Gene regulatory network inference: Data integration in dynamic models—A review
Hecker, Michael, Lambeck, Sandro, Toepfer, Susanne, van Someren, Eugene, Guthke, Reinhard·2009·Biosystems
Cited by (755)
Items 201–300 of 755
- Challenges and opportunities in network-based solutions for biological questionsMargaret G. Guo, Daniel N. Sosa, Russ Biagio Altman · 2021 · Briefings in Bioinformatics
- Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal developmentZheng Wang, Aditya Gudibanda, Ugochukwu C. Ugwuowo, Frances Trail, Jeffrey P. Townsend · 2018 · Fungal Biology Reviews
- Controlling large Boolean networks with single-step perturbationsAlexis Baudin, Soumya Paul, Cui Su, Jun Pang · 2019 · Bioinformatics
- Reconstruction of the temporal signaling network in Salmonella-infected human cellsGüngör Budak, Oyku Eren Ozsoy, Yeşim Aydın Son, Tolga Can, Nurcan Tunçbağ · 2015 · Frontiers in Microbiology
- Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression dataM. Wu, C. Chan · 2011 · Briefings in Bioinformatics
- Modeling Genome-Wide Dynamic Regulatory Network in Mouse Lungs with Influenza Infection Using High-Dimensional Ordinary Differential EquationsShuang Wu, Zhi‐Ping Liu, Xing Qiu, Hulin Wu · 2014 · PLoS ONE
- Prior knowledge driven Granger causality analysis on gene regulatory network discoveryShun Yao, Shinjae Yoo, Dantong Yu · 2015 · BMC Bioinformatics
- GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data propertiesAndreas Tjärnberg, Daniel C. Morgan, Matthew Studham, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer · 2017 · Molecular BioSystems
- Bayesian networks as a novel tool to enhance interpretability and predictive power of ecological modelsEdwin Hui, Richard Stafford, Iain Matthews, V. Anne Smith · 2021 · Ecological Informatics
- Quantum gene regulatory networksCristhian Roman-Vicharra, James J. Cai · 2023 · npj Quantum Information
- Reconstruction of Large-Scale Gene Regulatory Networks Using Bayesian Model AveragingHaseong Kim, Erol Gelenbe A · 2012 · IEEE Transactions on NanoBioscience
- Network-based approach reveals Y chromosome influences prostate cancer susceptibilityPegah Khosravi, Vahid Gazestani, Yazdan Asgari, Brian Law, Mehdi Sadeghi, Bahram Goliaei · 2014 · Computers in Biology and Medicine
- Fast integration-based prediction bands for ordinary differential equation modelsHelge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek · 2015 · Bioinformatics
- Adapted Boolean network models for extracellular matrix formationJohannes Wollbold, René Huber, Dirk Pohlers, Dirk Koczan, Reinhard Guthke, Raimund W. Kinne, Ulrike Gausmann · 2009 · BMC Systems Biology
- Spectral Clustering for Multiple Sparse Networks: ISharmodeep Bhattacharyya, Shirshendu Chatterjee · 2018 · arXiv (Cornell University)
- Discovery of Possible Gene Relationships through the Application of Self-Organizing Maps to DNA Microarray DatabasesRocio Chavez-Alvarez, Arturo Chavoya, Andres Méndez-Vázquez · 2014 · PLoS ONE
- Learning Asynchronous Boolean Networks From Single-Cell Data Using Multiobjective Cooperative Genetic ProgrammingShuhua Gao, Changkai Sun, Cheng Xiang, Kai‐Rong Qin, Tong Heng Lee · 2020 · IEEE Transactions on Cybernetics
- Improving gene regulatory network inference and assessment: The importance of using network structureJuan M. Escorcia-Rodríguez, Estefani Gaytan-Nuñez, Ericka M. Hernandez-Benitez, Andrea Zorro-Aranda, Marco A. Tello‐Palencia, Julio Augusto Freyre-González · 2023 · Frontiers in Genetics
- Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene DataDiana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani B, Johannes Geiselmann, Hidde de Jong · 2015 · PLoS Computational Biology
- Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coliValentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde de Jong · 2011 · Journal of Theoretical Biology
- Optimal Sparsity Criteria for Network InferenceAndreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer · 2013 · Journal of Computational Biology
- Tamoxifen Integromics and Personalized Medicine: Dynamic Modular Transformations Underpinning Response to Tamoxifen in Breast Cancer TreatmentKonstantina Dimitrakopoulou, Georgios Ν. Dimitrakopoulos, Kyriakos Sgarbas, Anastasios Bezerianos · 2013 · OMICS A Journal of Integrative Biology
- In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven ModelsJulia Zieringer, Ralf Takors · 2018 · Computational and Structural Biotechnology Journal
- Stabilization of Boolean control networks with state-triggered impulsesRongpei Zhou, Yuqian Guo, Xinzhi Liu, Weihua Gui · 2022 · Science China Information Sciences
- A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory NetworksFrancesco Zito, Vincenzo Cutello, Mario Francesco Pavone · 2023 · Entropy
- Integrative Biological Analysis For NeuropsychopharmacologyMark R. Emmett, Roger A. Kroes, Joseph R. Moskal, Charles A. Conrad, Waldemar Priebe, Fernanda Laezza, Anke Meyer‐Baese, Carol L Nilsson · 2013 · Neuropsychopharmacology
- Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thalianaGuangyou Duan, Dirk Walther, Waltraud X. Schulze · 2013 · Frontiers in Plant Science
- Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brainE. D. Petrovskiy, Olga Saik, Evgeny Tiys, Inna N. Lavrik, Nikolay Alexandrovich Kolchanov, В. А. Иванисенко · 2015 · BMC Genomics
- Identifying a Probabilistic Boolean Threshold Network From SamplesAvraham A. Melkman, Xiaoqing Cheng, Wai‐Ki Ching, Tatsuya Akutsu · 2017 · IEEE Transactions on Neural Networks and Learning Systems
- Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systemsAnthony Szedlak, Spencer Sims, Nicholas H. Smith, Giovanni Paternostro, Carlo Piermarocchi · 2017 · PLoS Computational Biology
- Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approachHosein Masoomy, Behrouz Askari, Samin Tajik, Abbas K. Rizi, Gholamreza Jafari · 2021 · Scientific Reports
- Measuring topological descriptors of complex networks under uncertaintySebastian Raimondo, Manlio De Domenico · 2021 · Physical review. E
- Explainable fault prediction using learning fuzzy cognitive mapsTaha Mansouri, Sunil Vadera · 2023 · Expert Systems
- Entropic Biological Score: a cell cycle investigation for GRNs inferenceFabrício Martins Lopes, Shubhra Sankar Ray, Ronaldo F. Hashimoto, Roberto Marcondes Cesar Junior · 2014 · Gene
- BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inferenceAurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent C. Duval, J.-C. Pesquet · 2015 · BMC Bioinformatics
- Latent Variable Time-varying Network InferenceFederico Tomasi, Veronica Tozzo, Saverio Salzo, Alessandro Verri · 2018 · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)
- Bayesian topology identification of linear dynamic networksShengling Shi, Giulio Bottegal, Paul M.J. Van den Hof · 2019 · European Control Conference (ECC)
- Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infectionKonstantina Dimitrakopoulou, Charalampos Tsimpouris, George D. Papadopoulos, Claudia Pommerenke, Esther Wilk, Kyriakos Sgarbas, Klaus Schughart, Anastasios Bezerianos · 2011 · Journal of Clinical Bioinformatics
- Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq DataDaniel S. Moore, Ricardo De Matos Simoes, Matthias Dehmer, Frank Emmert‐Streib · 2018 · Current Genomics
- Inferring network structures via signal LassoЛей Ши, Chen Shen, Libin Jin, Qi Shi, Zhen Wang, Stefano Boccaletti · 2021 · Physical Review Research
- PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorizationOmar Mahmood, Omar Mahmood, Richard Bonneau, Kyunghyun Cho · 2024 · Genome biology
- Robust Approaches for Genetic Regulatory Network Modeling and Intervention: A review of recent advancesRanadip Pal, Sonal Bhattacharya, Mehmet Umut Caglar · 2011 · IEEE Signal Processing Magazine
- Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiationMichael Weber, Ana M. Sotoca, Peter Kupfer, Reinhard Guthke, E.J.J. van Zoelen · 2013 · BMC Systems Biology
- Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein dataOana A. Tomescu, Diethard Mattanovich, Gerhard Thallinger · 2014 · BMC Systems Biology
- Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulationsAntoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand et al. · 2020 · BMC Bioinformatics
- Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpaMegan L. Matthews, Jack P. Wang, Ronald R. Sederoff, Vincent L. Chiang, Cranos Williams · 2020 · PLoS Computational Biology
- Dynamical models of biomarkers and clinical progression for personalized medicine: The HIV contextMélanie Prague, Daniel Commenges, Rodolphe Thiébaut · 2013 · Advanced Drug Delivery Reviews
- Stable Gene Regulatory Network Modeling From Steady-State DataJoy E. Larvie, Mohammad Sefidmazgi, Abdollah Homaifar, Scott Henry Harrison, Ali Karimoddini, Anthony Guiseppi‐Elie · 2016 · Bioengineering
- Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networksEmma J. Cooke, Richard S. Savage, David L. Wild · 2009 · Seminars in Cell and Developmental Biology
- In silico disease model: from simple networks to complex diseasesDebmalya Barh, Eugenia Ch. Yiannakopoulou, Emmanuel Oluwatobi Salawu, Atanu Bhattacharjee, Sudhir Chowbina, Joseph J. Nalluri, Preetam Ghosh, Vasco Azevedo · 2020 · Elsevier eBooks
- Analysis of time-series regulatory networksJun Ding, Ziv Bar‐Joseph · 2020 · Current Opinion in Systems Biology
- Using gene expression programming to infer gene regulatory networks from time-series dataYongqing Zhang, Yi‐Fei Pu, Haisen Zhang, Yabo Su, Lifang Zhang, Jiliu Zhou · 2013 · Computational Biology and Chemistry
- The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytesSebastian Vlaic, Wolfgang Schmidt‐Heck, Madlen Matz‐Soja, Eugenia Marbach, Jörg Linde, Anke Meyer‐Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt · 2012 · BMC Systems Biology
- Data simulation and regulatory network reconstruction from time-series microarray data using stepwise multiple linear regressionYiqian Zhou, Rehman Qureshi, Ahmet Saçan · 2012 · Network Modeling Analysis in Health Informatics and Bioinformatics
- Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual InformationVijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng · 2009 · International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing
- Combining Mathematical Models With Experimentation to Drive Novel Mechanistic Insights Into Macrophage FunctionJoanneke E. Jansen, Eamonn A. Gaffney, Jonathan Wagg, Mark Christopher Coles · 2019 · Frontiers in Immunology
- Stochastic models for inferring genetic regulation from microarray gene expression dataTianhai Tian · 2009 · Biosystems
- Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sourcesJin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Sachin Ranade, Hong Cui · 2016 · BMC Bioinformatics
- Reverse-engineering biological networks from large data setsJoseph L. Natale, David Hofmann, Damián G. Hernández, Ilya M. Nemenman · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory NetworksHao Zhu, Donna K. Slonim · 2024 · Journal of Computational Biology
- Constraint-based analysis of gene interactions using restricted boolean networks and time-series dataCarlos H. A. Higa, Vitor H. P. Louzada, Tales Pinheiro De Andrade, Ronaldo F. Hashimoto · 2011 · BMC Proceedings
- Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A VirusHimanshu Manchanda, Nora Seidel, Markus F. Blaess, Ralf Alexander Claus, Joerg Linde, Hortense Slevogt, Andreas Sauerbrei, Reinhard Guthke, Michaela Schmidtke · 2016 · Frontiers in Microbiology
- Predicting Phenotype from Genotype through Automatically Composed Petri NetsMary Ann Blätke, Monika Heiner A, Wolfgang Marwan · 2012 · Lecture notes in computer science
- Prediction of kinetic parameters from DNA-binding site sequences for modeling global transcription dynamics in Escherichia coliTimo Hardiman, Hannes Meinhold, Johannes F.-X. Hofmann, Jennifer Christina Ewald, Martin Siemann‐Herzberg, Matthias Reuß · 2009 · Metabolic Engineering
- Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular NetworksStalin Muñoz, Miguel Carrillo, Eugenio M. Azpeitia, David A. Rosenblueth · 2018 · Frontiers in Genetics
- Detecting direct associations in a network by information theoretic approachesJifan Shi, Juan Zhao, Tiejun Li, Luonan Chen · 2018 · Science China Mathematics
- Inferring Functional Connectivity From Time-Series of Events in Large Scale Network DeploymentsAntoine Messager, George Parisis, Istvan Zoltan Kiss, Robert Harper, Philip Tee, Luc Berthouze A · 2019 · IEEE Transactions on Network and Service Management
- Learning Laplacian Matrix from Graph Signals with Sparse Spectral RepresentationPierre Humbert, Batiste Le Bars, Laurent Oudre, Argyris Kalogeratos, Nicolas Vayatis · 2021 · HAL
- An integrated approach to infer dynamic protein-gene interactions – A case study of the human P53 proteinJunbai Wang, Qianqian Wu, Xiaohua Tony Hu, Tianhai Tian · 2016 · Methods
- A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networksTianchi Chen, M. Ali Al-Radhawi, Eduardo D. Sontag · 2020 · Epigenetics
- SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression dataAaron S. Wise, Ziv Bar‐Joseph · 2014 · Bioinformatics
- Epigenetic memories: structural marks or active circuits?Floriane Nicol‐Benoit, Pascale Le Goff, Yves Le Dréan, Florence Demay, Farzad Pakdel, Gilles Flouriot, Denis Michel · 2012 · Cellular and Molecular Life Sciences
- Identifying disease candidate genes via large-scale gene network analysisHaseong Kim, Taesung Park, Erol Gelenbe A · 2014 · International Journal of Data Mining and Bioinformatics
- Untangling statistical and biological models to understand network inference: the need for a genomics network ontologyFrank Emmert‐Streib, Matthias Dehmer, Benjamin Haibe‐Kains · 2014 · Frontiers in Genetics
- Construction of Transcriptional Regulatory Network of Alzheimer’s Disease Based on PANDA AlgorithmJieyuan Ding, Wei Kong, Xiaoyang Mou, Shuaiqun Wang · 2018 · Interdisciplinary Sciences Computational Life Sciences
- GENECI: A novel evolutionary machine learning consensus-based approach for the inference of gene regulatory networksAdrián Segura-Ortiz, José García-Nieto, José Francisco Aldana-Montes, Ismael Navas‐Delgado · 2023 · Computers in Biology and Medicine
- A Survey of Current Integrative Network Algorithms for Systems BiologyAndrew K. Rider, Nitesh V. Chawla, Scott Emrich · 2013 · Springer eBooks
- On the necessity of full-state measurement for state-space network reconstructionPhilip E. Paré, Vasu Chetty, Sean C. Warnick · 2013 · IEEE Global Conference on Signal and Information Processing
- A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virusLindsay C. DeMers, Neelam R. Redekar, Aardra Kachroo, S. A. Tolin, Song Li, M. A. Saghai Maroof · 2020 · PLoS ONE
- Gene network coherence based on prior knowledge using direct and indirect relationshipsFrancisco Gómez-Vela, José Antonio Lagares, Norberto Díaz–Díaz · 2015 · Computational Biology and Chemistry
- SFFS-MR: A Floating Search Strategy for GRNs InferenceFabrício Martins Lopes, David Martins, Júnior Barrera, Roberto Marcondes Cesar Junior · 2010 · Lecture notes in computer science
- Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency ResponseAlexandr Koryachko, Anna Matthiadis, DurreShahwar Muhammad, Jessica Foret, Siobhán M. Brady, Joel J. Ducoste, James M. Tuck, Terri A. Long, Cranos Williams · 2015 · PLoS ONE
- CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and CancerSimone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James M. Osborne, Joe Pitt‐Francis, Marco Antoniotti · 2015 · Cancer Informatics
- Mining Gene Regulatory Networks by Neural Modeling of Expression Time-SeriesMariano Rubiolo, Diego Humberto Milone, Georgina S. Stegmayer · 2015 · IEEE Transactions on Computational Biology and Bioinformatics
- FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEWIsmael Sánchez-Osorio, FERNANDO RAMOS, Pedro P. Mayorga, Edgar Dantán · 2013 · Journal of Bioinformatics and Computational Biology
- On the way toward systems biology of Aspergillus fumigatus infectionDaniela Albrecht, Olaf Kniemeyer, Franziska Mech, Matthias Gunzer, Axel A. Brakhage, Reinhard Guthke · 2011 · International Journal of Medical Microbiology
- A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction ChallengeJianhua Ruan · 2010 · PLoS ONE
- Integration of prior biological knowledge and epigenetic information enhances the prediction accuracy of the Bayesian Wnt pathwayShriprakash Sinha · 2014 · Integrative Biology
- Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapyMichael Weiss, Beatriz Peñalver Bernabé, S. Shin, Szilárd Asztalos, Sara J. Dubbury, Michael D. Mui, Abigail D. Bellis, Dennis A. Bluver, Debra A. Tonetti, Julio Sáez-Rodríguez et al. · 2014 · Integrative Biology
- Reverse engineering of gene regulatory networks from biological dataLizhi Liu, Fang‐Xiang Wu, Wen‐Jun Zhang · 2012 · Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery
- Gene co-opening network deciphers gene functional relationshipsWenran Li, Meng Wang, Jinghao Sun, Yong Wang, Rui Jiang · 2017 · Molecular BioSystems
- MKL-GRNI: A parallel multiple kernel learning approach for supervised inference of large-scale gene regulatory networksNisar Wani, Khalid Raza · 2021 · PeerJ Computer Science
- Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in CancerChristina Y. Yu, Antonina Mitrofanova · 2021 · Frontiers in Genetics
- Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosaAshley J. Vargas, John F Quackenbush, Kimberly Glass · 2016 · Genomics
- Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patientsPeter Kupfer, René Huber, Michael Weber, Sebastian Vlaic, Thomas Häupl, Dirk Koczan, Reinhard Guthke, Raimund W. Kinne · 2014 · BMC Medical Genomics
- The Regulatory Network Computational DeviceRui L. Lopes, Ernesto J. F. Costa · 2012 · Genetic Programming and Evolvable Machines
- Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimizationSaskia Trescher, Jannes Münchmeyer, Ulf Leser · 2017 · BMC Systems Biology
- Can dynamic network modelling be used to identify adaptive microbiomes?Joshua Garcia, Jenny Kao‐Kniffin · 2019 · Functional Ecology
- Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene NetworksFernando M. Delgado-Chaves, Francisco Gómez-Vela, Federico Divina, Miguel García-Torres, Domingo S. Rodríguez–Baena · 2020 · Genes
- Growing Seed Genes from Time Series Data and Thresholded Boolean Networks with PerturbationCarlos H. A. Higa, Tales Pinheiro De Andrade, Ronaldo F. Hashimoto · 2013 · IEEE Transactions on Computational Biology and Bioinformatics