A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives
Q Vanhaelen, AM Aliper, A Zhavoronkov - Molecular BioSystems, 2017 - pubs.rsc.org
Stem cells offer great promise within the field of regenerative medicine but despite
encouraging results, the large scale use of stem cells for therapeutic applications still faces …
encouraging results, the large scale use of stem cells for therapeutic applications still faces …
[图书][B] Computational methods for processing and analysis of biological pathways
This work offers a guided walkthrough of one of the most promising research areas in
modern life sciences, enabling a deeper understanding of involved concepts and …
modern life sciences, enabling a deeper understanding of involved concepts and …
Methods and approaches in the topology-based analysis of biological pathways
C Mitrea, Z Taghavi, B Bokanizad, S Hanoudi… - Frontiers in …, 2013 - frontiersin.org
The goal of pathway analysis is to identify the pathways significantly impacted in a given
phenotype. Many current methods are based on algorithms that consider pathways as …
phenotype. Many current methods are based on algorithms that consider pathways as …
Systems biology approaches to understanding stem cell fate choice
J Peltier, DV Schaffer - IET Systems Biology, 2010 - IET
Stem cells have the capability to self-renew and maintain their undifferentiated state or to
differentiate into one or more specialised cell types. Stem cell expansion and manipulation …
differentiate into one or more specialised cell types. Stem cell expansion and manipulation …
Inferring functional pathways from multi-perturbation data
Background: Recently, a conceptually new approach for analyzing gene networks, the
Functional Influence Network (FIN) was presented. The FIN approach uses the measured …
Functional Influence Network (FIN) was presented. The FIN approach uses the measured …
Dynamic pathway modeling of signal transduction networks: a domain-oriented approach
H Conzelmann, ED Gilles - Functional Proteomics: Methods and Protocols, 2008 - Springer
Mathematical models of biological processes become more and more important in biology.
The aim is a holistic understanding of how processes such as cellular communication, cell …
The aim is a holistic understanding of how processes such as cellular communication, cell …
A computational scheme connecting gene regulatory network dynamics with heterogeneous stem cell regeneration
Y Li, X Liang, J Lei - arXiv preprint arXiv:2404.11761, 2024 - arxiv.org
Stem cell regeneration is a vital biological process in self-renewing tissues, governing
development and tissue homeostasis. Gene regulatory network dynamics are pivotal in …
development and tissue homeostasis. Gene regulatory network dynamics are pivotal in …
Transition state characteristics during cell differentiation
RD Brackston, E Lakatos… - PLoS computational …, 2018 - journals.plos.org
Models describing the process of stem-cell differentiation are plentiful, and may offer insights
into the underlying mechanisms and experimentally observed behaviour. Waddington's …
into the underlying mechanisms and experimentally observed behaviour. Waddington's …
Computational processing and error reduction strategies for standardized quantitative data in biological networks
M Schilling, T Maiwald, S Bohl, M Kollmann… - The FEBS …, 2005 - Wiley Online Library
High‐quality quantitative data generated under standardized conditions is critical for
understanding dynamic cellular processes. We report strategies for error reduction, and …
understanding dynamic cellular processes. We report strategies for error reduction, and …
[HTML][HTML] Mathematical modeling of regulatory networks of intracellular processes–Aims and selected methods
M Kardynska, D Kogut, M Pacholczyk… - Computational and …, 2023 - Elsevier
Regulatory networks structure and signaling pathways dynamics are uncovered in time-and
resource consuming experimental work. However, it is increasingly supported by modeling …
resource consuming experimental work. However, it is increasingly supported by modeling …