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Multi-objective hybrid PSO using µ-fuzzy dominance

Praveen Koduru, Sanjoy Das, Stephen M. Welch
2007 Proceedings of the 9th annual conference on Genetic and evolutionary computation - GECCO '07  
The proposed algorithm is shown to perform better than MOPSO on several test problems as well as for the optimization of a genetic model for flowering time control in Arabidopsis.  ...  Adding the local search achieves faster convergence, an important feature in computationally intensive optimization of gene networks.  ...  Modeling Flowering Time Control in Arabidopsis In the molecular genetic model plant, Arabidopsis thaliana, three genes TERMINAL FLOWERING 1 (TFL1), APETALA 1 (AP1), and LEAFY (LFY) play a special role  ... 
doi:10.1145/1276958.1277125 dblp:conf/gecco/KoduruDW07 fatcat:qh65c52lv5fkzicqdssk4fj44i

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

James Kitchen, Robin Allaby
2013 Plants  
gene networks.  ...  Sedentism makes plants relevant candidates for spatially explicit modeling that is tied in with dynamical environments.  ...  A further example exists in Arabidopsis thaliana where a mutation in the EMBRYONIC FLOWER (EMF) genes EMF1 and EMF2 induces very early flowering but also a reduction in seed production [134] .  ... 
doi:10.3390/plants2010016 pmid:27137364 pmcid:PMC4844292 fatcat:znk6leg5wjdeznmevcyq6azzbi

A Hybrid Prediction Method for Plant lncRNA-Protein Interaction

Jael Sanyanda Wekesa, Yushi Luan, Ming Chen, Jun Meng
2019 Cells  
In particular, lncRNA-protein interaction has plausible relevance to gene expression regulation and in cellular processes such as pathogen resistance in plants.  ...  The selection of an optimal feature subset and subsequent efficient compression are significant challenges for deep learning models.  ...  For example, lncRNA COLDAIR in Arabidopsis thaliana regulates flowering time and floral organ formation during vernalization [4] .  ... 
doi:10.3390/cells8060521 pmid:31151273 pmcid:PMC6627874 fatcat:egqseuwyifhhld7wxlfaqcmo54

A model comparison study of the flowering time regulatory network in Arabidopsis

Charles CN Wang, Pei-Chun Chang, Ka-Lok Ng, Chun-Ming Chang, Phillip CY Sheu, Jeffrey JP Tsai
2014 BMC Systems Biology  
First, construction of dynamic models for gene regulatory networks requires the use of mathematic modeling that comprises equations of a large number of parameters.  ...  Conclusions: Three dynamic models were adopted to describe the dynamics of the gene regulatory network of the flowering transition process in Arabidopsis.  ...  Feng-Sheng Wang, Department of Chemical Engineering, National Chung Cheng University, Taiwan, for his advice on the S-system and parameter estimation methods.  ... 
doi:10.1186/1752-0509-8-15 pmid:24513114 pmcid:PMC3938817 fatcat:zamxcl3q3ndavlbu5lvlik6fxy

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

Dario Di Silvestre, Andrea Bergamaschi, Edoardo Bellini, PierLuigi Mauri
2018 Proteomes  
Proteomes 2018, 6, 27 2 of 34 level [7], while computational tools and algorithms assist biologists in data processing to extract the most relevant information in an objective way [8].  ...  (A) Like each living organism, it is assumed that plants are made up of networks integrated and communicating on a multiple scale.  ...  At the same time, the availability of multi-omic data allows for the elucidation of different aspects of the gene function.  ... 
doi:10.3390/proteomes6020027 pmid:29865292 pmcid:PMC6027444 fatcat:cs7o46lztfgtrh2bzi65hu7cti

Genetic Variants Detection Based on Weighted Sparse Group Lasso

Kai Che, Xi Chen, Maozu Guo, Chunyu Wang, Xiaoyan Liu
2020 Frontiers in Genetics  
approaches for genetic variants detection.  ...  Although the majority of existing methods for variants detection have good predictive performance in the average case, they can not precisely identify the variants present in a small number of target genes  ...  Experiments with both simulation and real data of SNPs related to the flowering time of A. thaliana demonstrated the effectiveness of our approach.  ... 
doi:10.3389/fgene.2020.00155 pmid:32194631 pmcid:PMC7063084 fatcat:lvt6ezzcoja6rptavxuwdwxrji

Hybrid of Restricted and Penalized Maximum Likelihood Method for Efficient Genome-Wide Association Study

Wenlong Ren, Zhikai Liang, Shu He, Jing Xiao
2020 Genes  
As a result, our method always had the highest average statistical power compared with multi-locus mixed-model (MLMM), fixed and random model circulating probability unification (FarmCPU), and genome-wide  ...  Secondly, we carried out penalized maximum likelihood (PML) on multi-locus LMM for markers with reasonably large effects.  ...  Lee and Lee [6] presented a web application for the network-based Arabidopsis genome-wide association boosting, which can identify weak association signals by integrating co-functional gene network information  ... 
doi:10.3390/genes11111286 pmid:33138126 fatcat:evqsbqdavffwho5evvwyhxvzsq

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

Emiliano Rodríguez-Mega, Alma Piñeyro-Nelson, Crisanto Gutierrez, Berenice García-Ponce, María De La Paz Sánchez, Estephania Zluhan-Martínez, Elena R. Álvarez-Buylla, Adriana Garay-Arroyo
2015 Developmental Dynamics  
We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks  ...  A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented  ...  Acknowledgments We are most grateful to Diana Romo for her help with logistical support.  ... 
doi:10.1002/dvdy.24268 pmid:25733163 fatcat:5adiyahuzze4vdvuwrzfcz262y

Examining the relationships between phenotypic plasticity and local environments with genomic structural equation models [article]

Malachy T. Campbell, Haipeng Yu, Mehdi Momen, Gota Morota
2019 bioRxiv   pre-print
between empirical phenotypes and environmental conditions using a mixed-effects structural equation model (SEM).  ...  We believe the frameworks presented in this manuscript can provide new insights into the genetic basis of local adaptation.  ...  To this end, we first predicted genomic values for each accession and trait using a Bayesian multi-trait model (MTM).  ... 
doi:10.1101/2019.12.11.873257 fatcat:ckm27n44zrarnd5pbxjdicdqnu

Improving drought tolerance in maize: a view from industry

H. Campos, M. Cooper, J.E. Habben, G.O. Edmeades, J.R. Schussler
2004 Field crops research (Print)  
Genomic tools and the use of model plants are considered indispensable tools in this search for new ways of optimizing maize yield under stress. #  ...  Genetic and crop physiological models of key processes are now being used to confirm the value of traits for target environments, and to suggest efficient breeding strategies.  ...  We also thank reviewers for their valuable comments on this manuscript.  ... 
doi:10.1016/j.fcr.2004.07.003 fatcat:m7khejdezzfvjm53kwlre4bqpa

Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs [chapter]

Peter Civan, Renaud Rincent, Alice Danguy-Des-Deserts, Jean-Michel Elsen, Sophie Bouchet
2021 Population Genomics  
In a breeding program, reduced phenotyping characterization allows to increase the number of tested parents and crosses (and global genetic variance) for a fixed budget.  ...  In that context, there is a growing demand for methodology to re-introduce useful variation into cultivated germplasm.  ...  It combines optimal contribution with optimal mating in a multi-objective problem that can be also optimized by heuristic algorithms.  ... 
doi:10.1007/13836_2021_97 fatcat:e364xlxu5nf7lltwkdkccyoyqa

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence

Dharmendra Singh, Priya Chaudhary, Jyoti Taunk, Chandan Kumar Singh, Deepti Singh, Ram Sewak Singh Tomar, Muraleedhar Aski, Noren Singh Konjengbam, Ranjeet Sharan Raje, Sanjay Singh, Rakesh Singh Sengar, Rajendra Kumar Yadav (+1 others)
2021 International Journal of Molecular Sciences  
Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand.  ...  regulation—has been widely used for abiotic stress amelioration in food legume crops.  ...  , ICAR-IARI, New Delhi for healthy discussions during the preparation of this article.  ... 
doi:10.3390/ijms221910535 pmid:34638885 fatcat:527ihatxi5hqleb2lngs32g7pm

Harnessing Crop Wild Diversity for Climate Change Adaptation

Andrés J Cortés, Felipe López-Hernández
2021 Genes  
However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated  ...  In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding.  ...  gain for abiotic stress tolerance per unit of time.  ... 
doi:10.3390/genes12050783 pmid:34065368 pmcid:PMC8161384 fatcat:xkcb3q4ycregdmmfy6flbsbzla

Identification of Evening Complex Associated Proteins inArabidopsisby Affinity Purification and Mass Spectrometry

He Huang, Sophie Alvarez, Rebecca Bindbeutel, Zhouxin Shen, Michael J. Naldrett, Bradley S. Evans, Steven P. Briggs, Leslie M. Hicks, Steve A. Kay, Dmitri A. Nusinow
2015 Molecular & Cellular Proteomics  
In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression  ...  Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana.  ...  Acknowledgments-We thank Doug Allen, Rebecca Bart, Dhruv Patel and Takato Imaizumi for critically reading the manuscript, Ivan Baxter and Toby Kellog for useful discussions, and Sarah Huss for technical  ... 
doi:10.1074/mcp.m115.054064 pmid:26545401 pmcid:PMC4762519 fatcat:dw5vw5lwwrdolgnpjuxny2zhmu

Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions

Dario Constantinescu, Mohamed-Mahmoud Memmah, Gilles Vercambre, Michel Génard, Valentina Baldazzi, Mathilde Causse, Elise Albert, Béatrice Brunel, Pierre Valsesia, Nadia Bertin
2016 Frontiers in Plant Science  
Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD.  ...  Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development  ...  Optimization Algorithm for Model Calibration and Design of Ideotypes The NSGA-II developed by Deb et al. (2002) has proven to be one of the most efficient algorithms for solving multi-objective problems  ... 
doi:10.3389/fpls.2016.01841 pmid:28018381 pmcid:PMC5145867 fatcat:u4ogqoek7vegnj7uhck2nnt6qa
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