Designs and their codes
Collision-based computing
Power Laws, Scale-Free Networks and Genome Biology (Molecular Biology Intelligence Unit)
Power Laws, Scale-Free Networks and Genome Biology (Molecular Biology Intelligence Unit)
A robust structural PGN model for control of cell-cycle progression stabilized by negative feedbacks
EURASIP Journal on Bioinformatics and Systems Biology
Genomic signal processing: the salient issues
EURASIP Journal on Applied Signal Processing
Error-correction capability of column-weight-three LDPC codes
IEEE Transactions on Information Theory
Factor graphs and the sum-product algorithm
IEEE Transactions on Information Theory
Low-density parity-check codes based on finite geometries: a rediscovery and new results
IEEE Transactions on Information Theory
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We introduce a class of finite systems models of gene regulatory networks exhibiting behavior of the cell cycle. The network is an extension of a Boolean network model. The system spontaneously cycles through a finite set of internal states, tracking the increase of an external factor such as cell mass, and also exhibits checkpoints in which errors in gene expression levels due to cellular noise are automatically corrected. We present a 7-gene network based on Projective Geometry codes, which can correct, at every given time, one gene expression error. The topology of a network is highly symmetric and requires using only simple Boolean functions that can be synthesized using genes of various organisms. The attractor structure of the Boolean network contains a single cycle attractor. It is the smallest nontrivial network with such high robustness. The methodology allows construction of artificial gene regulatory networks with the number of phases larger than in natural cell cycle.