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Refining transcriptional regulatory networks using network evolutionary models and gene histories

Xiuwei Zhang, Bernard ME Moret
2010 Algorithms for Molecular Biology  
Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models.  ...  Results: In this paper, we extend the evolutionary model so as to take into account gene duplications and losses, which are viewed as major drivers in the evolution of regulatory networks.  ...  Introduction Transcriptional regulatory networks are models of the cellular regulatory system that governs transcription.  ... 
doi:10.1186/1748-7188-5-1 pmid:20047657 pmcid:PMC2823753 fatcat:jv33yc5jafdjxc3uysqnqslhhu

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks [chapter]

Xiuwei Zhang, Bernard M. E. Moret
2011 Lecture Notes in Computer Science  
We therefore use an evolutionary approach to the inference of regulatory networks, which enables us to study evolutionary models for these networks as well as to improve the accuracy of inferred networks  ...  ProPhyC can be used with various network evolutionary models and any existing inference method.  ...  Introduction Transcriptional regulatory networks are models of the cellular regulatory system that governs transcription.  ... 
doi:10.1007/978-3-642-21260-4_33 fatcat:yc5byj4jnrdyxa4zgf2jcgbusy

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models [chapter]

Xiuwei Zhang, Bernard M. E. Moret
2009 Lecture Notes in Computer Science  
In previous work, we used a simple evolutionary model for regulatory networks and provided extensive simulation results showing that phylogenetic information, combined with such a model, could be used  ...  In this paper, we extend the evolutionary model so as to take into account gene duplications and losses, which are viewed as major drivers in the evolution of regulatory networks.  ...  INTRODUCTION Transcriptional regulatory networks are models of the cellular regulatory system that governs transcription.  ... 
doi:10.1007/978-3-642-04241-6_34 fatcat:mn6gzi6t6vhyvjxpovek5nh4iy

Refining Regulatory Networks through Phylogenetic Transfer of Information

Xiuwei Zhang, B. M. E. Moret
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
ProPhyC can be used with various network evolutionary models and any existing inference method.  ...  The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and timeconsuming, while computational methods to infer these networks provide only modest accuracy  ...  Jaebum Kim for providing much of the data we used for the Drosophila networks.  ... 
doi:10.1109/tcbb.2012.62 pmid:22547434 fatcat:6m7jtvfelfakvpajfoydppom4q

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

Dawn Thompson, Aviv Regev, Sushmita Roy
2015 Annual Review of Cell and Developmental Biology  
Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequences to functional data.  ...  We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence.  ...  A.R. is supported by HHMI, the NIH (R01CA119176-01, P50HG006193), and the Sloan Foundation. S.R. is supported by an NSF CAREER award (NSF DBI: 1350677) and a Sloan Foundation research fellowship.  ... 
doi:10.1146/annurev-cellbio-100913-012908 pmid:26355593 fatcat:sryxj3e2gvapnnnkmnzdhnyzr4

Extending the Reach of Phylogenetic Inference [chapter]

Bernard M. E. Moret
2013 Lecture Notes in Computer Science  
The new approaches include an extension of the time-tested and universally used comparative method, as well as applications of phylogenetic approaches to genomic transcripts and cell types, objects not  ...  It was also around that time that the development of computational approaches for the inference of phylogenies (evolutionary histories) started.  ...  We have successfully applied our ProPhyC tool to the refinement of regulatory networks and are currently using it for the refinement and prediction of protein contact networks in protein complexes.  ... 
doi:10.1007/978-3-642-40453-5_1 fatcat:ilmiouqtdnbzlodqtzumcnsywi

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Naomi Habib, Ilan Wapinski, Hanah Margalit, Aviv Regev, Nir Friedman
2012 Molecular Systems Biology  
Here, we introduce a novel approach to study cis-regulatory evolution, and use it to trace the regulatory history of 88 DNA motifs of transcription factors across 23 Ascomycota fungi.  ...  We explain these trends using a model with a strong selection to conserve the overall function of a transcription factor, and a much weaker selection over the specific genes it targets.  ...  Author contributions: NH, IW, HM, AR, and NF conceived and designed the study; NH and IW developed and applied the Cladeo-Scope framework; NH developed the models and performed the analyses; NH, IW, HM  ... 
doi:10.1038/msb.2012.50 pmid:23089682 pmcid:PMC3501536 fatcat:byubfqz675cqlcfecr5oh6ugxu

Conceptual and Methodological Biases in Network Models

Ehud Lamm
2009 Annals of the New York Academy of Sciences  
The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of the biological categories  ...  The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between "program  ...  The work presented in this paper is part of the author's PhD research, which was financially supported by The Cohn Institute For the History and Philosophy of Science and Ideas and The School of Philosophy  ... 
doi:10.1111/j.1749-6632.2009.05009.x pmid:19845645 fatcat:a7z6bdzounfuribjmlgg25y5ui

The analysis of Gene Regulatory Networks in plant evo-devo

Aurélie C. M. Vialette-Guiraud, Amélie Andres-Robin, Pierre Chambrier, Raquel Tavares, Charles P. Scutt
2016 Journal of Experimental Botany  
We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology.  ...  We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns,  ...  AV-G is also funded by an ENS-Lyon research and teaching position.  ... 
doi:10.1093/jxb/erw119 pmid:27006484 fatcat:jeazzckf5fev5kuwj6wtqaxxjq

Understanding Biological Regulation Through Synthetic Biology

Caleb J. Bashor, James J. Collins
2018 Annual Review of Biophysics  
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing.  ...  Here we outline research that uses the process of gene circuit engineering to advance biological discovery.  ...  could be used to address questions regarding the regulatory basis for phenotypic plasticity and evolutionary optimality.  ... 
doi:10.1146/annurev-biophys-070816-033903 pmid:29547341 fatcat:tj6bjg7nirebjkfppjdkzhtjku

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development

Mark Rebeiz, Nipam H. Patel, Veronica F. Hinman
2015 Annual review of genomics and human genetics (Print)  
Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space, and therefore determine the tissue specific genetic  ...  The molecular and genetic basis of the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades.  ...  VH was supported by grants IOS 0844948 and IOS 1024811. (NSF) and a Charles E. Kaufman award of the Pittsburgh Foundation  ... 
doi:10.1146/annurev-genom-091212-153423 pmid:26079281 fatcat:53ufkzamhbaahlwrods7g54hcy

A scalable multi-scale framework for parallel simulation and visualization of microbial evolution

Vadim Mozhayskiy, Bob Miller, Kwan-Liu Ma, Ilias Tagkopoulos
2011 Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11  
The simulator employs multi-scale models and data structures that capture a whole ecology of interactions between the environment, populations, organisms, and their respective gene regulatory and biochemical  ...  This dataset (stored in HDF5 format for scalability) includes all environmental and cellular parameters, cellular (division, death) and evolutionary events (mutations, Horizontal Gene Transfer).  ...  This work was supported in part by the National Science Foundation through TeraGrid resources (under grants number TG-ASC100043 and TG-ASC110007) and NSF-OCI grant 0941360.  ... 
doi:10.1145/2016741.2016749 fatcat:hhzzfuy4gbdhviqer4psbmlm7u

Exploring the miRNA Regulatory Network Using Evolutionary Correlations

Benedikt Obermayer, Erel Levine, Claus O. Wilke
2014 PLoS Computational Biology  
We thus provide a proof-of-principle method to understand regulatory networks from an evolutionary perspective.  ...  The increased statistical power of our phylogenetic model allows detection of evolutionary correlation in the conservation patterns of site pairs.  ...  Developed and implemented the computational approach: BO. Designed and performed research: BO EL.  ... 
doi:10.1371/journal.pcbi.1003860 pmid:25299225 pmcid:PMC4191876 fatcat:w66tbcsrn5gn7dkqfgf2fgqjzi

Eric Davidson: Steps to a gene regulatory network for development

Ellen V. Rothenberg
2016 Developmental Biology  
, then spent his life translating these process elements into molecularly definable terms through the architecture of gene regulatory networks.  ...  Eric Harris Davidson was a unique and creative intellectual force who grappled with the diversity of developmental processes used by animal embryos and wrestled them into an intelligible set of principles  ...  regulatory network models.  ... 
doi:10.1016/j.ydbio.2016.01.020 pmid:26825392 pmcid:PMC4828313 fatcat:zsonfddspbezlb4b7ezn7g576q

Adaptation of cells to new environments

Aaron N. Brooks, Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, Nitin S. Baliga
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Such studies provide spectacular insight into the mechanisms of adaptation, including rewiring of regulatory networks via natural selection of horizontal gene transfers, gene duplication, deletion, readjustment  ...  Here, we will discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.  ...  Acknowledgments This work was supported by grants from NIH (P50GM076547 and 1R01GM077398-01A2), DoE (ENIGMA MAGIC: DE-FG02-07ER64327), and NSF (DBI-0640950) to NSB.  ... 
doi:10.1002/wsbm.136 pmid:21197660 pmcid:PMC3081528 fatcat:l7khouleyrctxnicuahxshk67a
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