Modeling systems-level regulation of host immune responses

J Thakar, M Pilione, G Kirimanjeswara… - PLoS computational …, 2007 - journals.plos.org
Many pathogens are able to manipulate the signaling pathways responsible for the
generation of host immune responses. Here we examine and model a respiratory infection …

Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster

M Marques-Pita, LM Rocha - PloS one, 2013 - journals.plos.org
We present schema redescription as a methodology to characterize canalization in
automata networks used to model biochemical regulation and signalling. In our formulation …

Global stabilizing control of large-scale biomolecular regulatory networks

S An, SY Jang, SM Park, CK Lee, HM Kim… - …, 2023 - academic.oup.com
Motivation Cellular behavior is determined by complex non-linear interactions between
numerous intracellular molecules that are often represented by Boolean network models. To …

The cognitive phenotype of Down syndrome: insights from intracellular network analysis

A Ma'ayan, K Gardiner, R Iyengar - NeuroRx, 2006 - Springer
Down syndrome (DS) is caused by trisomy of chromosome 21. All individuals with DS exhibit
some level of cognitive dysfunction. It is generally accepted that these abnormalities are a …

Canalization and symmetry in Boolean models for genetic regulatory networks

CJO Reichhardt, KE Bassler - Journal of Physics A: Mathematical …, 2007 - iopscience.iop.org
Canalization of genetic regulatory networks has been argued to be favoured by evolutionary
processes due to the stability that it can confer to phenotype expression. We explore …

Regulatory patterns in molecular interaction networks

D Murrugarra, R Laubenbacher - Journal of theoretical biology, 2011 - Elsevier
Understanding design principles of molecular interaction networks is an important goal of
molecular systems biology. Some insights have been gained into features of their network …

Methods of Producing RPE Cells and Compositions of RPE Cells

C Malcuit, L Lemieux, W Holmes… - US Patent App. 12 …, 2011 - Google Patents
(54) METHODS OF PRODUCING RPE CELLS AND (60) Provisional application No.
60/998,668, filed on Oct. COMPOSITIONS OF RIPE CELLS 12, 2007, provisional application …

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling

A Graudenzi, G Caravagna, G De Matteis… - PLoS One, 2014 - journals.plos.org
Colorectal tumors originate and develop within intestinal crypts. Even though some of the
essential phenomena that characterize crypt structure and dynamics have been effectively …

Harmonic analysis of Boolean networks: determinative power and perturbations

R Heckel, S Schober, M Bossert - EURASIP Journal on Bioinformatics and …, 2013 - Springer
Consider a large Boolean network with a feed forward structure. Given a probability
distribution on the inputs, can one find, possibly small, collections of input nodes that …

Identification of genetic network dynamics with unate structure

R Porreca, E Cinquemani, J Lygeros… - …, 2010 - academic.oup.com
Motivation: Modern experimental techniques for time course measurement of gene
expression enable the identification of dynamical models of genetic regulatory networks. In …