Genetic Regulatory Networks

1Department of Electrical & Computer Engineering, College of Engineering, Texas A&M University, College Station, TX 77843-3128, USA 2Translation Genomics Research Institute, Phoenix, AZ 85004, USA 3Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan 4Digital Signal Processing Laboratory, Department of Electrical Engineering, “Politechnica” University of Bucharest, 060032 Bucharest, Romania 5Department of Electrical and Computer Engineering, Institute of Technology, University of Minnesota, Minneapolis, MN 55455, USA

[1]  P. Bourgine,et al.  Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.

[2]  J. Ji,et al.  Molecular profiling of hepatocellular carcinomas by cDNA microarray. , 2005, World Journal of Gastroenterology.

[3]  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.

[4]  J. N. R. Jeffers,et al.  Graphical Models in Applied Multivariate Statistics. , 1990 .

[5]  V. Hu.  The Cell Cycle , 1994, GWUMC Department of Biochemistry Annual Spring Symposia.

[6]  W. Yung,et al.  Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling. , 1999, Cancer research.

[7]  P Chambon,et al.  Systematic immunolocalization of retinoid receptors in developing and adult mouse eyes. , 2001, Investigative ophthalmology & visual science.

[8]  Patrik D'haeseleer,et al.  Genetic network inference: from co-expression clustering to reverse engineering , 2000, Bioinform..

[9]  Edward R. Dougherty,et al.  Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..

[10]  Daphne Koller,et al.  Rich probabilistic models for genomic data , 2004 .

[11]  James F. Lynch.  On the Threshold of Chaos in Random Boolean Cellular Automata , 1995, Random Struct. Algorithms.

[12]  J. Engel,et al.  Multiple, Distant Gata2 Enhancers Specify Temporally and Tissue-Specific Patterning in the Developing Urogenital System , 2004, Molecular and Cellular Biology.

[13]  Se-Jin Lee,et al.  Regulation of metanephric kidney development by growth/differentiation factor 11. , 2003, Developmental biology.

[14]  J. Reichen,et al.  Peginterferon alfa-2a in patients with chronic hepatitis C. , 2000, The New England journal of medicine.

[15]  E. Dougherty,et al.  Gene perturbation and intervention in probabilistic Boolean networks. , 2002, Bioinformatics.

[16]  Xiaobo Zhou,et al.  A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks , 2004, Bioinform..

[17]  Henry W. Altland,et al.  Regression Analysis: Statistical Modeling of a Response Variable , 1998, Technometrics.

[18]  Abraham Kandel,et al.  Foundations of Digital Logic Design , 1998 .

[19]  Aniruddha Datta,et al.  Intervention in context-sensitive probabilistic Boolean networks , 2005, Bioinform..

[20]  Akutsu,et al.  A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions. , 1998, Genome informatics. Workshop on Genome Informatics.

[21]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , .

[22]  Alfred O. Hero,et al.  Inference of Biologically Relevant Gene Influence Networks Using the Directed Information Criterion , 2006, 2006 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings.

[23]  Yong Xu,et al.  Interferon γ Repression of Collagen (COL1A2) Transcription Is Mediated by the RFX5 Complex* , 2003, Journal of Biological Chemistry.

[24]  Enders A. Robinson,et al.  Time Series Analysis and Applications , 1983 .

[25]  M.H. Sherif,et al.  An introduction to the analysis and processing of signals , 1985, Proceedings of the IEEE.

[26]  Edward R. Dougherty,et al.  Design of probabilistic Boolean networks under the requirement of contextual data consistency , 2006, IEEE Transactions on Signal Processing.

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

[28]  Andrew L. Rukhin,et al.  Analysis of Time Series Structure SSA and Related Techniques , 2002, Technometrics.

[29]  Melissa J Davis,et al.  J Am Soc Nephrol 15: 2344–2357, 2004 Identifying the Molecular Phenotype of Renal Progenitor Cells , 2022 .

[30]  Tong Wu,et al.  Cyclooxygenase-2 in hepatocellular carcinoma. , 2006, Cancer treatment reviews.

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

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

[33]  Oscar Moreno,et al.  Toward a Solution of the Reverse Engineering Problem Using FPGAs , 2006, Euro-Par Workshops.

[34]  Satoru Miyano,et al.  Finding Optimal Models for Small Gene Networks , 2003 .

[35]  Hao Li,et al.  Identification of gene expression patterns using planned linear contrasts , 2006, BMC Bioinformatics.

[36]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[37]  David Correa Martins,et al.  Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle , 2007 .

[38]  Peter D. Wendt,et al.  Modeling genetic regulatory networks with probabilistic Boolean networks , 2008 .

[39]  Martine Labbé,et al.  Identification of all steady states in large networks by logical analysis , 2003, Bulletin of mathematical biology.

[40]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[41]  Anja Vogler,et al.  An Introduction to Multivariate Statistical Analysis , 2004 .

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

[43]  Shoshana J. Wodak,et al.  Combining pattern discovery and discriminant analysis to predict gene co-regulation , 2004, Bioinform..

[44]  Shin Yamashita,et al.  Activin a produced by ureteric bud is a differentiation factor for metanephric mesenchyme. , 2003, Journal of the American Society of Nephrology : JASN.

[45]  Sui Huang.  Cell State Dynamics and Tumorigenesis in Boolean Regulatory Networks , 2006 .

[46]  Edward R. Dougherty,et al.  Reduction Mappings between Probabilistic Boolean Networks , 2004, EURASIP J. Adv. Signal Process..

[47]  R. Roeder,et al.  TIP30 has an intrinsic kinase activity required for up‐regulation of a subset of apoptotic genes , 2000, The EMBO journal.

[48]  Ilya Shmulevich,et al.  Binary analysis and optimization-based normalization of gene expression data , 2002, Bioinform..

[49]  T. Ørntoft,et al.  Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics , 2000, FEBS letters.

[50]  R. Blomhoff,et al.  Gene expression regulation by retinoic acid Published, JLR Papers in Press, August 16, 2002. DOI 10.1194/jlr.R100015-JLR200 , 2002, Journal of Lipid Research.

[51]  Kousuke Goto,et al.  ASIAN: a website for network inference , 2004, Bioinform..

[52]  Ilya Shmulevich,et al.  Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks , 2006, Signal Process..

[53]  Miodrag Živković.  A table of primitive binary polynomials , 1994 .

[54]  Xiaobo Zhou,et al.  Construction of genomic networks using mutual-information clustering and reversible-jump Markov-chain-Monte-Carlo predictor design , 2003, Signal Process..

[55]  Jürg Bähler,et al.  A logical circuit for the regulation of fission yeast growth modes. , 2005, Journal of Theoretical Biology.

[56]  Edward R. Dougherty,et al.  Coefficient of determination in nonlinear signal processing , 2000, Signal Process..

[57]  Kathy Chen,et al.  Network dynamics and cell physiology , 2001, Nature Reviews Molecular Cell Biology.

[58]  Marcel J. T. Reinders,et al.  A Comparison of Genetic Network Models , 2000, Pacific Symposium on Biocomputing.

[59]  Bernd Sturmfels,et al.  Monomial Dynamical Systems over Finite Fields , 2006, Complex Syst..

[60]  J R Lorsch,et al.  Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro , 1999, The EMBO journal.

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

[62]  M A Gerber,et al.  The natural history of community-acquired hepatitis C in the United States. The Sentinel Counties Chronic non-A, non-B Hepatitis Study Team. , 1992, The New England journal of medicine.

[63]  V. Iyer,et al.  Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[64]  T. Tsunoda,et al.  Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. , 2001, Cancer research.

[65]  Bruce J Aronow,et al.  A catalogue of gene expression in the developing kidney. , 2003, Kidney international.

[66]  A Zerbini,et al.  Is there a role for immunotherapy in hepatocellular carcinoma? , 2006, Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver.

[67]  Michael L. Bittner,et al.  Growing genetic regulatory networks from seed genes , 2004, Bioinform..

[68]  Eduardo D. Sontag,et al.  Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data , 2004, Bioinform..

[69]  A. Datta,et al.  Optimal infinite horizon control for probabilistic Boolean networks , 2006, ACC.

[70]  Yoshiyuki Sakaki,et al.  Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[71]  Katherine C. Chen,et al.  Integrative analysis of cell cycle control in budding yeast. , 2004, Molecular biology of the cell.

[72]  Oscar Moreno,et al.  A Parallel Solution to Reverse Engineering Genetic Networks , 2004, ICCSA.

[73]  Alberto de la Fuente,et al.  Discovery of meaningful associations in genomic data using partial correlation coefficients , 2004, Bioinform..

[74]  J. D. Engel,et al.  Rescue of the embryonic lethal hematopoietic defect reveals a critical role for GATA‐2 in urogenital development , 1998, The EMBO journal.

[75]  Lani F. Wu,et al.  Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters , 2002, Nature Genetics.

[76]  Satoru Miyano,et al.  Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model , 2003, Theor. Comput. Sci..

[77]  Zoubin Ghahramani,et al.  A Bayesian approach to reconstructing genetic regulatory networks with hidden factors , 2005, Bioinform..

[78]  Nir Friedman,et al.  Inferring Cellular Networks Using Probabilistic Graphical Models , 2004, Science.

[79]  Markus J. Herrgård,et al.  Reconciling gene expression data with known genome-scale regulatory network structures. , 2003, Genome research.

[80]  W. Just.  The steady state system problem is NP-hard even for monotone quadratic Boolean dynamical systems , 2006 .

[81]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[82]  Ning Xu,et al.  Influence of liver cancer on lipid and lipoprotein metabolism , 2005, Lipids in Health and Disease.

[83]  Korbinian Strimmer,et al.  An empirical Bayes approach to inferring large-scale gene association networks , 2005, Bioinform..

[84]  Berk Sunar,et al.  Comparison of Bit and Word Level Algorithms for Evaluating Unstructured Functions over Finite Rings , 2005, CHES.

[85]  E. Ling,et al.  High glucose alters the expression of genes involved in proliferation and cell-fate specification of embryonic neural stem cells , 2006, Diabetologia.

[86]  Q. Ouyang,et al.  The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[87]  Hiroyuki Toh,et al.  Statistical estimation of cluster boundaries in gene expression profile data , 2001, Bioinform..

[88]  M. Kenward,et al.  An Introduction to the Bootstrap , 2007 .

[89]  B. Elspas,et al.  The Theory of Autonomous Linear Sequential Networks , 1959 .

[90]  Aniruddha Datta,et al.  Generating Boolean networks with a prescribed attractor structure , 2005, Bioinform..

[91]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[92]  Geoffrey E. Hinton,et al.  Parameter estimation for linear dynamical systems , 1996 .

[93]  Alfred V. Aho,et al.  The Design and Analysis of Computer Algorithms , 1974 .

[94]  Edward R. Dougherty,et al.  Simulator for gene expression networks , 2001, SPIE BiOS.

[95]  Ilya Shmulevich,et al.  On Learning Gene Regulatory Networks Under the Boolean Network Model , 2003, Machine Learning.

[96]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[97]  I. Mian,et al.  Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in S. cerevisiae. , 2000, Physiological genomics.

[98]  N. Iizuka,et al.  MECHANISMS OF DISEASE Mechanisms of disease , 2022 .

[99]  Nir Friedman,et al.  Inferring subnetworks from perturbed expression profiles , 2001, ISMB.

[100]  Barbara Drossel.  Number of attractors in random Boolean networks. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[101]  Aniruddha Datta,et al.  External Control in Markovian Genetic Regulatory Networks , 2004, Machine Learning.

[102]  Michael K. Ng,et al.  A Control Model for Markovian Genetic Regulatory Networks , 2006, Trans. Comp. Sys. Biology.

[103]  Michael K. Ng,et al.  On construction of stochastic genetic networks based on gene expression sequences , 2005, Int. J. Neural Syst..

[104]  Edward R. Dougherty,et al.  CAN MARKOV CHAIN MODELS MIMIC BIOLOGICAL REGULATION , 2002 .

[105]  Satoru Miyano,et al.  Inferring gene networks from time series microarray data using dynamic Bayesian networks , 2003, Briefings Bioinform..

[106]  Alan David Hutson,et al.  Resampling Methods for Dependent Data , 2004, Technometrics.

[107]  Yufeng Wang,et al.  Reverse Engineering Yeast Gene Regulatory Networks using Graphical Models , 2006, 2006 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings.

[108]  Hiroaki Kitano,et al.  Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology , 2002, Current Genetics.

[109]  Hiroyuki Toh,et al.  Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling , 2003, Signal Process..

[110]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[111]  E. Dougherty,et al.  MODELING GENETIC REGULATORY NETWORKS: CONTINUOUS OR DISCRETE? , 2006 .

[112]  F. Leonardi,et al.  A NEW ANNOTATION TOOL FOR MALARIA BASED ON INFERENCE OF PROBABILISTIC GENETIC NETWORKS , 2004 .

[113]  Andrea Roli,et al.  Solving the Satisfiability Problem through Boolean Networks , 1999, AI*IA.

[114]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[115]  S. Kauffman.  Homeostasis and Differentiation in Random Genetic Control Networks , 1969, Nature.

[116]  L. You,et al.  Stochastic vs. deterministic modeling of intracellular viral kinetics. , 2002, Journal of theoretical biology.

[117]  M. Ng,et al.  Control of Boolean networks: hardness results and algorithms for tree structured networks. , 2007, Journal of theoretical biology.

[118]  M. Mackey,et al.  Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data. , 2003, Biophysical journal.

[119]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[120]  Jesper Tegnér,et al.  Growing Bayesian network models of gene networks from seed genes , 2005, ECCB/JBI.

[121]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[122]  K Sivakumar,et al.  General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. , 2000, Journal of biomedical optics.

[123]  W. Coleman,et al.  Mechanisms of human hepatocarcinogenesis. , 2003, Current molecular medicine.

[124]  David Botstein,et al.  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..

[125]  B. Drossel,et al.  Number and length of attractors in a critical Kauffman model with connectivity one. , 2004, Physical review letters.

[126]  Stuart J. Russell,et al.  Dynamic bayesian networks: representation, inference and learning , 2002 .

[127]  Roland Somogyi,et al.  Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation , 1996, Complex..

[128]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[129]  B. Samuelsson,et al.  Superpolynomial growth in the number of attractors in Kauffman networks. , 2003, Physical review letters.

[130]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[131]  Huai Li,et al.  Systematic intervention of transcription for identifying network response to disease and cellular phenotypes , 2006, Bioinform..

[132]  A. Rao,et al.  Gene expression elicited by NFAT in the presence or absence of cooperative recruitment of Fos and Jun , 2000, The EMBO journal.

[133]  Satoru Miyano,et al.  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.

[134]  Kousuke Goto,et al.  ASIAN: a web server for inferring a regulatory network framework from gene expression profiles , 2005, Nucleic Acids Res..

[135]  Tommi S. Jaakkola,et al.  Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks , 2000, Pacific Symposium on Biocomputing.

[136]  Edoardo Cervoni,et al.  Hepatitis C , 1998, The Lancet.

[137]  Edward R. Dougherty,et al.  From Boolean to probabilistic Boolean networks as models of genetic regulatory networks , 2002, Proc. IEEE.

[138]  Matthew J. Beal.  Variational algorithms for approximate Bayesian inference , 2003 .

[139]  Aurélien Mazurie,et al.  Gene networks inference using dynamic Bayesian networks , 2003, ECCB.

[140]  L. Glass,et al.  The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.

[141]  Karen Duca,et al.  An optimal control problem for in vitro virus competition , 2004, 2004 43rd IEEE Conference on Decision and Control (CDC) (IEEE Cat. No.04CH37601).

[142]  Anil K. Jain,et al.  Unsupervised Learning of Finite Mixture Models , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[143]  Erich Kaltofen,et al.  Subquadratic-time factoring of polynomials over finite fields , 1995, STOC '95.

[144]  Control in a family of Boolean networks , 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics.

[145]  Roger Germundsson,et al.  Symbolic algebraic discrete systems theory-applied to a fighter aircraft , 1995, Proceedings of 1995 34th IEEE Conference on Decision and Control.

[146]  R. Thomas,et al.  Laws for the dynamics of regulatory networks. , 1998, The International journal of developmental biology.

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

[148]  Joseph Naor,et al.  Approximating Minimum Feedback Sets and Multicuts in Directed Graphs , 1998, Algorithmica.

[149]  Kevin Murphy,et al.  Modelling Gene Expression Data using Dynamic Bayesian Networks , 2006 .

[150]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[151]  Stephen P. Brooks,et al.  Markov chain Monte Carlo method and its application , 1998 .

[152]  S. T. Buckland,et al.  An Introduction to the Bootstrap. , 1994 .

[153]  Ali S. Hadi,et al.  Finding Groups in Data: An Introduction to Chster Analysis , 1991 .

[154]  Aniruddha Datta,et al.  Intervention in Probabilistic Gene Regulatory Networks , 2006 .

[155]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[156]  H. Vincent Poor,et al.  Wireless Communication Systems: Advanced Techniques for Signal Reception , 2003 .

[157]  Ziv Bar-Joseph,et al.  Analyzing time series gene expression data , 2004, Bioinform..

[158]  S A Kauffman,et al.  Scaling in ordered and critical random boolean networks. , 2002, Physical review letters.

[159]  M. Honda,et al.  Differential gene expression between chronic hepatitis B and C hepatic lesion. , 2001, Gastroenterology.

[160]  B. R. McDonald.  Finite Rings With Identity , 1974 .

[161]  D. Slonim.  From patterns to pathways: gene expression data analysis comes of age , 2002, Nature Genetics.

[162]  E. Seto,et al.  Regulatory Factor for X-box Family Proteins Differentially Interact with Histone Deacetylases to Repress Collagen α2(I) Gene (COL1A2) Expression* , 2006, Journal of Biological Chemistry.

[163]  M. A. Aviño-Diaz,et al.  FINITE DYNAMICAL SYSTEMS, LINEAR AUTOMATA, AND FINITE FIELDS , 2006, math/0604534.

[164]  P. Barker,et al.  The MAGE proteins: Emerging roles in cell cycle progression, apoptosis, and neurogenetic disease , 2002, Journal of neuroscience research.

[165]  H Toh,et al.  System for Automatically Inferring a Genetic Netwerk from Expression Profiles , 2002, Journal of biological physics.

[166]  Araceli M. Huerta,et al.  From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[167]  Dirk Husmeier,et al.  Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks , 2003, Bioinform..

[168]  Sui Huang.  Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery , 1999, Journal of Molecular Medicine.

[169]  T. Kupper,et al.  Synergistic interactions of IL-1 and IL-6 in T cell activation. Mitogen but not antigen receptor-induced proliferation of a cloned T helper cell line is enhanced by exogenous IL-6. , 1989, Journal of immunology.

[170]  László Györfi,et al.  A Probabilistic Theory of Pattern Recognition , 1996, Stochastic Modelling and Applied Probability.

[171]  Stuart A. Kauffman,et al.  ORIGINS OF ORDER , 2019, Origins of Order.

[172]  James Douglas Engel,et al.  Gata3 loss leads to embryonic lethality due to noradrenaline deficiency of the sympathetic nervous system , 2000, Nature Genetics.

[173]  E.R. Dougherty,et al.  Research issues in genomic signal processing , 2005, IEEE Signal Processing Magazine.

[174]  S. Kauffman.  The large scale structure and dynamics of gene control circuits: an ensemble approach. , 1974, Journal of theoretical biology.

[175]  Marcel J. T. Reinders,et al.  Studying the Conditions for Learning Dynamic Bayesian Networks to Discover Genetic Regulatory Networks , 2003, Simul..

[176]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[177]  V. Moskvina,et al.  An Algorithm Based on Singular Spectrum Analysis for Change-Point Detection , 2003 .

[178]  Rolf Johannesson,et al.  Algebraic methods for signal processing and communications coding , 1995 .

[179]  Zoubin Ghahramani,et al.  Modeling T-cell activation using gene expression profiling and state-space models , 2004, Bioinform..

[180]  R. Bellazzi,et al.  Can we use linear Gaussian networks to model dynamic interactions among genes? Results from a simulation study , 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics.

[181]  Hiroyuki Toh,et al.  Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling , 2002, Bioinform..

[182]  Erkay Savas,et al.  Efficient Methods for Composite Field Arithmetic , 1999 .

[183]  S Fuhrman,et al.  Reveal, a general reverse engineering algorithm for inference of genetic network architectures. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[184]  Alfred O. Hero,et al.  Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays , 2004, EURASIP J. Adv. Signal Process..

[185]  A. Mochizuki.  An analytical study of the number of steady states in gene regulatory networks. , 2005, Journal of theoretical biology.

[186]  S. Thorgeirsson,et al.  Molecular prognostication of liver cancer: end of the beginning. , 2006, Journal of hepatology.

[187]  R. O. Stuart,et al.  Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development. , 2003, Kidney international.

[188]  D L Kreutzer,et al.  Despite large-scale T cell activation, only a minor subset of T cells responding in vitro to Actinobacillus actinomycetemcomitans differentiate into effector T cells. , 2000, Journal of periodontal research.

[189]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[190]  A. Kundaje,et al.  Learning Regulatory Networks from Sparsely Sampled Time Series Expression Data , 2002 .

[191]  Arne Storjohann,et al.  An O(n3) algorithm for the Frobenius normal form , 1998, ISSAC '98.

[192]  Nanny Wermuth,et al.  Algorithm AS 105: Fitting a Covariance Selection Model to a Matrix , 1977 .

[193]  Seungchan Kim,et al.  A nonlinear discrete dynamical model for transcriptional regulation: construction and properties. , 2004, Biophysical journal.

[194]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[195]  James E. Ferrell,et al.  Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations , 2005, Cell.

[196]  René A. Hernández Toledo.  Linear Finite Dynamical Systems , 2005 .

[197]  W. Leonard,et al.  The immediate-early gene product Egr-1 regulates the human interleukin-2 receptor beta-chain promoter through noncanonical Egr and Sp1 binding sites , 1997, Molecular and cellular biology.