PMID: 5803332Mar 1, 1969

Metabolic stability and epigenesis in randomly constructed genetic nets

Journal of Theoretical Biology
Stuart A Kauffman

Abstract

No abstract listed.

References

The template activity of chromatin

Oct 1, 1965·Journal of Cellular Physiology·J Bonner

Validity of a critical-item scale for schizophrenia on the MMPI

Jun 1, 1954·Journal of Consulting Psychology·H RUBIN

Citations

On the holistic approach in cellular and cancer biology: nonlinearity, complexity, and quasi-determinism of the dynamic cellular network

Jun 12, 1998·Journal of Surgical Oncology·P WaliszewskiJ Konarski

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

Jul 22, 1998·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Denis ThieffryJulio Collado-Vides

Origin of multicellular organisms as an inevitable consequence of dynamical systems

Oct 17, 2002·The Anatomical Record·C Furusawa, Kunihiko Kaneko

Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators

Jun 1, 1996·Biological cybernetics·Andreas Wagner

Linear analysis of switching nets

Jan 1, 1971·Kybernetik·P Cull

On the character of an distance between states in a binary switching net

Jan 1, 1982·Biological cybernetics·A E Gelfand, C C Walker

Control of switching nets

Sep 1, 1975·Biological cybernetics·P Cull

A neutral theory of biogenesis

Dec 1, 1981·Origins of Life·A Ferracin

On the theories of gene regulation and differentiation in eukaryotes

Jan 1, 1975·Acta Biotheoretica·N Düzgünes

Genetic nets and dissipative structures: an algebraic approach

Apr 1, 1974·Bulletin of Mathematical Biology·H M Martinez, G Carlsson

Isologous diversification: a theory of cell differentiation

Jan 1, 1997·Bulletin of Mathematical Biology·K Kaneko, T Yomo

Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution

Feb 13, 2010·Journal of Molecular Evolution·Dafyd J Jenkins, Dov J Stekel

A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development

May 9, 2012·Journal of Mathematical Biology·Giovanni De MatteisMarco Antoniotti

Formal methods for Hopfield-like networks

Feb 6, 2013·Acta Biotheoretica·Hedi Ben AmorNicolas Glade

MitomiRs, chloromiRs and modelling of the microRNA inhibition

Aug 29, 2013·Acta Biotheoretica·Jacques DemongeotA Henrion-Caude

Maximum number of fixed points in regulatory Boolean networks

Mar 1, 2008·Bulletin of Mathematical Biology·Julio Aracena

The dynamics of conjunctive and disjunctive Boolean network models

Jan 21, 2010·Bulletin of Mathematical Biology·Abdul Salam JarrahAlan Veliz-Cuba

Nested canalyzing depth and network stability

Dec 6, 2011·Bulletin of Mathematical Biology·Lori LayneMatthew Macauley

Deconstruction and dynamical robustness of regulatory networks: application to the yeast cell cycle networks

Nov 29, 2012·Bulletin of Mathematical Biology·Eric GolesGonzalo A Ruz

Remarks on the respective roles of logical parameters and time delays in asynchronous logic: an homage to El Houssine Snoussi

Mar 21, 2013·Bulletin of Mathematical Biology·R Thomas

Mathematical conditions for induced cell differentiation and trans-differentiation in adult cells

Apr 12, 2013·Bulletin of Mathematical Biology·Matan BodakerEduardo Mitrani

Logical modelling of regulatory networks, methods and applications

Jun 1, 2013·Bulletin of Mathematical Biology·Claudine Chaouiya, Elisabeth Remy

Monotone and near-monotone biochemical networks

Nov 13, 2008·Systems and Synthetic Biology·Eduardo D Sontag

Guiding the self-organization of random Boolean networks

Dec 1, 2011·Theory in Biosciences = Theorie in Den Biowissenschaften·Carlos Gershenson

Prediction of lethal and synthetically lethal knock-outs in regulatory networks

Aug 25, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Gunnar BoldhausKonstantin Klemm

Interactive modelling and simulation of biochemical networks

May 1, 1995·Computers in Biology and Medicine·R Hofestädt, F Meineke

Qualitative analysis of biochemical reaction systems

Jan 1, 1996·Computers in Biology and Medicine·V N ReddyM L Mavrovouniotis

Some remarks on the stability of the idiotypic network

Nov 1, 1977·Immunochemistry·J Hiernaux

Towards a rationale for neural stability: a model of neural computation and network architecture

Nov 1, 1980·International Journal of Bio-medical Computing·M C Fairhurst, G P Goutos

Predicting carcinogenicity with short-term tests: biological models and operational approaches

May 1, 1988·Mutation Research·R Benigni, A Giuliani

Information processing in molecular systems

Aug 1, 1972·Currents in Modern Biology·M Conrad

Endogenous oscillations in pathways of energy transduction as related to circadian rhythmicity and photoperiodic control

Jul 1, 1975·Bio Systems·E WagnerL Stroebele

Pigment color patterns of molluscs as an autonomous process generated by asynchronous automata

Jan 1, 1990·Bio Systems·Y P Gunji

Inter- and intracellular computation models based on Boolean vs. non-Boolean inconsistency

Jan 1, 1995·Bio Systems·Y P GunjiK Ito

The circular topology of rhythm in asynchronous random Boolean networks

Mar 12, 2004·Bio Systems·Philipp Rohlfshagen, E A Di Paolo

Dynamical and topological robustness of the mammalian cell cycle network: a reverse engineering approach

Nov 12, 2013·Bio Systems·Gonzalo A RuzGary B Fogel

An analytical study of the number of steady states in gene regulatory networks

May 12, 2005·Journal of Theoretical Biology·Atsushi Mochizuki

The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth

Apr 2, 2013·Journal of Theoretical Biology·Dov A PechenickJoshua L Payne

Turing on Super-Turing and adaptivity

Apr 16, 2013·Progress in Biophysics and Molecular Biology·Hava T Siegelmann

Stem cell states, fates, and the rules of attraction

May 12, 2009·Cell Stem Cell·Tariq EnverPeter W Andrews

The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

Jun 5, 2003·Journal of Theoretical Biology·Réka Albert, Hans G Othmer

Robust development as a consequence of generated positional information

Sep 6, 2003·Journal of Theoretical Biology·C Furusawa, Kunihiko Kaneko

Knowledge discovery in gene-expression-microarray data: mining the information output of the genome

Oct 8, 1999·Trends in Biotechnology·G Zweiger

Rhythmic and non-rhythmic attractors in asynchronous random Boolean networks

Apr 20, 2001·Bio Systems·E A Di Paolo

Enhancing evolvability with mutation buffering mediated through multiple weak interactions

Apr 12, 2003·Bio Systems·L Gwenn Volkert

The life of form. Emergent patterns of morphological transformation

Apr 1, 2000·Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie·B C Goodwin

A preprocessing method for inferring genetic interaction from gene expression data using Boolean algorithm

Oct 20, 2005·Journal of Bioscience and Bioengineering·Kazumi HakamadaTakeshi Kobayashi

Variation of scutellar bristles in Drosophila. XI. Selection for scutellar microchaetae and the correlated response of scutellar bristles

Apr 1, 1968·Genetical Research·W R Scowroft

Understanding biological functions through molecular networks

Jan 30, 2008·Cell Research·Jing-Dong Jackie Han

Executable cell biology

Nov 9, 2007·Nature Biotechnology·Jasmin Fisher, Thomas A Henzinger

Logic-based models in systems biology: a predictive and parameter-free network analysis method

Oct 18, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Michelle L WynnSantiago Schnell

Networks for systems biology: conceptual connection of data and function

Jun 7, 2011·IET Systems Biology·Frank Emmert-Streib, M Dehmer

Cell-cell interaction and diversity of emergent behaviours

Mar 17, 2011·IET Systems Biology·C DamianiA Colacci

Combinatorial explosion in model gene networks

Jun 5, 2003·Chaos·R. Edwards, Leon Glass

Symbolic dynamics and computation in model gene networks

Jun 5, 2003·Chaos·R. EdwardsLeon Glass

Extracting information from cDNA arrays

Jun 5, 2003·Chaos·Hanspeter HerzelJohannes Schuchhardt

Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits

Jun 5, 2003·Chaos·R Thomas, M. Kaufman

From topology to dynamics in biochemical networks

Jun 5, 2003·Chaos·Jeffrey J. Fox, Colin C. Hill

An adjustable aperiodic model class of genomic interactions using continuous time Boolean networks (Boolean delay equations)

Nov 8, 2003·Chaos·Hakan OktemKaren Egiazarian

Computation in gene networks

Mar 9, 2004·Chaos·Asa Ben-Hur, Hava T Siegelmann

Evolving complex dynamics in electronic models of genetic networks

Sep 28, 2004·Chaos·Jonathan MasonLeon Glass

The effect of network topology on the stability of discrete state models of genetic control

May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Andrew PomeranceWolfgang Losert

Some features of the spread of epidemics and information on a random graph

Feb 20, 2010·Proceedings of the National Academy of Sciences of the United States of America·Rick Durrett

Quantifying the Waddington landscape and biological paths for development and differentiation

May 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jin WangErkang Wang

Taming combinatorial explosion

Jun 28, 2000·Proceedings of the National Academy of Sciences of the United States of America·P Schuster

Model for constraint and control in biochemical networks

Jan 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·Stuart A Newman, S A Rice

Evolutionary games and computer simulations

Aug 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·B A Huberman, N S Glance

Emergence of homeostasis and "noise imprinting" in an evolution model

Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·M D Stern

Modeling and simulation of genetic regulatory systems: a literature review

Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong

A general modeling strategy for gene regulatory networks with stochastic dynamics

Dec 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Andre S RibeiroStuart A Kauffman

Discretization of time series data

Jun 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Elena DimitrovaReinhard C Laubenbacher

Computing combinatorial intervention strategies and failure modes in signaling networks

Jan 19, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Regina SamagaSteffen Klamt

Dynamical properties of a boolean model of gene regulatory network with memory

Jan 11, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alex GraudenziStuart A Kauffman

Gene expression complex networks: synthesis, identification, and analysis

May 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Fabrício Martins LopesLuciano Da F Costa

Robustness analysis of a Boolean model of gene regulatory network with memory

Mar 23, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alex GraudenziStuart A Kauffman

Reconstructing Boolean models of signaling

Jan 5, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Roded Sharan, Richard M Karp

A systems biology approach to cancer: fractals, attractors, and nonlinear dynamics

Feb 16, 2011·Omics : a Journal of Integrative Biology·Simona DinicolaMariano Bizzarri

Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science

Jul 11, 2009·Tissue Engineering. Part B, Reviews·Petros LenasFrank P Luyten

The executable pathway to biological networks

Feb 2, 2010·Briefings in Functional Genomics·Jasmin Fisher, Nir Piterman

Understanding cancer mechanisms through network dynamics

Jul 20, 2012·Briefings in Functional Genomics·Tammy M K ChengPaul A Bates

The Beta Workbench: a computational tool to study the dynamics of biological systems

May 9, 2008·Briefings in Bioinformatics·Lorenzo DemattéAlessandro Romanel

Estimating the divisibility of complex biological networks by sparseness indices

Jan 13, 2010·Briefings in Bioinformatics·Tommaso MazzaFerenc Jordán

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities

Jul 27, 2012·Briefings in Bioinformatics·Chang F QuoGil Alterovitz

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach

Nov 24, 2006·Bioinformatics·L Jason StegglesAnil Wipat

Boolean dynamics of genetic regulatory networks inferred from microarray time series data

Feb 3, 2007·Bioinformatics·Shawn MartinJean-Loup Faulon

Ensemble learning of genetic networks from time-series expression data

Nov 6, 2007·Bioinformatics·Dougu NamJihyun F Kim

Discerning static and causal interactions in genome-wide reverse engineering problems

May 10, 2008·Bioinformatics·Mattia ZampieriClaudio Altafini

Synchronous versus asynchronous modeling of gene regulatory networks

Jul 11, 2008·Bioinformatics·Abhishek GargGiovanni De Micheli

Coherent coupling of feedback loops: a design principle of cell signaling networks

Jul 4, 2008·Bioinformatics·Yung-Keun Kwon, Kwang-Hyun Cho

Modeling stochasticity and robustness in gene regulatory networks

May 30, 2009·Bioinformatics·Abhishek GargIoannis Xenarios

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources

Jul 3, 2009·Bioinformatics·Xiaofeng DaiAndre S Ribeiro

Identification of genetic network dynamics with unate structure

Mar 23, 2010·Bioinformatics·Riccardo PorrecaGiancarlo Ferrari-Trecate

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

Apr 10, 2010·Bioinformatics·Christoph MüsselHans A Kestler

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks

Apr 28, 2010·Bioinformatics·Noushin GhaffariEdward R Dougherty

Modeling and analyzing complex biological networks incooperating experimental information on both network topology and stable states

Jul 6, 2010·Bioinformatics·Yi Ming Zou

Inferring Boolean network structure via correlation

Apr 8, 2011·Bioinformatics·Markus MaucherHans A Kestler

Modeling mechanistic biological networks: an advanced Boolean approach

Dec 27, 2011·Bioinformatics·T Handorf, E Klipp

GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process

Jan 8, 2013·Bioinformatics·Marco AntoniottiGiancarlo Mauri

BooleSim: an interactive Boolean network simulator

Oct 1, 2013·Bioinformatics·Matthias BöckEdda Klipp

Use of network analysis to capture key traits affecting tomato organoleptic quality

Jun 12, 2009·Journal of Experimental Botany·Paola CarliMaria R Ercolano

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Nov 13, 2012·Nucleic Acids Research·Deepak BalasubramanianKalai Mathee

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

Sep 4, 2012·Nucleic Acids Research·Isaac CrespoAntonio Del Sol

Simplification and its consequences in biological modelling: conclusions from a study of calcium oscillations in hepatocytes

Jul 20, 2006·Journal of the Royal Society, Interface·James P J HetheringtonRobert M Seymour

Boolean network models of cellular regulation: prospects and limitations

May 30, 2008·Journal of the Royal Society, Interface·Stefan Bornholdt

Biological switches and clocks

Jun 5, 2008·Journal of the Royal Society, Interface·John J TysonJill Sible

Distributed robustness in cellular networks: insights from synthetic evolved circuits

Sep 18, 2008·Journal of the Royal Society, Interface·Javier Macia, Ricard V Solé

Digital clocks: simple Boolean models can quantitatively describe circadian systems

Apr 14, 2012·Journal of the Royal Society, Interface·Ozgur E AkmanPeter Ghazal

The relationship between modularity and robustness in signalling networks

Sep 21, 2013·Journal of the Royal Society, Interface·Tien-Dzung Tran, Yung-Keun Kwon

Robustness as an evolutionary principle

Jun 21, 2001·Proceedings. Biological Sciences·Stefan Bornholdt, Kim Sneppen

Physics and complexity

Feb 4, 2010·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·David Sherrington

Robust dynamics in minimal hybrid models of genetic networks

Oct 6, 2010·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Theodore J PerkinsLeon Glass

Extracellular matrix, mechanotransduction and structural hierarchies in heart tissue engineering

Jun 26, 2007·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kevin K Parker, Donald E Ingber

Estimating coarse gene network structure from large-scale gene perturbation data

Feb 6, 2002·Genome Research·Andreas Wagner

A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles

Oct 16, 2004·The Plant Cell·Carlos Espinosa-SotoElena R Alvarez-Buylla

A data-driven integrative model of sepal primordium polarity in Arabidopsis

Dec 27, 2011·The Plant Cell·Camilo La RotaFrançoise Monéger

A complex control circuit. Regulation of immunity in temperate bacteriophages

Dec 1, 1976·European Journal of Biochemistry·R ThomasL Lambert

Mathematical biology education: beyond calculus

Aug 1, 2009·Science·Raina Robeva, Reinhard Laubenbacher

Computational approaches for analyzing information flow in biological networks

Apr 19, 2012·Science Signaling·Boris KholodenkoWalter Kolch

The duration of T cell stimulation is a critical determinant of cell fate and plasticity

Nov 7, 2013·Science Signaling·Natasa Miskov-ZivanovJames R Faeder

Boolean versus continuous dynamics in modules with two feedback loops

Oct 26, 2012·The European Physical Journal. E, Soft Matter·Eva AckermannBarbara Drossel

On construction of stochastic genetic networks based on gene expression sequences

Sep 28, 2005·International Journal of Neural Systems·Wai-Ki ChingT Akutsu

On cooperative quasi-equilibrium models of transcriptional regulation

Jul 20, 2007·Journal of Bioinformatics and Computational Biology·Eric Mjolsness

Functional motifs in biochemical reaction networks

Jan 9, 2010·Annual Review of Physical Chemistry·John J Tyson, Béla Novák

Algorithms for finding small attractors in Boolean networks

Feb 7, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Shu-Qin ZhangMichael K Ng

Inference of a probabilistic Boolean network from a single observed temporal sequence

Mar 28, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Stephen MarshallEdward R Dougherty

Comparison of gene regulatory networks via steady-state trajectories

Mar 1, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Marcel BrunEdward R Dougherty

Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data

Jun 28, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Wentao ZhaoEdward R Dougherty

Inference of gene regulatory networks based on a universal minimum description length

Apr 26, 2008·EURASIP Journal on Bioinformatics & Systems Biology·John DoughertyJaakko Astola

Algorithms and complexity analyses for control of singleton attractors in Boolean networks

Sep 17, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Morihiro HayashidaWai-Ki Ching

Optimal constrained stationary intervention in gene regulatory networks

Jun 3, 2008·EURASIP Journal on Bioinformatics & Systems Biology·B FaryabiEdward R Dougherty

Intervention in context-sensitive probabilistic Boolean networks revisited

May 1, 2009·EURASIP Journal on Bioinformatics & Systems Biology·B FaryabiEdward R Dougherty

Adaptive dynamics of regulatory networks: size matters

Apr 1, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Dirk RepsilberMats Björklund

Polynomial-time algorithm for controllability test of a class of boolean biological networks

Oct 5, 2010·EURASIP Journal on Bioinformatics & Systems Biology·Koichi KobayashiKunihiko Hiraishi

Verification and optimal control of context-sensitive probabilistic Boolean networks using model checking and polynomial optimization

Mar 4, 2014·TheScientificWorldJournal·Koichi Kobayashi, Kunihiko Hiraishi

Dynamical systems approach to endothelial heterogeneity

Jun 23, 2012·Circulation Research·Erzsébet Ravasz Regan, William C Aird

Complex organization in multicellularity as a necessity in evolution

May 12, 2001·Artificial Life·C Furusawa, K Kaneko

The evolution and understanding of hierarchical complexity in biology from an algebraic perspective

Aug 16, 2000·Artificial Life·Chrystopher L Nehaniv, J L Rhodes

Shapes in the shadow: evolutionary dynamics of morphogenesis

Aug 16, 2000·Artificial Life·P Hogeweg

Artificial chemistries--a review

Nov 20, 2001·Artificial Life·P DittrichW Banzhaf

From machine and tape to structure and function: formulation of a reflexively computing system

Sep 7, 2006·Artificial Life·Chris Salzberg

Genetic regulatory network models of biological clocks: evolutionary history matters

Jan 4, 2008·Artificial Life·Johannes F KnabeMaria J Schilstra

Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks

May 21, 2008·Artificial Life·Attila Egri-Nagy, Chrystopher L Nehaniv

Modular random Boolean networks

Jul 19, 2011·Artificial Life·Rodrigo Poblanno-Balp, Carlos Gershenson

A simple computational cell: coupling boolean gene and protein networks

Feb 24, 2012·Artificial Life·Larry Bull

Evolving Boolean networks with structural dynamism

Sep 4, 2012·Artificial Life·Larry Bull

Robustness, evolvability, and the logic of genetic regulation

Feb 5, 2013·Artificial Life·Joshua L PayneAndreas Wagner

Bespoke physics for living technology

Jul 31, 2013·Artificial Life·David H Ackley

Complex networks

Jul 19, 2011·Artificial Life·Carlos Gershenson, Mikhail Prokopenko

Connectivity, dynamics, and memory in reservoir computing with binary and analog neurons

Dec 24, 2009·Neural Computation·Lars BüsingRobert Legenstein

Applications of a formal approach to decipher discrete genetic networks

Jul 22, 2010·BMC Bioinformatics·Fabien CorblinLaurent Trilling

Reverse engineering gene regulatory network from microarray data using linear time-variant model

Mar 5, 2010·BMC Bioinformatics·Mitra KabirHitoshi Iba

Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks

Oct 22, 2010·BMC Bioinformatics·Vijender ChaitankarChaoyang Zhang

Techniques for analysing pattern formation in populations of stem cells and their progeny

Oct 14, 2011·BMC Bioinformatics·John A FozardHelen M Byrne

A genetic algorithm-based Boolean delay model of intracellular signal transduction in inflammation

Mar 5, 2011·BMC Bioinformatics·Chu Chun KangDavid Shan Hill Wong

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail

Oct 2, 2012·BMC Bioinformatics·Katrin KolczykCarsten Conradi

Comparison of co-expression measures: mutual information, correlation, and model based indices

Dec 12, 2012·BMC Bioinformatics·Lin SongSteve Horvath

Visualization of protein interaction networks: problems and solutions

Feb 13, 2013·BMC Bioinformatics·Giuseppe AgapitoMario Cannataro

Probabilistic estimation of microarray data reliability and underlying gene expression

Sep 12, 2003·BMC Bioinformatics·Sven BilkeMikael Sigvardsson

Simulation of microarray data with realistic characteristics

Jul 20, 2006·BMC Bioinformatics·Matti NykterOlli Yli-Harja

A methodology for the structural and functional analysis of signaling and regulatory networks

Feb 9, 2006·BMC Bioinformatics·Steffen KlamtErnst D Gilles

Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks

Jul 14, 2007·BMC Bioinformatics·Chang Sik Kim

Boolean networks using the chi-square test for inferring large-scale gene regulatory networks

Feb 3, 2007·BMC Bioinformatics·Haseong KimTaesung Park

Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling

Oct 16, 2007·BMC Bioinformatics·Yung-Keun KwonKwang-Hyun Cho

Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks

Dec 6, 2007·BMC Bioinformatics·Peng LiYouping Deng

Multistable and multistep dynamics in neutrophil differentiation

Mar 2, 2006·BMC Cell Biology·Hannah H ChangSui Huang

Model transcriptional networks with continuously varying expression levels

Dec 21, 2011·BMC Evolutionary Biology·Mauricio O CarneiroDaniel L Hartl

Genetic and environmental factors affecting cryptic variations in gene regulatory networks

Apr 30, 2013·BMC Evolutionary Biology·Watal M IwasakiMasakado Kawata

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

May 28, 2009·BMC Genomics·Carito GuziolowskiAnne Siegel

Application of Max-SAT-based ATPG to optimal cancer therapy design

Nov 21, 2012·BMC Genomics·Pey-Chang Kent Lin, Sunil P Khatri

Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium

Dec 19, 2013·BMC Microbiology·Jesper T RosenkrantzCarmen Pin

Boolean genetic network model for the control of C. elegans early embryonic cell cycles

Feb 26, 2014·Biomedical Engineering Online·Xiaotai HuangHong Yan

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

Jun 28, 2013·Cell Communication and Signaling : CCS·Regina Samaga, Steffen Klamt

Recent development and biomedical applications of probabilistic Boolean networks

Jul 3, 2013·Cell Communication and Signaling : CCS·Panuwat TrairatphisanThomas Sauter

Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks

Sep 14, 2011·EURASIP Journal on Bioinformatics & Systems Biology·Elena DimitrovaAbdul Salam Jarrah

Properties of Boolean networks and methods for their tests

Jan 15, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Johannes Georg KlotzSteffen Schober

Inferring Boolean network states from partial information

Sep 7, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Guy Karlebach

Harmonic analysis of Boolean networks: determinative power and perturbations

May 7, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Reinhard HeckelMartin Bossert

Boolean network-based model of the Bcl-2 family mediated MOMP regulation

Jun 19, 2013·Theoretical Biology & Medical Modelling·Tomas TokarJozef Ulicny

A method for the generation of standardized qualitative dynamical systems of regulatory networks

Mar 18, 2006·Theoretical Biology & Medical Modelling·Luis Mendoza, Ioannis Xenarios

A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies

Feb 14, 2006·Theoretical Biology & Medical Modelling·Benjamin RibbaSantiago Schnell

Dynamic models of immune responses: what is the ideal level of detail?

Aug 24, 2010·Theoretical Biology & Medical Modelling·Juilee ThakarRanran Zhang

Boolean network simulations for life scientists

Nov 19, 2008·Source Code for Biology and Medicine·István AlbertRéka Albert

Structural and functional analysis of cellular networks with CellNetAnalyzer

Apr 6, 2007·BMC Systems Biology·Steffen KlamtErnst D Gilles

Qualitative networks: a symbolic approach to analyze biological signaling networks

Apr 6, 2007·BMC Systems Biology·Marc A SchaubJasmin Fisher

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response

Mar 4, 2008·BMC Systems Biology·Areejit Samal, Sanjay Jain

Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

Nov 19, 2008·BMC Systems Biology·Mariana BenítezElena R Alvarez-Buylla

Dynamical modeling of the cholesterol regulatory pathway with Boolean networks

Nov 26, 2008·BMC Systems Biology·Gwenael Kervizic, Laurent Corcos

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation

Feb 19, 2009·BMC Systems Biology·Albert C HuangIlya Shmulevich

Information processing in the transcriptional regulatory network of yeast: functional robustness

Mar 21, 2009·BMC Systems Biology·Frank Emmert-Streib, Matthias Dehmer

Adapted Boolean network models for extracellular matrix formation

Jul 23, 2009·BMC Systems Biology·Johannes WollboldUlrike Gausmann

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Sep 30, 2009·BMC Systems Biology·Dominik M WittmannFabian J Theis

Snazer: the simulations and networks analyzer

Jan 9, 2010·BMC Systems Biology·Tommaso MazzaCorrado Priami

Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation

Sep 11, 2010·BMC Systems Biology·Li ShenWei Wang

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

Oct 6, 2010·BMC Systems Biology·Eugenio AzpeitiaElena R Alvarez-Buylla

Information propagation within the Genetic Network of Saccharomyces cerevisiae

Oct 28, 2010·BMC Systems Biology·Sharif ChowdhuryAndre S Ribeiro

A novel gene network inference algorithm using predictive minimum description length approach

Jun 11, 2010·BMC Systems Biology·Vijender ChaitankarChaoyang Zhang

Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles

Jul 13, 2011·BMC Systems Biology·John JackImran Shah

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae

Apr 14, 2011·BMC Systems Biology·Shengchao Ding, Wei Wang

Inference of gene regulatory networks from time series by Tsallis entropy

May 7, 2011·BMC Systems Biology·Fabrício Martins LopesRoberto M Cesar

A deterministic map of Waddington's epigenetic landscape for cell fate specification

May 31, 2011·BMC Systems Biology·Sudin BhattacharyaMelvin E Andersen

Stochastic Boolean networks: an efficient approach to modeling gene regulatory networks

Aug 30, 2012·BMC Systems Biology·Jinghang Liang, Jie Han

A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network

Sep 29, 2012·BMC Systems Biology·Changki HongInsik Shin

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Oct 20, 2012·BMC Systems Biology·Camille TerfveJulio Saez-Rodriguez

On optimal control policy for probabilistic Boolean network: a state reduction approach

Oct 12, 2012·BMC Systems Biology·X ChenWai-Ki Ching

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

Jan 3, 2013·BMC Systems Biology·Michael WeberDominik Driesch

Path2Models: large-scale generation of computational models from biochemical pathway maps

Nov 5, 2013·BMC Systems Biology·Finja BüchelNicolas Le Novère

Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks

Dec 20, 2013·BMC Systems Biology·Isaac CrespoAntonio Del Sol

Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

May 11, 2011·BMC Proceedings·Carlos H A HigaRonaldo F Hashimoto

Unraveling nature's networks

Oct 2, 2003·Genome Biology·Lev Soinov, Misha Kapushesky

Evolution of biological interaction networks: from models to real data

Dec 30, 2011·Genome Biology·Mark G F Sun, Philip M Kim

Mathematical biology modules based on modern molecular biology and modern discrete mathematics

Sep 3, 2010·CBE Life Sciences Education·Raina RobevaAlexander Enyedi

High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification

Jan 1, 2011·Journal of the American Statistical Association·Tao LuHulin Wu

Non-genetic heterogeneity of cells in development: more than just noise

Nov 13, 2009·Development·Sui Huang

A mutual support mechanism through intercellular movement of CAPRICE and GLABRA3 can pattern the Arabidopsis root epidermis

Sep 26, 2008·PLoS Biology·Natasha Saint SavageNicholas A M Monk

A logical model provides insights into T cell receptor signaling

Aug 29, 2007·PLoS Computational Biology·Julio Saez-RodriguezBurkhart Schraven

Evolution of evolvability in gene regulatory networks

Jul 12, 2008·PLoS Computational Biology·Anton Crombach, P Hogeweg

Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors

Mar 14, 2009·PLoS Computational Biology· ManuJ Reinitz

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

Aug 8, 2009·PLoS Computational Biology·Regina SamagaSteffen Klamt

Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary

Nov 26, 2009·PLoS Computational Biology·Dominik M WittmannFabian J Theis

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data

Dec 10, 2009·PLoS Computational Biology·Alexander MitsosLeonidas G Alexopoulos

Estimating the stochastic bifurcation structure of cellular networks

Mar 12, 2010·PLoS Computational Biology·Carl SongTheodore J Perkins

Reliability of transcriptional cycles and the yeast cell-cycle oscillator

Jul 16, 2010·PLoS Computational Biology·Volkan SevimJoshua E S Socolar

Minimal models of multidimensional computations

Apr 2, 2011·PLoS Computational Biology·Jeffrey D FitzgeraldTatyana O Sharpee

The roots of bioinformatics in theoretical biology

Apr 13, 2011·PLoS Computational Biology·P Hogeweg

Integrating quantitative knowledge into a qualitative gene regulatory network

Sep 22, 2011·PLoS Computational Biology·Jérémie BourdonAnne Siegel

Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia

Nov 22, 2011·PLoS Computational Biology·Assieh SaadatpourRéka Albert

Quantifying and analyzing the network basis of genetic complexity

Jul 14, 2012·PLoS Computational Biology·Ethan G Thompson, Timothy Galitski

Criticality is an emergent property of genetic networks that exhibit evolvability

Sep 13, 2012·PLoS Computational Biology·Christian Torres-SosaMaximino Aldana

Constraint and contingency in multifunctional gene regulatory circuits

Jun 14, 2013·PLoS Computational Biology·Joshua L Payne, Andreas Wagner

Modeling integrated cellular machinery using hybrid Petri-Boolean networks

Nov 19, 2013·PLoS Computational Biology·Natalie BerestovskyLuay Nakhleh

Optimal signal processing in small stochastic biochemical networks

Oct 25, 2007·PloS One·Etay ZivChris H Wiggins

Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram

Feb 14, 2008·PloS One·Jonathan E McDunnJ Perren Cobb

Boolean network model predicts cell cycle sequence of fission yeast

Feb 28, 2008·PloS One·Maria Davidich, Stefan Bornholdt

Critical dynamics in genetic regulatory networks: examples from four kingdoms

Jun 19, 2008·PloS One·Enrique BallezaMaximino Aldana

A publish-subscribe model of genetic networks

Sep 20, 2008·PloS One·Brett CalcottPaul A Hohenlohe

Timing robustness in the budding and fission yeast cell cycles

Feb 4, 2010·PloS One·Karan ManglaMark A Horowitz

Classification of genes and putative biomarker identification using distribution metrics on expression profiles

Feb 9, 2010·PloS One·Hung-Chung HuangVincent VanBuren

Prepatterning in the stem cell compartment

Jun 10, 2010·PloS One·Peter D TongePeter W Andrews

Attraction basins as gauges of robustness against boundary conditions in biological complex systems

Aug 12, 2010·PloS One·Jacques DemongeotSylvain Sené

Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed

Aug 21, 2010·PloS One·Masa TsuchiyaKumar Selvarajoo

A dynamical model of genetic networks for cell differentiation

Apr 6, 2011·PloS One·Marco VillaniRoberto Serra

Analysing dynamical behavior of cellular networks via stochastic bifurcations

Jun 8, 2011·PloS One·Anna ZakharovaAneta Koseska

Discrete dynamics model for the speract-activated Ca2+ signaling network relevant to sperm motility

Aug 23, 2011·PloS One·Jesús EspinalGustavo Martínez-Mekler

Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network

Aug 20, 2011·PloS One·Jan KrumsiekFabian J Theis

Additive functions in boolean models of gene regulatory network modules

Dec 2, 2011·PloS One·Christian DarabosM Giacobini

Oscillatory protein expression dynamics endows stem cells with robust differentiation potential

Nov 11, 2011·PloS One·Narito SuzukiKunihiko Kaneko

Statistical properties and robustness of biological controller-target networks

Jan 12, 2012·PloS One·Jacob D FealaGiovanni Paternostro

Analysis and practical guideline of constraint-based boolean method in genetic network inference

Jan 25, 2012·PloS One·Treenut SaithongAsawin Meechai

Bagging statistical network inference from large-scale gene expression data

Apr 6, 2012·PloS One·Ricardo de Matos Simoes, Frank Emmert-Streib

Understanding communication signals during mycobacterial latency through predicted genome-wide protein interactions and boolean modeling

Mar 27, 2012·PloS One·Shubhada R HegdeShekhar C Mande

Most networks in Wagner's model are cycling

Apr 19, 2012·PloS One·Ricardo PinhoMarcus W Feldman

Hub-centered gene network reconstruction using automatic relevance determination

May 10, 2012·PloS One·Matthias BöckLars Kaderali

Assessment method for a power analysis to identify differentially expressed pathways

May 26, 2012·PloS One·Shailesh Tripathi, Frank Emmert-Streib

Process-driven inference of biological network structure: feasibility, minimality, and multiplicity

Jul 21, 2012·PloS One·Guanyu WangChen Zeng

A model-based method for gene dependency measurement

Jul 26, 2012·PloS One·Qing ZhangDianjing Guo

Robustness and information propagation in attractors of Random Boolean Networks

Aug 4, 2012·PloS One·Jason Lloyd-PriceAndre S Ribeiro

Inference of biological pathway from gene expression profiles by time delay boolean networks

Sep 7, 2012·PloS One·Tung-Hung Chueh, Henry Horng-Shing Lu

From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation

Jan 10, 2013·PloS One·Xiaojie QiuTieliu Shi

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways

Dec 12, 2012·PloS One·Alexander MitsosLeonidas G Alexopoulos

Reverse engineering Boolean networks: from Bernoulli mixture models to rule based systems

Jan 4, 2013·PloS One·Mehreen SaeedHaroon Atique Babri

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks

Feb 26, 2013·PloS One·Giulio CaravagnaAlberto d'Onofrio

Balance between noise and information flow maximizes set complexity of network dynamics

Mar 22, 2013·PloS One·Tuomo Mäki-MarttunenMatti Nykter

Network class superposition analyses

Apr 9, 2013·PloS One·Carl A B PearsonRahul Simha

Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development

May 3, 2013·PloS One·Hauke BuschStefan A Rensing

Dynamics of cell-fate determination and patterning in the vascular bundles of Arabidopsis thaliana

Jun 1, 2013·PloS One·Mariana Benítez, Jan Hejátko

Bounds on the average sensitivity of nested canalizing functions

Jun 7, 2013·PloS One·Johannes Georg KlotzSteffen Schober

Dynamics of random Boolean networks under fully asynchronous stochastic update based on linear representation

Jun 21, 2013·PloS One·Chao Luo, Xingyuan Wang

Layered signaling regulatory networks analysis of gene expression involved in malignant tumorigenesis of non-resolving ulcerative colitis via integration of cross-study microarray profiles

Jul 5, 2013·PloS One·Shengjun FanXuejun Li

Majority rules with random tie-breaking in Boolean gene regulatory networks

Aug 8, 2013·PloS One·Claudine ChaouiyaRicardo Lima

A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks

Apr 11, 2014·PloS One·Wensheng GuoMingyu Sun

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

May 30, 2014·PloS One·Alex GraudenziMarco Antoniotti

Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions

Jul 25, 2014·PloS One·Philippe C FauconXiao Wang

Roumen Tsanev, pioneer of the early days of nucleic acid gel electrophoresis and histone code epigenetics

Apr 29, 2003·Biological Chemistry·Doncho Z StaynovWalter Schaffner

Genomics, complexity and drug discovery: insights from Boolean network models of cellular regulation

Sep 6, 2001·Pharmacogenomics·S Huang

Genetic network modeling

Aug 8, 2002·Pharmacogenomics·E P van SomerenM J T Reinders

Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation

Feb 1, 2008·HFSP Journal·Ralf BlosseyAndrew Phillips

A possible mechanism for evading temperature quantum decoherence in living matter by feshbach resonance

Jul 1, 2009·International Journal of Molecular Sciences·Nicola PocciaAntonio Bianconi

optPBN: an optimisation toolbox for probabilistic Boolean networks

Jul 2, 2014·PloS One·Panuwat TrairatphisanThomas Sauter

Tracking of time-varying genomic regulatory networks with a LASSO-Kalman smoother

Feb 13, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Jehandad KhanHassan M Fathallah-Shaykh

Detection of attractors of large Boolean networks via exhaustive enumeration of appropriate subspaces of the state space

Dec 18, 2013·BMC Bioinformatics·Nikolaos Berntenis, Martin Ebeling

Synchronization of coupled large-scale Boolean networks

Apr 5, 2014·Chaos·Fangfei Li

Relaxation dynamics and frequency response of a noisy cell signaling network

Jan 5, 2011·Chaos·P RuéJordi Garcia-Ojalvo

Introduction to focus issue: quantitative approaches to genetic networks

Jul 5, 2013·Chaos·Réka AlbertLeon Glass

Propagation of external regulation and asynchronous dynamics in random Boolean networks

Jul 7, 2007·Chaos·H MahmoudiR Zecchina

Criticality in conserved dynamical systems: experimental observation vs. exact properties

Apr 6, 2013·Chaos·Dimitrije MarkovićAndré Schuelein

Exponential cluster synchronization of impulsive delayed genetic oscillators with external disturbances

Jan 10, 2012·Chaos·Wenbing ZhangWu Zhu

An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks

Jul 5, 2013·Chaos·Jorge G T Zañudo, Réka Albert

Generic Properties of Random Gene Regulatory Networks

Oct 21, 2014·Quantitative Biology·Zhiyuan LiChao Tang

Construction of a Boolean model of gene and protein regulatory network with memory

Jan 22, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Meng YangTianguang Chu

Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review

Jan 29, 2014·Journal of Bioinformatics and Computational Biology·Ismael Sánchez-OsorioEdgar Dantan

In vitro regulatory models for systems biology

May 8, 2013·Biotechnology Advances·Anthony J GenotYannick Rondelez

Gene perturbation and intervention in context-sensitive stochastic Boolean networks

Jun 3, 2014·BMC Systems Biology·Peican ZhuJie Han

Dynamic pattern evolution on scale-free networks

Jul 12, 2005·Proceedings of the National Academy of Sciences of the United States of America·Haijun Zhou, Reinhard Lipowsky

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

Dec 3, 2013·Bioinformatics·Sebastian DümckeAchim Tresch

A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty

Apr 9, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Mohammadmahdi R Yousefi, Edward R Dougherty

A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure

Apr 11, 2014·Journal of the Royal Society, Interface·Sam F GreenburyS E Ahnert

An extended gene protein/products Boolean network model including post-transcriptional regulation

Aug 1, 2014·Theoretical Biology & Medical Modelling·Alfredo BensoAlessandro Vasciaveo

The role of certain Post classes in Boolean network models of genetic networks

Sep 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ilya ShmulevichWei Zhang

The yeast cell-cycle network is robustly designed

Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang

Defining an essential transcription factor program for naïve pluripotency

Jun 7, 2014·Science·S-J DunnAustin Smith

A natural class of robust networks

Jul 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Maximino Aldana, Philippe Cluzel

Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity

Apr 1, 2014·Molecular Biology and Evolution·Lu ChenAraxi O Urrutia

Characterizing cancer subtypes as attractors of Hopfield networks

Jan 11, 2014·Bioinformatics·Stefan R Maetschke, Mark A Ragan

Structure and function of the feed-forward loop network motif

Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Shmoolik Mangan, Uri Alon

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

May 23, 2013·Biochimica Et Biophysica Acta·Faiz M KhanJulio Vera

Eukaryotic cells are dynamically ordered or critical but not chaotic

Sep 13, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ilya ShmulevichMaximino Aldana

Stochastic gene expression as a many-body problem

Feb 28, 2003·Proceedings of the National Academy of Sciences of the United States of America·Masaki Sasai, Peter G Wolynes

Asynchronous stochastic Boolean networks as gene network models

Jun 18, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Peican Zhu, Jie Han

Controllability of asynchronous Boolean multiplex control networks

Oct 3, 2014·Chaos·Chao LuoHong Liu

Review on statistical methods for gene network reconstruction using expression data

Apr 15, 2014·Journal of Theoretical Biology·Y X Rachel Wang, Haiyan Huang

Social insect colony as a biological regulatory system: modelling information flow in dominance networks

Oct 17, 2014·Journal of the Royal Society, Interface·Anjan K NandiKunal Bhattacharya

Hierarchical closeness efficiently predicts disease genes in a directed signaling network

Dec 3, 2014·Computational Biology and Chemistry·Tien-Dzung Tran, Yung-Keun Kwon

Evolution of communication protocols using an artificial regulatory network

Aug 26, 2014·Artificial Life·W Garrett Mitchener

Evolving functional and structural dynamism in coupled Boolean networks

Apr 16, 2014·Artificial Life·Larry Bull

Robustness in regulatory interaction networks. A generic approach with applications at different levels: physiologic, metabolic and genetic

Jan 9, 2010·International Journal of Molecular Sciences·Jacques DemongeotSylvain Sené

Cancer systems biology: signal processing for cancer research

Mar 29, 2011·Chinese Journal of Cancer·Olli Yli-HarjaWei Zhang

Optimal control of gene regulatory networks with effectiveness of multiple drugs: a Boolean network approach

Sep 24, 2013·BioMed Research International·Koichi Kobayashi, Kunihiko Hiraishi

Epigenetic memories: structural marks or active circuits?

Feb 15, 2012·Cellular and Molecular Life Sciences : CMLS·Floriane Nicol-BenoîtDenis Michel

Optimal control for probabilistic Boolean networks

Mar 18, 2010·IET Systems Biology·Q LiuT Zhou

Controllability of Boolean networks via input controls under Harvey's update scheme

Mar 5, 2016·Chaos·Chao LuoYuanJie Zheng

Sampled-Data State Feedback Stabilization of Boolean Control Networks

Feb 19, 2016·Neural Computation·Yang LiuJianquan Lu

Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis

Oct 16, 2014·BMC Systems Biology·Johannes WollboldOlaf Wolkenhauer

Understanding disease mechanisms with models of signaling pathway activities

Oct 26, 2014·BMC Systems Biology·Patricia Sebastian-LeonJoaquín Dopazo

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

Feb 6, 2016·BMC Bioinformatics·Andrea ParoniMarco Antoniotti

Boolean Models of Biological Processes Explain Cascade-Like Behavior

Jan 30, 2016·Scientific Reports·Hao ChenChen Zeng

Epigenetic resolution of the 'curse of complexity' in adaptive evolution of complex traits

Jun 3, 2014·The Journal of Physiology·Alexander V Badyaev

Approaches to in vitro tissue regeneration with application for human disease modeling and drug development

May 6, 2014·Drug Discovery Today·Mohammad R EbrahimkhaniJeffrey T Borenstein

Complete synchronization of temporal Boolean networks

Apr 13, 2013·Neural Networks : the Official Journal of the International Neural Network Society·Fangfei Li, Xiwen Lu

On the number of different dynamics in Boolean networks with deterministic update schedules

Feb 7, 2013·Mathematical Biosciences·Julio AracenaM Montalva

A new approach for global controllability of higher order Boolean control network

Jan 10, 2013·Neural Networks : the Official Journal of the International Neural Network Society·Hao Chen, Jitao Sun

Bayesian estimation of the discrete coefficient of determination

Jan 26, 2016·EURASIP Journal on Bioinformatics & Systems Biology·Ting Chen, Ulisses M Braga-Neto

Dreaming of mathematical neuroscience for half a century

Oct 25, 2012·Neural Networks : the Official Journal of the International Neural Network Society·Shun-ichi Amari

Controllability and optimal control of a temporal Boolean network

Jul 13, 2012·Neural Networks : the Official Journal of the International Neural Network Society·Fangfei Li, Jitao Sun

The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks

Dec 14, 2011·Journal of Theoretical Biology·Dov A PechenickJason H Moore

Regulatory patterns in molecular interaction networks

Aug 30, 2011·Journal of Theoretical Biology·David Murrugarra, Reinhard C Laubenbacher

"Immunetworks", intersecting circuits and dynamics

Mar 29, 2011·Journal of Theoretical Biology·Jacques DemongeotFlorence Thuderoz

Structure-function relations are subtle in genetic regulatory networks

Feb 19, 2011·Mathematical Biosciences·Michael E Wall

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks

Mar 2, 2011·Bio Systems·Andre S RibeiroOlli Yli-Harja

Logical and symbolic analysis of robust biological dynamics

Oct 22, 2010·Current Opinion in Genetics & Development·Leon Glass, Hava T Siegelmann

Evolution of form and function in a model of differentiated multicellular organisms with gene regulatory networks

Sep 15, 2010·Bio Systems·Daniel Lobo, Francisco J Vico

Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks

Oct 16, 2010·Journal of Theoretical Biology·Jan-Ke LarssonRobert Forchheimer

Attractor analysis of asynchronous Boolean models of signal transduction networks

Jul 28, 2010·Journal of Theoretical Biology·Assieh SaadatpourRéka Albert

Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks

Jul 27, 2010·Journal of Theoretical Biology·Dominik M WittmannFabian J Theis

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

Aug 11, 2010·Journal of Theoretical Biology·Sam F GreenburyArd A Louis

Boolean modeling identifies Greatwall/MASTL as an important regulator in the AURKA network of neuroblastoma

Dec 1, 2015·Cancer Letters·Meike DahlhausChristian Beltinger

Diseases as network perturbations

Aug 17, 2010·Current Opinion in Biotechnology·Antonio Del SolDavid Galas

Stochastic stability of Markovian jumping uncertain stochastic genetic regulatory networks with interval time-varying delays

May 1, 2010·Mathematical Biosciences·P BalasubramaniamR Krishnasamy

Higher order Boolean networks as models of cell state dynamics

Mar 23, 2010·Journal of Theoretical Biology·Elke K MarkertAlexei Vazquez

On the dynamics of random Boolean networks subject to noise: attractors, ergodic sets and cell types

Apr 20, 2010·Journal of Theoretical Biology·R SerraA Colacci

Receptor cross-talk in angiogenesis: mapping environmental cues to cell phenotype using a stochastic, Boolean signaling network model

Mar 24, 2010·Journal of Theoretical Biology·Amy L BauerThimo Rohlf

Anomalies in the transcriptional regulatory network of the yeast Saccharomyces cerevisiae

Dec 17, 2009·Journal of Theoretical Biology·M Tuğrul, A Kabakçioğlu

Identification of potential targets in biological signalling systems through network perturbation analysis

Jan 19, 2010·Bio Systems·Francisco AzuajeDaniel R Wagner

Stochastic and delayed stochastic models of gene expression and regulation

Nov 4, 2009·Mathematical Biosciences·Andre S Ribeiro

Morphogenesis by coupled regulatory networks: reliable control of positional information and proportion regulation

Aug 1, 2009·Journal of Theoretical Biology·Thimo Rohlf, Stefan Bornholdt

Comparing different ODE modelling approaches for gene regulatory networks

Aug 12, 2009·Journal of Theoretical Biology·A PolynikisM di Bernardo

Statistical mechanics of the neocortex

Aug 22, 2009·Progress in Biophysics and Molecular Biology·Michael A Buice, Jack D Cowan

Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch

Jun 9, 2009·Journal of Theoretical Biology·Andre S RibeiroOlli Yli-Harja

A model of sequential branching in hierarchical cell fate determination

Jul 21, 2009·Journal of Theoretical Biology·David V FosterStuart A Kauffman

Dynamics of unperturbed and noisy generalized Boolean networks

Jul 21, 2009·Journal of Theoretical Biology·Ch DarabosM Giacobini

Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective

Jul 15, 2009·Seminars in Cell & Developmental Biology·Sui HuangStuart A Kauffman

Robust filtering for stochastic genetic regulatory networks with time-varying delay

Apr 28, 2009·Mathematical Biosciences·Guoliang WeiXiaohui Liu

Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving

May 9, 2009·Journal of Theoretical Biology·Zhongxing Mai, Haiyan Liu

On the robustness of update schedules in Boolean networks

Jun 10, 2009·Bio Systems·Julio AracenaLilian Salinas

Reliability of regulatory networks and its evolution

Mar 4, 2009·Journal of Theoretical Biology·Stefan Braunewell, Stefan Bornholdt

Gene regulatory network inference: data integration in dynamic models-a review

Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke

Statistical Detection of Intrinsically Multivariate Predictive Genes

Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ting Chen, Ulisses M Braga-Neto

Modelling evolutionary cell behaviour using neural networks: application to tumour growth

Nov 26, 2008·Bio Systems·P Gerlee, A R A Anderson

Intrinsic properties of Boolean dynamics in complex networks

Nov 19, 2008·Journal of Theoretical Biology·Shu-Ichi KinoshitaHiroaki S Yamada

The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model

Aug 12, 2008·Journal of Theoretical Biology·Maria Davidich, Stefan Bornholdt

The flux-summation theorem and the 'evolution of dominance'

Aug 19, 2008·Journal of Theoretical Biology·Paul S Agutter

Logic models of pathway biology

May 13, 2008·Drug Discovery Today·Steven WattersonPeter Ghazal

Towards a general theory of adaptive walks on rugged landscapes

Sep 7, 1987·Journal of Theoretical Biology·Stuart A Kauffman, S Levin

Chaotic gene regulatory networks can be robust against mutations and noise

Apr 18, 2008·Journal of Theoretical Biology·Volkan Sevim, Per Arne Rikvold

Comparative study of the transcriptional regulatory networks of E. coli and yeast: structural characteristics leading to marginal dynamic stability

Aug 19, 2007·Journal of Theoretical Biology·Deok-Sun Lee, Heiko Rieger

Noisy attractors and ergodic sets in models of gene regulatory networks

Jun 5, 2007·Journal of Theoretical Biology·Andre S Ribeiro, Stuart A Kauffman

Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models

Mar 14, 2007·Journal of Theoretical Biology·Rui ZhuStuart A Kauffman

A Markovian approach to the control of genetic regulatory networks

Feb 27, 2007·Bio Systems·Peter C Y Chen, Jeremy W Chen

Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity

Jan 6, 2007·Journal of Theoretical Biology·Stefan Braunewell, Stefan Bornholdt

Data identification for improving gene network inference using computational algebra

Oct 5, 2014·Bulletin of Mathematical Biology·Elena Dimitrova, Brandilyn Stigler

Piecewise linear and Boolean models of chemical reaction networks

Nov 22, 2014·Bulletin of Mathematical Biology·Alan Veliz-CubaKrešimir Josić

Biological networks: the microscope of the twenty-first century?

Nov 4, 2015·Frontiers in Genetics·Frank Emmert-Streib, Matthias Dehmer

Function does not follow form in gene regulatory circuits

Aug 21, 2015·Scientific Reports·Joshua L Payne, Andreas Wagner

Dynamical approaches to modeling developmental gene regulatory networks

Jun 17, 2009·Birth Defects Research. Part C, Embryo Today : Reviews·Nicholas Geard, Kai Willadsen

Gene networks and liar paradoxes

Sep 2, 2009·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mark Isalan

Network modeling of signal transduction: establishing the global view

Oct 22, 2008·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Hans A KestlerMichael Kühl

Inference, validation, and dynamic modeling of transcription networks in multipotent hematopoietic cells

Apr 20, 2007·Annals of the New York Academy of Sciences·Shamit SonejiGillian May

Signal integration in the galactose network of Escherichia coli

Jul 17, 2007·Molecular Microbiology·Szabolcs SemseySankar Adhya

Reverse engineering of gene networks with LASSO and nonlinear basis functions

Apr 8, 2009·Annals of the New York Academy of Sciences·Mika GustafssonJesper Tegnér

A gene network simulator to assess reverse engineering algorithms

Apr 8, 2009·Annals of the New York Academy of Sciences·Barbara Di CamilloClaudio Cobelli

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models

Nov 20, 2015·Bioinformatics·Martin PirklRainer Spang

The inheritance of process: a dynamical systems approach

Oct 13, 2012·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Johannes JaegerNick Monk

Network biology: a direct approach to study biological function

Jan 5, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Frank Emmert-Streib, Galina Glazko

A general strategy for cellular reprogramming: the importance of transcription factor cross-repression

Jul 23, 2013·Stem Cells·Isaac Crespo, Antonio Del Sol

Plant systems biology: network matters

Feb 12, 2011·Plant, Cell & Environment·Mikaël LucasMalcolm J Bennett

Using network biology to bridge pharmacokinetics and pharmacodynamics in oncology

Sep 6, 2013·CPT: Pharmacometrics & Systems Pharmacology·D C Kirouac, M D Onsum

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

Nov 22, 2011·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Sui Huang

Toward an integrated software platform for systems pharmacology

Oct 24, 2013·Biopharmaceutics & Drug Disposition·Samik GhoshHiroaki Kitano

Blood flow and endothelial cell phenotype regulation during sprouting angiogenesis

Aug 2, 2015·Medical & Biological Engineering & Computing·Hossein BazmaraArman Rahmim

Identification of Potential Drug Targets in Cancer Signaling Pathways using Stochastic Logical Models

Mar 19, 2016·Scientific Reports·Peican ZhuJie Han

Leveraging systems biology approaches in clinical pharmacology

Aug 29, 2013·Biopharmaceutics & Drug Disposition·Ioannis N MelasLeonidas G Alexopoulos

Drawing a Waddington landscape to capture dynamic epigenetics

Oct 12, 2013·Biology of the Cell·Floriane Nicol-BenoitDenis Michel

Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

Oct 2, 2014·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Réka Albert, Juilee Thakar

Boolean networks with multiexpressions and parameters

Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yi Ming Zou

Synchronization of Boolean Networks with Different Update Schemes

Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hao ZhangXiaohui Lin

Synchronization in an array of output-coupled Boolean networks with time delay

Nov 25, 2014·IEEE Transactions on Neural Networks and Learning Systems·Jie ZhongJinde Cao

Complete synchronization of Boolean networks

May 1, 2012·IEEE Transactions on Neural Networks and Learning Systems·Rui Li, Tianguang Chu

Growing seed genes from time series data and thresholded Boolean networks with perturbation

May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Carlos H A HigaRonaldo F Hashimoto

Algebraic representation of asynchronous multiple-valued networks and its dynamics

Dec 18, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Chao Luo, Xingyuan Wang

Stochastic multiple-valued gene networks

Apr 1, 2014·IEEE Transactions on Biomedical Circuits and Systems·Peican Zhu, Jie Han

Controllability and observability of Boolean control networks with time-variant delays in states

May 9, 2014·IEEE Transactions on Neural Networks and Learning Systems·Lijun Zhang, Kuize Zhang

Inferring connectivity of genetic regulatory networks using information-theoretic criteria

May 3, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wentao ZhaoEdward R Dougherty

Search for steady states of piecewise-linear differential equation models of genetic regulatory networks

May 3, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hidde de Jong, Michel Page

Multiscale binarization of gene expression data for reconstructing Boolean networks

Apr 6, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Martin HopfensitzHans A Kestler

Parameter estimation using meta-heuristics in systems biology: a comprehensive review

Apr 6, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jianyong SunCharlie Hodgman

A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data

Feb 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Theodore J Perkins, Michael T Hallett

SimBioNeT: a simulator of biological network topology

Aug 24, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Barbara Di CamilloClaudio Cobelli

A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures

May 18, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kyriakos Kentzoglanakis, Matthew Poole

A SAT-based algorithm for finding attractors in synchronous Boolean networks

Jul 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Elena Dubrova, Maxim Teslenko

Designing logical rules to model the response of biomolecular networks with complex interactions: an application to cancer modeling

Aug 25, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Carito GuziolowskiAnne Siegel

State-space analysis of Boolean networks

Feb 23, 2010·IEEE Transactions on Neural Networks·Daizhan Cheng, Hongsheng Qi

An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations

Apr 6, 2016·Frontiers in Physiology·Masaki Nakagawa, Yuichi Togashi

Modeling genetic networks from clonal analysis

Aug 11, 2004·Journal of Theoretical Biology·Radhakrishnan NagarajanCharlotte A Peterson

Splitting the dynamics of large biochemical interaction networks

Dec 2, 2004·Journal of Theoretical Biology·Elisabeth Pécou

Model construction of Boolean network via observed data

Feb 24, 2011·IEEE Transactions on Neural Networks·Daizhan ChengZhiqiang Li

A computational algebra approach to the reverse engineering of gene regulatory networks

Jul 13, 2004·Journal of Theoretical Biology·Reinhard C Laubenbacher, Brandilyn Stigler

Observability of Boolean control networks with state time delays

Apr 27, 2011·IEEE Transactions on Neural Networks·Fangfei LiQi-Di Wu

Boolean dynamics of biological networks with multiple coupled feedback loops

Jan 30, 2007·Biophysical Journal·Yung-Keun Kwon, Kwang-Hyun Cho

The effect of negative feedback loops on the dynamics of boolean networks

Apr 1, 2008·Biophysical Journal·Eduardo SontagAbdul Salam Jarrah

Robustness and evolvability in genetic regulatory networks

Dec 26, 2006·Journal of Theoretical Biology·Maximino AldanaOsbaldo Resendiz

Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks

Nov 2, 2015·Bioinformatics·Eduardo PalmaJulio Aracena

The emergence of goals in a self-organizing network: a non-mentalist model of intentional actions

Sep 5, 2006·Neural Networks : the Official Journal of the International Neural Network Society·Yoram Louzoun, Henri Atlan

An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification

Dec 17, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mohammad Shahrokh Esfahani, Edward R Dougherty

Synchronization of Asynchronous Switched Boolean Network

Dec 17, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hao ZhangXiaohui Lin

Size and connectivity as emergent properties of a developing immune network

Apr 7, 1991·Journal of Theoretical Biology·R J de Boer, A S Perelson

Hyperoxidant states cause microbial cell differentiation by cell isolation from dioxygen

Jan 23, 1990·Journal of Theoretical Biology·W Hansberg, J Aguirre

Boolean networks with biologically relevant rules show ordered behavior

Dec 26, 2006·Bio Systems·S NikolajewaT Wilhelm

Adaptive properties of living beings: proposal for a generic mechanism. (Self-programming machines III)

Mar 21, 2006·Comptes rendus biologies·J P Moulin

An analysis of the class of gene regulatory functions implied by a biochemical model

Dec 31, 2005·Bio Systems·John GrefenstetteStuart A Kauffman

Dynamical properties of model gene networks and implications for the inverse problem

Jan 3, 2006·Bio Systems·Theodore J PerkinsLeon Glass

Dynamical modeling of biological regulatory networks

Jan 3, 2006·Bio Systems·Claudine ChaouiyaDenis Thieffry

The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli

Jan 13, 2006·Journal of Molecular Biology·Shmoolik ManganUri Alon

Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation

Nov 24, 2005·Bio Systems·K MorgenthalR Steuer

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

Apr 7, 2007·Signal Processing·Harri LähdesmäkiOlli Yli-Harja

Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli

Jun 25, 2005·Journal of Theoretical Biology·Cheol-Min GhimByungnam Kahng

Designing Experiments to Discriminate Families of Logic Models

Sep 22, 2015·Frontiers in Bioengineering and Biotechnology·Santiago VidelaCarito Guziolowski

Consistent stabilizability of switched Boolean networks

Jun 22, 2013·Neural Networks : the Official Journal of the International Neural Network Society·Haitao Li, Yuzhen Wang

Anergy in self-directed B lymphocytes: A statistical mechanics perspective

May 17, 2014·Journal of Theoretical Biology·Elena AgliariDaniele Tantari

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

May 24, 2015·Bioinformatics·David HenriquesJulio R Banga

Towards patient stratification and treatment in the autoimmune disease lupus erythematosus using a systems pharmacology approach

Apr 16, 2016·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·M Leire Ruiz-CerdáJosé David Gómez-Mantilla

Dynamical properties of gene regulatory networks involved in long-term potentiation

Aug 25, 2015·Frontiers in Molecular Neuroscience·Gonzalo S NidoJoanna M Williams

Forced synchronization of autonomous dynamical Boolean networks

Sep 4, 2015·Chaos·R R Rivera-DurónDaniel J Gauthier

HSM - a hybrid system based approach for modelling intracellular networks

Dec 26, 2012·Gene·Alvis BrazmaJuris Viksna

Integration of cellular signals in chattering environments

May 16, 2012·Progress in Biophysics and Molecular Biology·P RuéA J Pons

Kolmogorov complexity of epithelial pattern formation: the role of regulatory network configuration

Mar 19, 2013·Bio Systems·Nicholas S FlannGregory J Podgorski

The incorporation of epigenetics in artificial gene regulatory networks

Mar 19, 2013·Bio Systems·Alexander P TurnerAndy M Tyrrell

Characterising neurological time series data using biologically motivated networks of coupled discrete maps

Mar 19, 2013·Bio Systems·Michael A LonesD R Stuart Jamieson

Microenvironment-evoked cell lineage conversion: Shifting the focus from internal reprogramming to external forcing

May 9, 2012·Ageing Research Reviews·Ji LinWei-dong Han

Modeling and visualizing cell type switching

May 17, 2014·Computational and Mathematical Methods in Medicine·Ahmadreza GhaffarizadehNicholas S Flann

Activation of Apoptotic Signal in Endothelial Cells through Intracellular Signaling Molecules Blockade in Tumor-Induced Angiogenesis

Sep 9, 2015·BioMed Research International·Hossein BazmaraAli Elkamel

Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences

Jul 27, 2015·BMC Systems Biology·Sergio Pérez-LanderoJorge Nieto-Sotelo

Delayed transition to new cell fates during cellular reprogramming

May 2, 2014·Developmental Biology·Xianrui ChengDavid R McClay

Regulation by transcription factors in bacteria: beyond description

Dec 17, 2008·FEMS Microbiology Reviews·Enrique BallezaJulio Collado-Vides

Symmetry structure in discrete models of biochemical systems: natural subsystems and the weak control hierarchy in a new model of computation driven by interactions

Jun 17, 2015·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Chrystopher L NehanivMaria J Schilstra

Structural determinants of criticality in biological networks

May 26, 2015·Frontiers in Physiology·Sergi ValverdeJordi Garcia-Ojalvo

Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia

Jun 20, 2015·Theoretical Biology & Medical Modelling·María Camila Álvarez-SilvaAndrés Fernando González Barrios

Neutral space analysis for a Boolean network model of the fission yeast cell cycle network

Feb 28, 2015·Biological Research·Gonzalo A RuzEric Goles

A Boolean gene regulatory model of heterosis and speciation

Apr 19, 2015·BMC Evolutionary Biology·Peter Martin Ferdinand EmmrichVera Pancaldi

A proposal for using the ensemble approach to understand genetic regulatory networks

Sep 15, 2004·Journal of Theoretical Biology·Stuart A Kauffman

Host-pathogen systems biology

Apr 4, 2006·Drug Discovery Today·Christian V Forst

Control of complex networks requires both structure and dynamics

Apr 19, 2016·Scientific Reports·Alexander J Gates, Luis M Rocha

A Boolean algorithm for reconstructing the structure of regulatory networks

Oct 20, 2004·Metabolic Engineering·Sarika MehraGeorge Karypis

Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates

May 15, 2015·BMC Systems Biology·Jose Davila-VelderrainElena R Alvarez-Buylla

The Need for Formally Defining "Modern Medicine" by Means of Experimental Design

May 6, 2016·Frontiers in Genetics·Frank Emmert-StreibOlli Yli-Harja

Evolving Boolean regulatory networks with epigenetic control

Dec 24, 2013·Bio Systems·Larry Bull

From ABC genes to regulatory networks, epigenetic landscapes and flower morphogenesis: making biological sense of theoretical approaches

Nov 20, 2009·Seminars in Cell & Developmental Biology·Elena R Alvarez-BuyllaPablo Padilla-Longoria

Multistable switches and their role in cellular differentiation networks

Aug 1, 2014·BMC Bioinformatics·Ahmadreza GhaffarizadehGregory J Podgorski

Gap Gene Regulatory Dynamics Evolve along a Genotype Network

Jan 23, 2016·Molecular Biology and Evolution·Anton CrombachJohannes Jaeger

Synthetic biology: evolution or revolution? A co-founder's perspective

Oct 16, 2013·Current Opinion in Chemical Biology·Timothy S Gardner, Kristy Hawkins

Cooperative development of logical modelling standards and tools with CoLoMoTo

Jan 27, 2015·Bioinformatics·Aurélien NaldiClaudine Chaouiya

Multi-scale modeling in biology: how to bridge the gaps between scales?

Jun 28, 2011·Progress in Biophysics and Molecular Biology·Zhilin QuMelissa Nivala

A computer scientist's view on mobile DNA: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro

Jul 23, 2013·Physics of Life Reviews·Larry Bull

In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system

Dec 24, 1998·Chemistry & Biology·T EllingerJ S McCaskill

Refining network reconstruction based on functional reliability

Mar 19, 2014·Journal of Theoretical Biology·Yunjun ZhangZhi Geng

A sub-space greedy search method for efficient Bayesian Network inference

Jul 12, 2011·Computers in Biology and Medicine·Qing ZhangDianjing Guo

Punctuated evolution and robustness in morphogenesis

Jul 6, 2014·Bio Systems·D GrigorievA Weber

Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

Apr 7, 2007·Developmental Biology·Sui HuangTariq Enver

Engineering and Biology: Counsel for a Continued Relationship

Jun 19, 2015·Biological Theory·Brett CalcottAndreas Wagner

The Comet Cometh: Evolving Developmental Systems

Mar 24, 2015·Biological Theory·Johannes JaegerWerner Callebaut

Poised for survival: criticality, natural selection, and excitation-transcription coupling

Jan 28, 2015·The International Journal of Biochemistry & Cell Biology·Ron Wallace

Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications

Mar 15, 2015·Frontiers in Cell and Developmental Biology·Karl J NiklasStuart A Newman

Temporal-logic analysis of microglial phenotypic conversion with exposure to amyloid-β

Nov 20, 2014·Molecular BioSystems·Thomas J Anastasio

Homeopathic effect: a network perspective

Oct 10, 2002·Homeopathy : the Journal of the Faculty of Homeopathy·J L Torres

Learning delayed influences of biological systems

Feb 3, 2015·Frontiers in Bioengineering and Biotechnology·Tony RibeiroChiaki Sakama

Toward synthesizing executable models in biology

Jan 8, 2015·Frontiers in Bioengineering and Biotechnology·Jasmin FisherRastislav Bodik

Counteraction of the multifunctional restriction factor tetherin

May 2, 2014·Frontiers in Microbiology·Daniel Sauter

Universal scaling laws for hierarchical complexity in languages, organisms, behaviors and other combinatorial systems

Jul 11, 2001·Journal of Theoretical Biology·M A Changizi

Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation

Mar 29, 2000·Journal of Theoretical Biology·P Hogeweg

Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling

Jul 26, 2014·Journal of the American Statistical Association·Hulin WuHua Liang

In silico determination of the effect of multi-target drugs on calcium dynamics signaling network underlying sea urchin spermatozoa motility

Aug 28, 2014·PloS One·Jesús Espinal-EnríquezGustavo Martínez-Mekler

Control of asymmetric Hopfield networks and application to cancer attractors

Aug 30, 2014·PloS One·Anthony SzedlakCarlo Piermarocchi

Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation

Aug 27, 2015·PLoS Computational Biology·Tadashi MiyamotoKunihiko Kaneko

Automated Synthesis and Analysis of Switching Gene Regulatory Networks

May 15, 2016·Bio Systems·Yoli ShavitHillel Kugler

A full bayesian approach for boolean genetic network inference

Jan 1, 2015·PloS One·Shengtong HanXiaodan Fan

Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord

Nov 15, 2014·PloS One·Anna LovricsKrisztián A Kovács

Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence

Jun 15, 2016·Scientifica·Abhinandan KhanGoutam Saha

Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells

Aug 15, 2014·PLoS Computational Biology·Huilei XuAvi Ma'ayan

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

Jun 13, 2015·PloS One·Johan Kerkhofs, Liesbet Geris

Dynamical modeling of the cell cycle and cell fate emergence in Caulobacter crescentus

Nov 5, 2014·PloS One·César Quiñones-VallesAgustino Martínez-Antonio

Logical Modeling and Dynamical Analysis of Cellular Networks

Jun 16, 2016·Frontiers in Genetics·Wassim Abou-JaoudéClaudine Chaouiya

Stability depends on positive autoregulation in Boolean gene regulatory networks

Nov 7, 2014·PLoS Computational Biology·Ricardo PinhoMarcus W Feldman

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

Jun 12, 2016·Bio Systems·R P Vivek-Ananth, Areejit Samal

Data-driven optimizations for model checking of multi-valued regulatory networks

Jun 15, 2016·Bio Systems·Adam StreckHeike Siebert

Qualitative dynamics semantics for SBGN process description

Jun 17, 2016·BMC Systems Biology·Adrien RougnyLoïc Paulevé

Modular genetic regulatory networks increase organization during pattern formation

Jun 22, 2016·Bio Systems·Hamid MohamadlouNicholas S Flann

The reverse control of irreversible biological processes

Jun 22, 2016·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Kwang-Hyun ChoSang-Min Park

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems

Aug 12, 2015·PloS One·Sherif H Elmeligy AbdelhamidS S Ravi

Cell fate reprogramming by control of intracellular network dynamics

Apr 8, 2015·PLoS Computational Biology·Jorge G T Zañudo, Réka Albert

Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

Jul 2, 2016·Physics of Life Reviews·Olivier C MartinM Zagorski

Using synchronous Boolean networks to model several phenomena of collective behavior

Dec 20, 2014·PloS One·Stepan Kochemazov, Alexander Semenov

Super-transient scaling in time-delay autonomous Boolean network motifs

Oct 27, 2016·Chaos·Otti D'HuysDaniel J Gauthier

Control of Large-Scale Boolean Networks via Network Aggregation

Aug 11, 2015·IEEE Transactions on Neural Networks and Learning Systems·Yin ZhaoDaizhan Cheng

A Method to Identify and Analyze Biological Programs through Automated Reasoning

Sep 27, 2016·NPJ Systems Biology and Applications·Boyan YordanovStephen Emmott

Modelling and analysis of the feeding regimen induced entrainment of hepatocyte circadian oscillators using petri nets

Mar 20, 2015·PloS One·Samar Hayat Khan Tareen, Jamil Ahmad

Logical Reduction of Biological Networks to Their Most Determinative Components

Jul 16, 2016·Bulletin of Mathematical Biology·Mihaela T Matache, Valentin Matache

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space

Jul 22, 2016·Journal of the Royal Society, Interface·S E Ahnert, T M A Fink

Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors

Jul 28, 2016·Bio Systems·Satya Swarup SamalOvidiu Radulescu

Time-Delayed Models of Gene Regulatory Networks

Nov 18, 2015·Computational and Mathematical Methods in Medicine·K ParmarS J Hogan

Discrete dynamic modeling of cellular signaling networks

Nov 10, 2009·Methods in Enzymology·Réka Albert, Rui-Sheng Wang

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming

Aug 4, 2016·Bio Systems·M OstrowskiCarito Guziolowski

Evolutionary Developmental Biology (Evo-Devo) Research in Latin America

Aug 6, 2016·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Sylvain MarcelliniFederico D Brown

An efficient approach of attractor calculation for large-scale Boolean gene regulatory networks

Aug 16, 2016·Journal of Theoretical Biology·Qinbin HeBin Lin

Recurrent neural network based hybrid model for reconstructing gene regulatory network

Aug 30, 2016·Computational Biology and Chemistry·Khalid Raza, Mansaf Alam

Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation

Aug 21, 2016·BMC Systems Biology·Xiao Gan, Réka Albert

State feedback control design for Boolean networks

Sep 3, 2016·BMC Systems Biology·Rongjie LiuYu-Fang Jin

A Bayesian Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway

Sep 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Priya S VenkatAniruddha Datta

Identification of control targets in Boolean molecular network models via computational algebra

Sep 25, 2016·BMC Systems Biology·David MurrugarraReinhard C Laubenbacher

Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks

Oct 8, 2016·Scientific Reports·Pablo VillegasMiguel A Muñoz

An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

Oct 9, 2016·BMC Systems Biology·Sang-Mok Choo, Kwang-Hyun Cho

Modifiable automata self-modifying automata

Sep 1, 1992·Acta Biotheoretica·J P Moulin

Dynamical Robustness against Multiple Mutations in Signaling Networks

Nov 4, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yung-Keun KwonKwang-Hyun Cho

Fixed-points in random Boolean networks: The impact of parallelism in the Barabási-Albert scale-free topology case

Oct 22, 2016·Bio Systems·P Moisset de EspanésI Rapaport

Flexible and robust networks

Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Sergey A Vakulenko, Ovidiu Radulescu

On the limit cycle structure of threshold boolean networks over complete graphs

Jul 10, 2004·International Journal of Neural Systems·George Voutsadakis

Inference of gene regulatory networks using boolean-network inference methods

Dec 17, 2009·Journal of Bioinformatics and Computational Biology·Graham J Hickman, T Charlie Hodgman

Partial Synchronization of Interconnected Boolean Networks

Jan 19, 2016·IEEE Transactions on Cybernetics·Hongwei ChenJianquan Lu

Exact Identification of the Structure of a Probabilistic Boolean Network from Samples

Dec 15, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiaoqing ChengT Akutsu

ViSiBooL-visualization and simulation of Boolean networks with temporal constraints

Nov 1, 2016·Bioinformatics·Julian D SchwabHans A Kestler

A Network Model to Describe the Terminal Differentiation of B Cells

Jan 12, 2016·PLoS Computational Biology·Akram Méndez, Luis Mendoza

An Efficient Steady-State Analysis Method for Large Boolean Networks with High Maximum Node Connectivity

Dec 31, 2015·PloS One·Changki HongInsik Shin

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Jan 23, 2016·PLoS Computational Biology·Ezio Bartocci, Pietro Lió

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling

Nov 17, 2015·PloS One·Holger FröhlichUlrike Korf

Controllability and observability of Boolean networks arising from biology

Mar 3, 2015·Chaos·Rui LiTianguang Chu

A Qualitative Model of the Differentiation Network in Chondrocyte Maturation: A Holistic View of Chondrocyte Hypertrophy

Sep 1, 2016·PloS One·Johan KerkhofsLiesbet Geris

Artificial Epigenetic Networks: Automatic Decomposition of Dynamical Control Tasks Using Topological Self-Modification

Jan 8, 2016·IEEE Transactions on Neural Networks and Learning Systems·Alexander P TurnerMichael A Lones

Advanced Boolean modeling of biological networks applied to systems pharmacology

Jan 12, 2017·Bioinformatics·Itziar Irurzun-AranaJosé David Gómez-Mantilla

Phenotypic robustness and the assortativity signature of human transcription factor networks

Aug 15, 2014·PLoS Computational Biology·Dov A PechenickJason H Moore

A novel mutual information-based Boolean network inference method from time-series gene expression data

Feb 9, 2017·PloS One·Shohag Barman, Yung-Keun Kwon

Synchronization of Arbitrarily Switched Boolean Networks

Dec 2, 2015·IEEE Transactions on Neural Networks and Learning Systems·Hongwei ChenJinde Cao

Noncommutative Biology: Sequential Regulation of Complex Networks

Aug 26, 2016·PLoS Computational Biology·William Letsou, Long Cai

Synchronization Analysis of Master-Slave Probabilistic Boolean Networks

Sep 1, 2015·Scientific Reports·Jianquan LuJinde Cao

Inferring modulators of genetic interactions with epistatic nested effects models

Apr 14, 2017·PLoS Computational Biology·Martin PirklFlorian Markowetz

A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana

Apr 21, 2017·PLoS Computational Biology·Mónica L García-GómezElena R Alvarez-Buylla

Controllability of time-delayed Boolean multiplex control networks under asynchronous stochastic update

Dec 18, 2014·Scientific Reports·Chao LuoHong Liu

toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map

Dec 19, 2014·Scientific Reports·Clemente F AriasJosé A Cuesta

Synchronization in output-coupled temporal Boolean networks

Sep 6, 2014·Scientific Reports·Jianquan LuJürgen Kurths

Molecular network control through boolean canalization

Jan 12, 2016·EURASIP Journal on Bioinformatics & Systems Biology·David Murrugarra, Elena S Dimitrova

Robust Reachability of Boolean Control Networks

Jan 24, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Fangfei Li, Yang Tang

Differentiation of malignant to benign cells

Jun 1, 1971·Journal of Theoretical Biology·Stuart A Kauffman

Boolean formalization of genetic control circuits

Dec 1, 1973·Journal of Theoretical Biology·R Thomas

Ecosystem stability: a result from an abstract simulation

Jun 1, 1974·Journal of Theoretical Biology·M P Austin, B G Cook

A graph-theoretical analysis of metabolic regulation

Jan 21, 1983·Journal of Theoretical Biology·M C Kohn, W J Letzkus

Structure of regulatory networks and diversity of gene expression patterns

Nov 9, 2007·Journal of Theoretical Biology·Atsushi Mochizuki

A clock and wavefront model for control of the number of repeated structures during animal morphogenesis

May 21, 1976·Journal of Theoretical Biology·J Cooke, E C Zeeman

Discrete systems, cell-cell interactions and color pattern of animals. II. Clonal theory and cellular automata

Apr 21, 1987·Journal of Theoretical Biology·G CochoF Soto

The large scale structure and dynamics of gene control circuits: an ensemble approach

Mar 1, 1974·Journal of Theoretical Biology·Stuart A Kauffman

Regulatory network for cell shape changes during Drosophila ventral furrow formation

Sep 6, 2005·Journal of Theoretical Biology·Julio AracenaVerónica Cambiazo

A criticism of catastrophe modelling of the differentiative process in amphibian development

Dec 21, 1977·Journal of Theoretical Biology·M J Pearson, D I McLaren

System theoretic analysis of models: computer simulation of a living cell

Oct 1, 1970·Journal of Theoretical Biology·B P Zeigler, R Weinberg

Circular causality

Sep 22, 2006·Systems Biology·R Thomas

Boolean dynamics of Kauffman models with a scale-free network

Apr 6, 2007·Journal of Theoretical Biology·Kazumoto IguchiHiroaki S Yamada

Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

Jan 20, 2015·Molecular BioSystems·Santhust KumarAreejit Samal

The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks

Feb 12, 2017·Scientific Reports·Eugenio AzpeitiaLuis Mendoza

The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic

Jun 3, 2017·Traffic·Allen P LiuCostin N Antonescu

Bistability and Asynchrony in a Boolean Model of the L-arabinose Operon in Escherichia coli

Jun 24, 2017·Bulletin of Mathematical Biology·Andy Jenkins, Matthew Macauley

Design of Probabilistic Boolean Networks Based on Network Structure and Steady-State Probabilities

Jun 14, 2016·IEEE Transactions on Neural Networks and Learning Systems·Koichi Kobayashi, Kunihiko Hiraishi

GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis

Jun 22, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ricardo De Souza JacominiAnna Helena Reali Costa

FALCON: a toolbox for the fast contextualization of logical networks

Jul 5, 2017·Bioinformatics·Sébastien De LandtsheerThomas Sauter

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations

Jan 1, 2013·Plants·James L Kitchen, Robin G Allaby

Systems biology - the broader perspective

Jan 1, 2013·Cells·Jonathan Bard

Synchronization for the Realization-Dependent Probabilistic Boolean Networks

Jan 28, 2017·IEEE Transactions on Neural Networks and Learning Systems·Hongwei ChenJianlong Qiu

Identifying a Probabilistic Boolean Threshold Network From Samples

Jan 28, 2017·IEEE Transactions on Neural Networks and Learning Systems·Avraham A MelkmanT Akutsu

Classification of State Trajectories in Gene Regulatory Networks

Oct 16, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Alireza KarbalaygharehEdward R Dougherty

A Boolean network of the crosstalk between IGF and Wnt signaling in aging satellite cells

Mar 30, 2018·PloS One·Lea SiegleHans A Kestler

Network motifs in the transcriptional regulation network of Escherichia coli

Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon

Kinetic models of hematopoietic differentiation

Apr 17, 2018·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Victor Olariu, Carsten Peterson

How Criticality of Gene Regulatory Networks Affects the Resulting Morphogenesis under Genetic Perturbations

Apr 18, 2018·Artificial Life·Hyobin Kim, Hiroki Sayama

Networking opportunity

Feb 13, 2004·Nature·Ian Stewart

The phenotype control kernel of a biomolecular regulatory network

Apr 7, 2018·BMC Systems Biology·Sang-Mok ChooKwang-Hyun Cho

Genomic approaches in dissecting complex biological pathways

Mar 16, 2004·Pharmacogenomics·Ning Sun, Hongyu Zhao

Beyond cancer genes: colorectal cancer as robust intrinsic states formed by molecular interactions

Nov 10, 2017·Open Biology·Ruoshi YuanXiaomei Zhu

Moving beyond the genome with computer modeling

May 17, 2018·Personalized Medicine·Patrik Christen

Collective dynamics of 'small-world' networks

Jun 12, 1998·Nature·D J Watts, S H Strogatz

Estimation of delays in generalized asynchronous Boolean networks

Jul 29, 2016·Molecular BioSystems·Haimabati Das, Ritwik Layek

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems

Nov 28, 2017·BMC Bioinformatics·Levi D McclennyUlisses M Braga-Neto

An improved Bayesian network method for reconstructing gene regulatory network based on candidate auto selection

Dec 9, 2017·BMC Genomics·Linlin XingYin Zhang

Perspectives on theory at the interface of physics and biology

Dec 8, 2017·Reports on Progress in Physics·William Bialek

A systems pharmacology model for inflammatory bowel disease

Mar 8, 2018·PloS One·Violeta Balbas-MartinezIñaki F Trocóniz

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer

Sep 19, 2015·Cancer Informatics·Simone RubinacciMarco Antoniotti

Controllability and Synchronization Analysis of Identical-Hierarchy Mixed-Valued Logical Control Networks

Jun 21, 2016·IEEE Transactions on Cybernetics·Jie ZhongDaniel W C Ho

Potts-glass model of layered feedforward neural networks

Jan 15, 1992·Physical Review. a·G M ShimM Y Choi

Dynamics of complex systems: scaling laws for the period of boolean networks

Sep 16, 2000·Physical Review Letters·Réka Albert, A L Barabasi

Power-Law Distributions in Some Random Boolean Networks

Aug 19, 1996·Physical Review Letters·A Bhattacharjya, S Liang

Inhomogeneous magnetization in dilute asymmetric and symmetric systems

May 9, 1988·Physical Review Letters·I Kanter

Mutual information in a dilute, asymmetric neural network model

Apr 20, 2001·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·E Greenfield, H Lecar

Synchronization of Kauffman networks

Apr 20, 2001·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·L G Morelli, D H Zanette

Frequency distributions in population genetics parallel those in statistical physics

Jan 1, 1995·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·P G Higgs

Damage spreading in the mixed spin Ising model

Jan 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ce-Jun LiuJia-Zhen Hu

Chaos in neural networks with a nonmonotonic transfer function

Apr 24, 2002·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·D CaroppoS Stramaglia

Damage spreading transition in glasses: a probe for the ruggedness of the configurational landscape

Apr 24, 2002·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·M Heerema, F Ritort

Physical aspects of evolutionary optimization and adaptation

Sep 15, 1989·Physical Review A: General Physics·W FontanaP Schuster

Construction and analysis of gene-gene dynamics influence networks based on a Boolean model

Jan 13, 2018·BMC Systems Biology·Maulida MazayaYung-Keun Kwon

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors

Jan 4, 2018·BMC Bioinformatics·Shahin BolukiEdward R Dougherty

A toolbox for discrete modelling of cell signalling dynamics

Jun 2, 2018·Integrative Biology : Quantitative Biosciences From Nano to Macro·Yasmin Z PatersonJasmin Fisher

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation

Apr 25, 2018·Database : the Journal of Biological Databases and Curation·Amel BekkarIsaac Crespo

Evolution of developmental canalization in networks of competing boolean nodes

Aug 25, 2004·Physical Review Letters·K E BasslerYong Lee

Activities and sensitivities in boolean network models

Aug 25, 2004·Physical Review Letters·Ilya Shmulevich, Stuart A Kauffman

Single-Input Pinning Controller Design for Reachability of Boolean Networks

Jun 15, 2017·IEEE Transactions on Neural Networks and Learning Systems·Fangfei LiHamid Reza Karimi

Normalization and Solvability of Dynamic-Algebraic Boolean Networks

Jul 18, 2017·IEEE Transactions on Neural Networks and Learning Systems·Yang LiuJianquan Lu

Delayed Feedback Control for Stabilization of Boolean Control Networks With State Delay

Jun 27, 2017·IEEE Transactions on Neural Networks and Learning Systems·Rongjian LiuZheng-Guang Wu

Stability and Guaranteed Cost Analysis of Time-Triggered Boolean Networks

Sep 8, 2017·IEEE Transactions on Neural Networks and Learning Systems·Min MengKie Chung Cheung

Modeling the evolution of complex genetic systems: the gene network family tree

Dec 17, 2014·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·J L Fierst, Patrick C Phillips

Exploring complex networks

Mar 22, 2001·Nature·S H Strogatz

Modelling cellular behaviour

Feb 24, 2001·Nature·D Endy, R Brent

Event-Triggered Control for the Disturbance Decoupling Problem of Boolean Control Networks

Sep 9, 2017·IEEE Transactions on Cybernetics·Bowen LiLi Yu

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Aug 31, 2018·Science China. Life Sciences·Shunong BaiHong Qian

Affective family interactions and their associations with adolescent depression: A dynamic network approach

Nov 21, 2017·Development and Psychopathology·Nadja BodnerEva Ceulemans

Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era

Jun 20, 2018·Integrative and Comparative Biology·Selene L Fernandez-ValverdeRené Alexander Ramos-Díaz

Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks

Mar 2, 2016·PloS One·Karl FogelmarkCarl Troein

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data

Oct 30, 2018·PLoS Computational Biology·Misbah RazzaqCarito Guziolowski

Boosting functionality of synthetic DNA circuits with tailored deactivation

Nov 16, 2016·Nature Communications·Kevin MontagneYannick Rondelez

Generating probabilistic Boolean networks from a prescribed transition probability matrix

Dec 2, 2009·IET Systems Biology·W-K ChingN-K Tsing

Optimal control policy for probabilistic Boolean networks with hard constraints

Mar 19, 2009·IET Systems Biology·W-K ChingA S Wong

Inference of Boolean networks under constraint on bidirectional gene relationships

May 20, 2009·IET Systems Biology·G VahediEdward R Dougherty

On approximate stochastic control in genetic regulatory networks

Jan 22, 2008·IET Systems Biology·B FaryabiEdward R Dougherty

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks

Nov 6, 2018·Bioinformatics·Ruiqing ZhengJianxin Wang

A roadmap towards personalized immunology

Feb 10, 2018·NPJ Systems Biology and Applications·Sylvie DelhalleFeng Q He

Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease

Jan 23, 2018·NPJ Systems Biology and Applications·Jorge JúlvezStephen G Oliver

Symbiotic emergence of metazoans

Apr 18, 1970·Nature·H Timourian

Homeostasis and differentiation in random genetic control networks

Oct 11, 1969·Nature·Stuart A Kauffman

Finding community structure in very large networks

Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aaron ClausetCristopher Moore

Scale-free network with Boolean dynamics as a function of connectivity

Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A Castro e SilvaJ F F Mendes

Dynamic modeling and analysis of cancer cellular network motifs

Jun 16, 2011·Integrative Biology : Quantitative Biosciences From Nano to Macro·Mathieu Cloutier, Edwin Wang

Early gene regulation of osteogenesis in embryonic stem cells

Oct 9, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Glen R KirkhamLee D K Buttery

Microbial evolution in vivo and in silico: methods and applications

Oct 26, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Vadim Mozhayskiy, Ilias Tagkopoulos

The origins of cancer robustness and evolvability

Oct 15, 2010·Integrative Biology : Quantitative Biosciences From Nano to Macro·Tianhai TianAngus Harding

Developmental logic and its evolution

Feb 1, 1987·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Stuart A Kauffman

Order-disorder phase transition in random-walk networks

May 21, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·F J Ballesteros, B Luque

Cell fates as high-dimensional attractor states of a complex gene regulatory network

May 21, 2005·Physical Review Letters·Sui HuangDonald E Ingber

Computational models reconstruct gene regulatory networks

Dec 17, 2008·Molecular BioSystems·Anastasios Bezerianos, Ioannis A Maraziotis

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

Dec 3, 2009·Molecular Systems Biology·Julio Saez-RodriguezPeter K Sorger

Forcing cells to change lineages

Dec 4, 2009·Nature·Thomas Graf, Tariq Enver

Analytical results for the statistical distribution related to a memoryless deterministic walk: dimensionality effect and mean-field models

Oct 4, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·César Augusto Sangaletti Terçariol, Alexandre Souto Martinez

Externally controlled attractor selection in a high-dimensional system

Oct 4, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Frederick H Willeboordse, Kunihiko Kaneko

Noise in a Small Genetic Circuit that Undergoes Bifurcation

May 4, 2006·Complexity·Trent ToulouseStuart A Kauffman

Biology by numbers: mathematical modelling in developmental biology

Apr 19, 2007·Nature Reviews. Genetics·Claire J Tomlin, Jeffrey D Axelrod

Core percolation and onset of complexity in boolean networks

Feb 21, 2006·Physical Review Letters·L CorrealeR Zecchina

Exhaustive percolation on random networks

Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Björn Samuelsson, Joshua E S Socolar

Plant behaviour in response to the environment: information processing in the solid state

Apr 23, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Salva Duran-Nebreda, George W Bassel

Software for systems biology: from tools to integrated platforms

Nov 4, 2011·Nature Reviews. Genetics·Samik GhoshHiroaki Kitano

Basin entropy in Boolean network ensembles

May 16, 2007·Physical Review Letters·Peter Krawitz, Ilya Shmulevich

Sub-block order parameter in a driven Ising lattice gas using block distribution functions

May 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Wooseop KwakD P Landau

Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions

Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Andre S Ribeiro

Critical dynamics of randomly assembled and diluted threshold networks

Jun 4, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Karl E Kürten, John W Clark

Influence of memory in deterministic walks in random media: analytical calculation within a mean-field approximation

Oct 15, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·César Augusto Sangaletti Terçariol, Alexandre Souto Martinez

A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis

Feb 23, 2010·Molecular BioSystems·Karthik RamanNagasuma Chandra

Boolean modeling in systems biology: an overview of methodology and applications

Sep 27, 2012·Physical Biology·Rui-Sheng WangRéka Albert

Computational capabilities of random automata networks for reservoir computing

May 18, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·David SnyderChristof Teuscher

Limited imitation contagion on random networks: chaos, universality, and unpredictability

Apr 12, 2013·Physical Review Letters·Peter Sheridan DoddsChristopher M Danforth

Minimal model for stem-cell differentiation

Oct 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yusuke Goto, Kunihiko Kaneko

Emergence of diverse life cycles and li