Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering

[1]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[2]  H. Hironaka Resolution of Singularities of an Algebraic Variety Over a Field of Characteristic Zero: II , 1964 .

[3]  J. MacQueen Some methods for classification and analysis of multivariate observations , 1967 .

[4]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[5]  Bruno Buchberger,et al.  The Construction of Multivariate Polynomials with Preassigned Zeros , 1982, EUROCAM.

[6]  Teo Mora,et al.  The Gröbner Fan of an Ideal , 1988, J. Symb. Comput..

[7]  Anil K. Jain,et al.  Algorithms for Clustering Data , 1988 .

[8]  Ron Kohavi,et al.  Supervised and Unsupervised Discretization of Continuous Features , 1995, ICML.

[9]  Michael Kalkbrener,et al.  Converting Bases with the Gröbner Walk , 1997, J. Symb. Comput..

[10]  David A. Cox,et al.  Ideals, Varieties, and Algorithms , 1997 .

[11]  Alexander J. Hartemink,et al.  Principled computational methods for the validation discovery of genetic regulatory networks , 2001 .

[12]  A. Giuliani,et al.  The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data , 2001, FEBS letters.

[13]  P. Brazhnik,et al.  Gene networks: how to put the function in genomics. , 2002, Trends in biotechnology.

[14]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[15]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[16]  U. Alon,et al.  Detailed map of a cis-regulatory input function , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[17]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.

[18]  R. Laubenbacher,et al.  Boolean Monomial Dynamical Systems , 2004, math/0403166.

[19]  R. Laubenbacher,et al.  A computational algebra approach to the reverse engineering of gene regulatory networks. , 2003, Journal of theoretical biology.

[20]  Timothy S Gardner,et al.  Reverse-engineering transcription control networks. , 2005, Physics of life reviews.

[21]  V. Thorsson,et al.  Reverse Engineering Galactose Regulation in Yeast through Model Selection , 2005, Statistical applications in genetics and molecular biology.

[22]  M. Gustafsson,et al.  Constructing and analyzing a large-scale gene-to-gene regulatory network Lasso-constrained inference and biological validation , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[23]  Stefan Bornholdt,et al.  Less Is More in Modeling Large Genetic Networks , 2005, Science.

[24]  Bruno Buchberger,et al.  Bruno Buchberger's PhD thesis 1965: An algorithm for finding the basis elements of the residue class ring of a zero dimensional polynomial ideal , 2006, J. Symb. Comput..

[25]  U. Alon,et al.  Plasticity of the cis-Regulatory Input Function of a Gene , 2006, PLoS biology.

[26]  Rekha R. Thomas,et al.  Computing Gröbner fans , 2007, Math. Comput..

[27]  Abdul Salam Jarrah,et al.  Reverse-engineering of polynomial dynamical systems , 2007, Adv. Appl. Math..

[28]  Abdul Salam Jarrah,et al.  A Gröbner fan method for biochemical network modeling , 2007, ISSAC '07.

[29]  D. di Bernardo,et al.  How to infer gene networks from expression profiles , 2007, Molecular systems biology.

[30]  Yu-Chun Lin,et al.  ' s response to reviews Title : Identifying Significant Genetic Regulatory Networks in the Prostate Cancer from Microarray Data Based on Transcription Factor Analysis and Conditional Independency , 2009 .

[31]  John McGee,et al.  Discretization of Time Series Data , 2005, J. Comput. Biol..

[32]  D. MacLean,et al.  A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System , 2010, PloS one.

[33]  Elena S. Dimitrova Estimating the Volumes of the Cones in a Gröbner Fan , 2010, Math. Comput. Sci..

[34]  Z. Burda,et al.  Distribution of essential interactions in model gene regulatory networks under mutation-selection balance. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[35]  C. Franceschi,et al.  Encoding the states of interacting proteins to facilitate biological pathways reconstruction , 2010, Biology Direct.

[36]  Abdul Salam Jarrah,et al.  Polynomial algebra of discrete models in systems biology , 2010, Bioinform..

[37]  B. Stigler,et al.  Boolean Models Can Explain Bistability in the lac Operon , 2008, J. Comput. Biol..

[38]  Abdul Salam Jarrah,et al.  Parameter estimation for Boolean models of biological networks , 2009, Theor. Comput. Sci..

[39]  W. W. Adams,et al.  An Introduction to Gröbner Bases , 2012 .