Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

PMID: 11847074Feb 16, 2002

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

Bioinformatics

Ilya ShmulevichWei Zhang

Abstract

Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of global network dynamics; (iii) is able to cope with uncertainty, both in the data and the model selection; and (iv) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes. We introduce Probabilistic Boolean Networks (PBN) that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty. We show how the dynamics of these networks can be studied in the probabilistic context of Markov chains, with standard Boolean networks being special cases. Then, we discuss the relationship between PBNs and Bayesian networks--a family of graphical models that explicitly represent probabilistic relationships between variables. We show how probabilistic dependencies between a gene and its parent genes, constituting the basic building blocks of Bayesian networks, can be obtained from PBNs. Finally, we present methods for quantifying the influence of genes on other genes, within the context of PBNs. Examples illustrating the above concepts are presented throughou...Continue Reading

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Identification of mouse heart transcriptomic network sensitive to various heart diseases

Mar 6, 2008·Biotechnology Journal·Seong-Eui HongDo Han Kim

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

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

Transforming omics data into context: bioinformatics on genomics and proteomics raw data

Jun 2, 2006·Electrophoresis·Paul PercoBernd Mayer

Robust control of uncertain nonlinear switched genetic regulatory networks with time delays: A redesign approach

Mar 1, 2016·Mathematical Biosciences·Hojjatullah Moradi, Vahid Johari Majd

Network inference by combining biologically motivated regulatory constraints with penalized regression

Apr 8, 2009·Annals of the New York Academy of Sciences·Fabio ParisiFelix Naef

Modeling of gene regulatory network dynamics using threshold logic

Apr 8, 2009·Annals of the New York Academy of Sciences·Tejaswi GowdaSeungchan Kim

The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms

Mar 18, 2011·Environmental Microbiology·Rafael Silva-RochaVíctor de Lorenzo

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

Mar 19, 2016·Scientific Reports·Peican ZhuJie Han

Algorithmic and analytical methods in network biology

Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Mehmet Koyutürk

In silico models of cancer

Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Lucas B EdelmanNathan D Price

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

Inference of biological S-system using the separable estimation method and the genetic algorithm

Oct 5, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Li-Zhi LiuW J Zhang

Inferring gene regulatory networks via nonlinear state-space models and exploiting sparsity

Feb 22, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Amina NoorHazem N Nounou

Transient dynamics of reduced-order models of genetic regulatory networks

Mar 14, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ranadip Pal, Sonal Bhattacharya

Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug

Jul 19, 2013·IEEE Transactions on Bio-medical Engineering·Mohammadmahdi R YousefiEdward R Dougherty

Nonparametric network design and analysis of disease genes in oral cancer progression

Mar 13, 2014·IEEE Journal of Biomedical and Health Informatics·K KalantzakiD I Fotiadis

Incorporation of Biological Pathway Knowledge in the Construction of Priors for Optimal Bayesian Classification

Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mohammad Shahrokh Esfahani, Edward R Dougherty

Statistical detection of boolean regulatory relationships

Jan 5, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ting Chen, Ulisses M Braga-Neto

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

A model for cancer tissue heterogeneity

Feb 22, 2014·IEEE Transactions on Bio-medical Engineering·Anwoy MohantyVijayanagaram Venkatraj

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

GSGS: a computational approach to reconstruct signaling pathway structures from gene sets

Oct 26, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Lipi AcharyaDongxiao Zhu

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

A hybrid systems framework for cellular processes

May 13, 2005·Bio Systems·Kwang-Hyun ChoOlaf Wolkenhauer

Genetic networks and soft computing

Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sushmita MitraYoichi Hayashi

Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior

Jul 27, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiaoning Qian, Edward R Dougherty

Construction of gene networks with hybrid approach from expression profile and gene ontology

Oct 1, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Liping JingYing Liu

Automated large-scale control of gene regulatory networks

Oct 28, 2009·IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society·Mehmet TanFaruk Polat

Extracting gene-gene interactions through curve fitting

Sep 22, 2012·IEEE Transactions on Nanobioscience·Ranajit DasC A Murthy

Intervention in gene regulatory networks via a stationary mean-first-passage-time control policy

Oct 8, 2008·IEEE Transactions on Bio-medical Engineering·Golnaz VahediEdward R Dougherty

Optimal intervention strategies for cyclic therapeutic methods

Mar 11, 2009·IEEE Transactions on Bio-medical Engineering·Golnaz VahediEdward R Dougherty

Multi-scale modeling of cell survival and death mediated by the p53 network: a systems pharmacology framework

Aug 25, 2015·Molecular BioSystems·Yuan WangYonghua Wang

Reconstructing directed signed gene regulatory network from microarray data

Aug 2, 2011·IEEE Transactions on Bio-medical Engineering·Peng Qiu, Sylvia K Plevritis

Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic

Nov 2, 2011·IEEE Transactions on Bio-medical Engineering·Fang-Han HsuEdward R Dougherty

Control of Boolean networks: hardness results and algorithms for tree structured networks

Oct 31, 2006·Journal of Theoretical Biology·Tatsuya AkutsuMichael K Ng

A Conjugate Exponential Model for Cancer Tissue Heterogeneity

Mar 15, 2015·IEEE Journal of Biomedical and Health Informatics·Anwoy MohantyJijayanagaram Venkatraj

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

Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes

Jul 28, 2006·Bio Systems·Xutao DengMihaela T Matache

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

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

Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data

Jan 9, 2015·IET Systems Biology·Li-Zhi LiuWen-Jun Zhang

Cellular metabolic network analysis: discovering important reactions in Treponema pallidum

Oct 24, 2015·BioMed Research International·Xueying ChenHong Qu

Neural model of gene regulatory network: a survey on supportive meta-heuristics

Apr 7, 2016·Theory in Biosciences = Theorie in Den Biowissenschaften·Surama Biswas, Sriyankar Acharyya

Learning restricted Boolean network model by time-series data

Aug 6, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Hongjia OuyangWenbin Liu

Stochastic S-system modeling of gene regulatory network

Sep 18, 2015·Cognitive Neurodynamics·Ahsan Raja ChowdhuryRob Evans

A pattern-oriented specification of gene network inference processes

Sep 17, 2013·Computers in Biology and Medicine·Nestor W TrepodeJunior Barrera

Deconstructing stem cell population heterogeneity: single-cell analysis and modeling approaches

Sep 17, 2013·Biotechnology Advances·Jincheng Wu, Emmanuel S Tzanakakis

Reverse engineering systems models of regulation: discovery, prediction and mechanisms

Jan 3, 2012·Current Opinion in Biotechnology·Justin AshworthNitin S Baliga

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks

Aug 12, 2015·BMC Systems Biology·Tomoya MoriEdda Klipp

Computational cancer biology: education is a natural key to many locks

Jan 16, 2015·BMC Cancer·Frank Emmert-StreibPeter Hamilton

Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery

Apr 14, 2005·BMC Bioinformatics·Leslie R Grate

A multiorganism based method for Bayesian gene network estimation

Dec 21, 2010·Bio Systems·Zaher DawyHady Ali Zeineddine

The complex fluctuations of probabilistic Boolean networks

Jul 23, 2013·Bio Systems·Yuan-ming GaoWenbin Liu

Transcriptome analysis in cardiomyocyte-specific differentiation of murine embryonic stem cells reveals transcriptional regulation network

Jul 25, 2014·Gene Expression Patterns : GEP·Lin GanBernd Denecke

Experimental and computational methods for the analysis and modeling of signaling networks

Nov 21, 2012·New Biotechnology·Pier Federico Gherardini, Manuela Helmer-Citterich

Cooperative development of logical modelling standards and tools with CoLoMoTo

Jan 27, 2015·Bioinformatics·Aurélien NaldiClaudine Chaouiya

Challenges for modeling global gene regulatory networks during development: insights from Drosophila

Oct 31, 2009·Developmental Biology·Bartek Wilczynski, Eileen E M Furlong

The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data

Feb 6, 2008·Journal of Biomedical Informatics·Xiaogang RuanEdmund F Perozzi

Methodologies for the modeling and simulation of biochemical networks, illustrated for signal transduction pathways: a primer

Feb 1, 2015·Bio Systems·Nesma ElKalaawy, Amr Wassal

From biological pathways to regulatory networks

Dec 17, 2010·Molecular BioSystems·Ritwik Kumar LayekEdward R Dougherty

Functional genomics analysis reveals a MYC signature associated with a poor clinical prognosis in liposarcomas

Jan 28, 2015·The American Journal of Pathology·Dat TranBrad A Bryan

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology

Sep 16, 2014·Frontiers in Genetics·Frank Emmert-StreibBenjamin Haibe-Kains

Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling

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

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

An efficient algorithm to identify the optimal one-bit perturbation based on the basin-of-state size of Boolean networks

May 20, 2016·Scientific Reports·Mingxiao HuWenbin Liu

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

The p75 neurotrophin receptor is a central regulator of glioma invasion

Aug 19, 2007·PLoS Biology·Angela L M JohnstonDonna L Senger

Two-Way Gene Interaction From Microarray Data Based on Correlation Methods

Sep 14, 2016·Iranian Red Crescent Medical Journal·Hamid Alavi MajdNasibeh Khayyer

Logical Modeling and Dynamical Analysis of Cellular Networks

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

Effective gene expression data generation framework based on multi-model approach

Jul 20, 2016·Artificial Intelligence in Medicine·Utku SirinReda Alhajj

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

Jun 17, 2016·Bioinformatics·Jukka IntosalmiHarri Lähdesmäki

Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET

Jun 10, 2015·PloS One·Ana RodriguezAntonio Del Sol

Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies?

May 20, 2015·PloS One·Saurabh VashishthaNancy G Klimas

Estimation of delays in generalized asynchronous Boolean networks

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

Integrated molecular analysis suggests a three-class model for low-grade gliomas: a proof-of-concept study

Oct 20, 2009·Genomics·Nicholas F MarkoRobert J Weil

Recurrent neural network based hybrid model for reconstructing gene regulatory network

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

Glioblastoma: clinical, radiological and biological prognostic factors

Sep 28, 2010·Neuro-Chirurgie·D Fontaine, P Paquis

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 VenkatA Datta

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

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

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

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

A systems biology approach to drug discovery

Mar 25, 2008·Advances in Genetics·Jun ZhuEric E Schadt

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

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

Gene Regulatory Network Inferences Using a Maximum-Relevance and Maximum-Significance Strategy

Nov 10, 2016·PloS One·Wei LiuXiangtao Chen

Inference of Gene Regulatory Network Based on Local Bayesian Networks

Aug 2, 2016·PLoS Computational Biology·Fei LiuLuonan Chen

The Evolutionary Origins of Hierarchy

Jun 10, 2016·PLoS Computational Biology·Henok MengistuJeff Clune

A Probabilistic Boolean Network Approach for the Analysis of Cancer-Specific Signalling: A Case Study of Deregulated PDGF Signalling in GIST

May 28, 2016·PloS One·Panuwat TrairatphisanThomas Sauter

A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data

Feb 2, 2017·BMC Bioinformatics·Shupeng GuiHongyu Miao

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

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

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 MelkmanTatsuya Akutsu

Kinetic models of hematopoietic differentiation

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

The value of prior knowledge in machine learning of complex network systems

Oct 17, 2017·Bioinformatics·Dana FerrantiDavid Craft

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

Dec 9, 2017·BMC Genomics·Linlin XingYin Zhang

Improving GRN re-construction by mining hidden regulatory signals

Nov 11, 2017·IET Systems Biology·Ming ShiHong-Qiang Wang

Model checking optimal finite-horizon control for probabilistic gene regulatory networks

Jan 4, 2018·BMC Systems Biology·Ou WeiWenyuan Liao

A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data

Jan 1, 2015·Cancer Informatics·André FonsecaJunior Barrera

Data Requirements for Model-Based Cancer Prognosis Prediction

Jan 1, 2015·Cancer Informatics·Lori A Dalton, Mohammadmahdi R Yousefi

Network-based identification of biomarkers coexpressed with multiple pathways

Nov 14, 2014·Cancer Informatics·Nancy Lan Guo, Ying-Wooi Wan

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

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

A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection

May 31, 2018·Statistical Methods in Medical Research·Michelle CareyHulin Wu

Activities and sensitivities in boolean network models

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

A robust gene regulatory network inference method base on Kalman filter and linear regression

Jul 13, 2018·PloS One·Jamshid Pirgazi, Ali Reza Khanteymoori

Gene Regulatory Networks Reconstruction Using the Flooding-Pruning Hill-Climbing Algorithm

Jul 11, 2018·Genes·Linlin XingLei Zhang

Quantifying the notions of canalizing and master genes in a gene regulatory network-a Boolean network modeling perspective

Jul 28, 2018·Bioinformatics·Eunji KimEdward R Dougherty

Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling

Sep 1, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hongjie WuMin Jiang

Batch Mode TD($\lambda$ ) for Controlling Partially Observable Gene Regulatory Networks

Aug 3, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Utku SirinReda Alhajj

Reviving the Two-State Markov Chain Approach

May 24, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Andrzej Mizera Qixia Yuan

Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy

Mar 10, 2018·PLoS Biology·Eunjung KimAlexander R A Anderson

Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae

Oct 6, 2017·PloS One·Maria SimakHenry Horng-Shing Lu

Reverse engineering of gene regulatory networks

Jun 27, 2007·IET Systems Biology·K H ChoJ Kim

Linear matrix inequalities approach to reconstruction of biological networks

Jun 27, 2007·IET Systems Biology·C CosentinoF Amato

Modelling codependence in biological systems

Mar 21, 2007·IET Systems Biology·J J MandelW Dubitzky

Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks

Apr 20, 2007·IET Systems Biology·C ChristensenRéka Albert

On approximate stochastic control in genetic regulatory networks

Jan 22, 2008·IET Systems Biology·B FaryabiEdward R Dougherty

Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data

Jul 23, 2014·BMC Bioinformatics·Narsis A Kiani, Lars Kaderali

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

Sep 6, 2014·BMC Systems Biology·Naomi KochiMihaela T Matache

Biological Resource Centers and Systems Biology

Feb 17, 2010·Bioscience·Yufeng Wang, Timothy G Lilburn

Discerning Functional Connections in the Pulsed Neural Networks with the Dynamic Bayesian Network Structure Search Method Based on a Genetic Algorithm

Jun 19, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chaoxuan DongChao-Yi Dong

Boolean modeling in systems biology: an overview of methodology and applications

Sep 27, 2012·Physical Biology·Rui-Sheng WangRéka Albert

Increasing the efficiency of fuzzy logic-based gene expression data analysis

Feb 22, 2003·Physiological Genomics·Habtom RessomRency S Varghese

Executable pathway analysis using ensemble discrete-state modeling for large-scale data

Sep 4, 2019·PLoS Computational Biology·Rohith PalliJuilee Thakar

Inference of time-delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method

Nov 9, 2017·Oncotarget·Bin YuMing-Hui Wang

Boolean network modeling in systems pharmacology

Jan 8, 2018·Journal of Pharmacokinetics and Pharmacodynamics·Peter BloomingdaleDonald E Mager

A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma.

Jul 23, 2020·GigaScience·Boris AguilarIlya Shmulevich

An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference

Jan 1, 2015·Microarrays·Xu WangErchin Serpedin

Immuno-hybrid algorithm: a novel hybrid approach for GRN reconstruction

Jan 1, 2016·3 Biotech·A S Jereesh, V K Govindan

Mathematical and Computational Modeling in Complex Biological Systems

Apr 8, 2017·BioMed Research International·Zhiwei JiXiaoliang Zhu

Dynamics and robustness of the cardiac progenitor cell induced pluripotent stem cell network during cell phenotypes transition

Mar 18, 2017·IET Systems Biology·Yuangen YaoMing Yi

Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming

Jul 25, 2017·Algorithms for Molecular Biology : AMB·Louis Fippo FitimeLoïc Paulevé

Automatic Screening for Perturbations in Boolean Networks

May 10, 2018·Frontiers in Physiology·Julian D Schwab, Hans A Kestler

Single-cell RNA sequencing technologies and bioinformatics pipelines

Aug 10, 2018·Experimental & Molecular Medicine·Byungjin HwangDuhee Bang

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

Feb 13, 2019·Frontiers in Microbiology·Damien EveillardJérémie Bourdon

Pinning Control for the p53-Mdm2 Network Dynamics Regulated by p14ARF

Sep 29, 2020·Frontiers in Physiology·Oscar J SuarezEsteban A Hernandez-Vargas

Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets

Jan 1, 2008·Bioinformatics and Biology Insights·Laura A HeckerM Heather West Greenlee

Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum

Mar 19, 2016·The New Phytologist·Li GuoLi-Jun Ma

COMPUTATIONAL METHODS FOR ASYNCHRONOUS BASINS

Feb 6, 2017·Discrete and Continuous Dynamical Systems. Series B·Ian H Dinwoodie

Stability of Signaling Pathways during Aging-A Boolean Network Approach

Dec 21, 2017·Biology·Julian D SchwabHans A Kestler

Analysis Tools for Interconnected Boolean Networks With Biological Applications

Jun 14, 2018·Frontiers in Physiology·Madalena Chaves, Laurent Tournier

Construction of Discrete Model of Human Pluripotency in Predicting Lineage-Specific Outcomes and Targeted Knockdowns of Essential Genes

Jul 25, 2018·Scientific Reports·Priyanka NaradAbhishek Sengupta

A Novel Data-Driven Boolean Model for Genetic Regulatory Networks

Oct 16, 2018·Frontiers in Physiology·Leshi ChenSandhya Samarasinghe

Representing dynamic biological networks with multi-scale probabilistic models

Jan 25, 2019·Communications Biology·Alexander GroßHans A Kestler

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

Mar 12, 2019·Current Topics in Medicinal Chemistry·Alexiou AthanasiosGhulam Md Ashraf

A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps

Oct 17, 2019·Journal of Bioinformatics and Computational Biology·Luowen Liu, Jing Liu

Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean

Dec 4, 2019·Frontiers in Plant Science·Faqiang WuYoshie Hanzawa

Modeling Approaches Reveal New Regulatory Networks in Aspergillus fumigatus Metabolism

Jul 18, 2020·Journal of Fungi·Enzo AcerbiTeresa Zelante

Exact solving and sensitivity analysis of stochastic continuous time Boolean models

Jun 13, 2020·BMC Bioinformatics·Mihály KoltaiEmmanuel Barillot

RefBool: a reference-based algorithm for discretizing gene expression data

Mar 24, 2017·Bioinformatics·Sascha JungAntonio Del Sol

Template-based intervention in Boolean network models of biological systems

Jul 19, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Michael P Verdicchio, Seungchan Kim

Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms

Nov 29, 2016·Frontiers in Neuroscience·David MurrugarraAlex N Mueller

Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty

Aug 11, 2018·Cancer Informatics·Mahdi ImaniEdward R Dougherty

Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways

Jun 7, 2018·Frontiers in Physiology·Sébastien De LandtsheerThomas Sauter

Optimal stabilization of Boolean networks through collective influence

May 20, 2018·Physical Review. E·Jiannan WangZhiming Zheng

TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network

Jul 11, 2019·Journal of Bioinformatics and Computational Biology·Jamshid PirgaziMaryam Jalilkhani

Feedback analysis identifies a combination target for overcoming adaptive resistance to targeted cancer therapy

Mar 12, 2020·Oncogene·Sang-Min ParkKwang-Hyun Cho

D3GRN: a data driven dynamic network construction method to infer gene regulatory networks

Dec 29, 2019·BMC Genomics·Xiang ChenJianxin Wang

ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics

Aug 2, 2019·Bioinformatics·Ning ShiShan He

Gut-host Crosstalk: Methodological and Computational Challenges

Feb 5, 2020·Digestive Diseases and Sciences·Ivan Ivanov

Simulating heterogeneous populations using Boolean models

Jun 9, 2018·BMC Systems Biology·Brian C RossJames C Costello

Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection

Sep 16, 2017·Frontiers in Physiology·Martina CantoneJulio Vera

Emergence of diversity in homogeneous coupled Boolean networks

Jun 17, 2018·Physical Review. E·Chris KangIlya Shmulevich

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ

Jun 4, 2019·BMC Bioinformatics·Dace RuklisaJuris Viksna

Flexible Nets: a modeling formalism for dynamic systems with uncertain parameters

Jan 1, 2019·Discrete Event Dynamic Systems·Jorge Júlvez, Stephen G Oliver

Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

Feb 26, 2020·BMC Genomics·Li GuoKai Ye

Optimal cancer prognosis under network uncertainty

Jan 27, 2015·EURASIP Journal on Bioinformatics & Systems Biology·Mohammadmahdi R Yousefi, Lori A Dalton

Phenotype Classification Using Moment Features of Single-Cell Data

Jun 9, 2018·Cancer Informatics·Chao SimaEdward R Dougherty

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism

May 10, 2017·Royal Society Open Science·Anastasia I LavrovaSvetlana V Babak

Time-lagged Ordered Lasso for network inference

Dec 31, 2018·BMC Bioinformatics·Phan Nguyen, Rosemary Braun

Stability of Boolean networks: the joint effects of topology and update rules

Sep 13, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shane SquiresEdward Ott

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries

Nov 29, 2020·Database : the Journal of Biological Databases and Curation·Braja Gopal PatraAshraf Yaseen

Drug2ways: Reasoning over causal paths in biological networks for drug discovery.

Dec 3, 2020·PLoS Computational Biology·Daniel Rivas-BarraganDaniel Domingo-Fernández

Concepts in Boolean network modeling: What do they all mean?

Apr 8, 2020·Computational and Structural Biotechnology Journal·Julian D SchwabHans A Kestler

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