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Scatter Search Applied to the Inference of a Development Gene Network

Amir Abdol, Damjan Cicin-Sain, Jaap Kaandorp, Anton Crombach
2017 Computation  
From this we conclude that for poorly-studied developmental systems, scatter search is a valuable tool for exploration and accelerates the elucidation of gene regulatory networks.  ...  We compare the hybrid approach to simulated annealing, a method of network inference with a proven track record.  ...  We thankfully acknowledge the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center, which is part of the Red Española de Supercomputación.  ... 
doi:10.3390/computation5020022 fatcat:vnecgmwpkfaupmpauf2z75giny

Réseaux de systèmes évolutifs / Network in evolutionary systems

Anton Crombach
2019 Annuaire du Collège de France : Résumé Des Cours et Travaux  
., Kaandorp J.A. et Crombach A., « Scatter search applied to the inference of a development gene network », Computation , vol. 5, n o 2, 2017, p. 22, DOI : 10.3390/computation5020022.  ...  Kaandorp (Univ. of Amsterdam) on the design and implementation of a hybrid network inference method, using the novel method of scatter search optimization.  ... 
doi:10.4000/annuaire-cdf.14704 fatcat:rdcs4ulb4fd7vpwfp5efeaf2xu

Identification of gene interactions associated with disease from gene expression data using synergy networks

John Watkinson, Xiaodong Wang, Tian Zheng, Dimitris Anastassiou
2008 BMC Systems Biology  
High levels of synergy in gene pairs indicates possible membership of the two genes in a shared pathway and leads to a graphical representation of inferred gene-gene interactions associated with disease  ...  , in the form of a "synergy network."  ...  Acknowledgements We thank John Walker and Garret Hampton for providing us with CEL values of the prostate cancer expression data set that we used for validation.  ... 
doi:10.1186/1752-0509-2-10 pmid:18234101 pmcid:PMC2258206 fatcat:ez3xpp3uknat7k7xu2znghydlq

Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

Tingting Qin, Lam C Tsoi, Kellie J Sims, Xinghua Lu, W Zheng
2012 BMC Systems Biology  
The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven  ...  Results: We applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition.  ...  John Schwacke for providing us with the R code to generate the plot of protein phosphorylation activity.  ... 
doi:10.1186/1752-0509-6-s3-s3 pmid:23282239 pmcid:PMC3524013 fatcat:i7w5tdqjyjanvigkkv6ag43idq

Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data

Jiajun Zhang, Qing Nie, Tianshou Zhou
2019 Frontiers in Genetics  
It also infers both marker gene networks and their dynamic changes as well as dynamic characteristics of transcriptional bursting along the cell-state transition trajectories.  ...  We developed a multifunction new method, Topographer, to construct a "quantitative" Waddington's landscape of single-cell transcriptomic data.  ...  FUNDING This work was partially supported by the National Natural Science Foundation of China (11931019, 11775314, 91530320, 11631005), and the Science and Technology Program of Guangzhou ACKNOWLEDGMENTS  ... 
doi:10.3389/fgene.2019.01280 pmid:31921315 pmcid:PMC6935941 fatcat:axfom33mq5dixihaosqqu6k5iq

Interactive exploration of integrated biological datasets using context-sensitive workflows

Fabian Horn, Martin Rittweger, Jan Taubert, Artem Lysenko, Christopher Rawlings, Reinhard Guthke
2014 Frontiers in Genetics  
Network inference utilizes experimental high-throughput data for the reconstruction of molecular interaction networks where new relationships between the network entities can be predicted.  ...  We applied the Ondex system to the integration of publicly available data for Aspergillus nidulans and analyzed transcriptome data.  ...  The introduction starts with a survey of network inference methods and qualitative assessment of inferred networks.  ... 
doi:10.3389/fgene.2014.00021 pmid:24600467 pmcid:PMC3929842 fatcat:pzzmhnzljvhwtg6qwfgblojb7m

Topographer Reveals Dynamic Mechanisms of Cell Fate Decisions from Single-Cell Transcriptomic Data [article]

Jiajun Zhang, Tianshou Zhou, Qing Nie
2018 bioRxiv   pre-print
It also infers both marker gene networks and their dynamic changes as well as dynamic characteristics of transcriptional bursting along the cell-state transition trajectories.  ...  We developed a multifunction new method, Topographer to construct a "quantitative" Waddington's landscape of single-cell transcriptomic data.  ...  Xiaoming Lai's partial computer program codes for the manuscript. This work was  ... 
doi:10.1101/251207 fatcat:hqy5ep6mrngzznppelx3u2aeaq

Memetic Algorithms in Bioinformatics [chapter]

Regina Berretta, Carlos Cotta, Pablo Moscato
2012 Studies in Computational Intelligence  
They use a binary genetic algorithm to evolve the topology of the network, and an evolution strategy to do local search on the parameters of the model representing the network.  ...  Two local searches are applied, the first one work inverting branches of subtrees and the second one employs a pairwise interchange local search. They test the MA in instances with up to 500 genes.  ... 
doi:10.1007/978-3-642-23247-3_16 fatcat:cbhccq5bzzbyrbm7pxxhaa7pqu

State of the Art of Fuzzy Methods for Gene Regulatory Networks Inference

Tuqyah Abdullah Al Qazlan, Aboubekeur Hamdi-Cherif, Chafia Kara-Mohamed
2015 The Scientific World Journal  
To address one of the most challenging issues at the cellular level, this paper surveys the fuzzy methods used in gene regulatory networks (GRNs) inference.  ...  GRNs represent causal relationships between genes that have a direct influence, trough protein production, on the life and the development of living organisms and provide a useful contribution to the understanding  ...  Acknowledgment This work is supported by the Deanship of Scientific Research at Qassim University, Saudi Arabia, as part of the research project with ID no. 1223-2012.  ... 
doi:10.1155/2015/148010 pmid:25879048 pmcid:PMC4386676 fatcat:kjdq6dmcwre4rp7vp2ye3hmeja

Network constrained clustering for gene microarray data

D. Zhu, A. O Hero, H. Cheng, R. Khanna, A. Swaroop
2005 Bioinformatics  
Our approach tends to group functionally related genes into a tight cluster. We illustrate our approach and compare it to the traditional clustering approaches on a retinal gene expression dataset.  ...  Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective.  ...  Transitive co-expression analysis can be viewed as one possible way to apply network analysis techniques for inferring functional relationships among genes [2] .  ... 
doi:10.1093/bioinformatics/bti655 pmid:16141248 fatcat:jciyev4gi5h5hnu7u2b2qo6dte

Network-Based Method for Identifying Co-Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues

Lei Chen, Hongying Pan, Yu-Hang Zhang, Kaiyan Feng, XiangYin Kong, Tao Huang, Yu-Dong Cai
2017 Genes  
A total of seventeen genes were inferred by the method, which were deemed to contribute to co-regeneration of at least two tissues.  ...  Three procedures were applied in the network-based method.  ...  Conflicts of Interest: The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish  ... 
doi:10.3390/8100252 fatcat:2c2jiuz7ebdfzhukasdgbtagfu

Network-Based Method for Identifying Co-Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues

Lei Chen, Hongying Pan, Yu-Hang Zhang, Kaiyan Feng, XiangYin Kong, Tao Huang, Yu-Dong Cai
2017 Genes  
A total of seventeen genes were inferred by the method, which were deemed to contribute to co-regeneration of at least two tissues.  ...  Three procedures were applied in the network-based method.  ...  Conflicts of Interest: The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish  ... 
doi:10.3390/genes8100252 pmid:28974058 pmcid:PMC5664102 fatcat:7wdyglogszeobcshhuhrlbnzau

Estimation of Gene Regulatory Networks from Cancer Transcriptomics Data

Seong Beom Cho
2021 Processes  
In addition, more systematic methods for validation of the estimated GRNs need to be developed in the context of cancer biology.  ...  In this review, methods for inference of gene regulatory networks (GRNs) from transcriptomics data that are used in cancer research are introduced.  ...  discovery rate of edges using mixture model [49] , fast inference of the GGM using scaled lasso regression [44] , and combing a greedy search algorithm to identify the network structure of the GGM in  ... 
doi:10.3390/pr9101758 fatcat:2lxa6q6epncvjgtje7wuhnztdi

A Review of Software for Predicting Gene Function

Swee Kuan Loh, Swee Thing Low, Mohd Saberi Mohamad, Safaai Deris, Shahreen Kasim, Choon Yee Wen, Zuwairie Ibrahim, Bambang Susilo, Yusuf Hendrawan, Agustin Krisna Wardani
2015 International Journal of Bio-Science and Bio-Technology  
A rich resource of information on functional genomics data can be applied to annotating the thousands of unknown gene functions that can be retrieved from most sequenced.  ...  High-throughput sequencing can lead to increased understanding of proteins and genes. We can infer networks of functional couplings from direct and indirect interactions.  ...  Acknowledgements We would like to thank the Universiti Teknologi Malaysia for supporting this research through a GUP research grant (Grant number: Q.J130000.2507.05H50) and a Matching grant (Grant number  ... 
doi:10.14257/ijbsbt.2015.7.2.06 fatcat:nedrong7bzhqrgzqhholgfguyq

Syn-Lethality: An Integrative Knowledge Base of Synthetic Lethality towards Discovery of Selective Anticancer Therapies

Xue-juan Li, Shital K. Mishra, Min Wu, Fan Zhang, Jie Zheng
2014 BioMed Research International  
Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets  ...  It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms.  ...  It is the first attempt to apply the experimentally verified SL pairs to construct a SL network.  ... 
doi:10.1155/2014/196034 pmid:24864230 pmcid:PMC4016865 fatcat:3swxozrfcjdr5ff3lwhafpgyri
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