoretical Biology & Medical Modelling·Virginia A FolcikCharles G Orosz
Dec 24, 2009·Briefings in Bioinformatics·Peter M A Sloot, Alfons G Hoekstra
Apr 7, 2010·Journal of Theoretical Biology·Katherine WendelsdorfStephen Eubank
May 8, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Martin Meier-SchellersheimFrederick Klauschen
Dec 28, 2010·Nature Methods·Michael W SneddonThierry Emonet
Sep 19, 2012·IEEE Transactions on Nanobioscience·Katherine V WendelsdorfMadhav Marathe
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Adria CarboJosep Bassaganya-Riera
Mar 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Hao YeGeorge Sugihara

❮ Previous
Next ❯

Citations

Feb 26, 2016·Frontiers in Nutrition·Meghna VermaJosep Bassaganya-Riera
Oct 7, 2015·Frontiers in Nutrition·David B AllisonClaus Vögele
Apr 27, 2016·Current Opinion in Biotechnology·Jessica S Yu, Neda Bagheri
Aug 18, 2016·Frontiers in Immunology·Abigail BassonFabio Cominelli
Mar 8, 2018·PloS One·Violeta Balbas-MartinezIñaki F Trocóniz
Jun 12, 2019·GigaScience·Meghna VermaRaquel Hontecillas
Jul 2, 2019·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Yoram Vodovotz, Gary An
Dec 12, 2019·BMC Bioinformatics·Mozhgan Kabiri ChimehPaul Richmond
May 11, 2018·IET Systems Biology·Snehal B Shinde, Manish P Kurhekar

❮ Previous
Next ❯

Methods Mentioned

BETA
imaging techniques

Software Mentioned

CellDesigner
ENISI Visual
Basic Immune Simulator , BIS
GridVaueLayer
MSM
Rhapsody
ValueLayer
ParIMM
ENISE HPC
Swarm

Related Concepts

Related Feeds

Actin, Myosin & Cell Movement

Contractile forces generated by the actin-myosin cytoskeleton are critical for morphogenesis, but the cellular and molecular mechanisms of contraction have been elusive for many cell shape changes and movements. Here is the latest research on the roles of actin and myosin in cell movement.

Anthrax Vaccines

Three different types of anthrax vaccines are available; a live-attenuated, an alum-precipitated cell-free filtrate and a protein recombinant vaccine. The effectiveness between the three is uncertain, but the live-attenuated have shown to reduce the risk of anthrax with low adverse events. Here is the latest research on anthrax vaccines.

Anthrax

Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Here is the latest research on Anthrax.

Anthrax Vaccines (ASM)

Three different types of anthrax vaccines are available; a live-attenuated, an alum-precipitated cell-free filtrate and a protein recombinant vaccine. The effectiveness between the three is uncertain, but the live-attenuated have shown to reduce the risk of anthrax with low adverse events. Here is the latest research on anthrax vaccines.

Related Papers

Annual Review of Biomedical Engineering
Thomas S DeisboeckVittorio Cristini
Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Lucas B EdelmanNathan D Price
© 2021 Meta ULC. All rights reserved