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Biological Networks: Comparison, Conservation, and Evolutionary Trees [chapter]

Benny Chor, Tamir Tuller
2006 Lecture Notes in Computer Science  
We describe a new approach for comparing cellular-biological networks, and finding conserved regions in two or more such networks.  ...  We also found conserved regions among more than a dozen metabolic networks, and among two protein interaction networks.  ...  Acknowledgements We would like to thank Nadir Ashkenazi, Nathan Nelson, Eytan Ruppin, Roded Sharan, and Tomer Shlomi for helpful discussions.  ... 
doi:10.1007/11732990_3 fatcat:m4iax2zefvakncrh5jlb35nnwm

Measuring the Evolutionary Rewiring of Biological Networks

Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein, Berend Snel
2011 PLoS Computational Biology  
family trees, co-authorships and linux-kernel function dependencies.  ...  We have accumulated a large amount of biological network data and expect even more to come.  ...  Acknowledgments We thank Chao Cheng, Tara Gianoulis, Kevin Yip, Roger Alexander, and Pedro Alves for helpful discussions. Author Contributions  ... 
doi:10.1371/journal.pcbi.1001050 pmid:21253555 pmcid:PMC3017101 fatcat:dzjmwqrc3nhkhpf7v2eindihde

Modeling cellular machinery through biological network comparison

Roded Sharan, Trey Ideker
2006 Nature Biotechnology  
However, and although sequence comparison has long been a staple of biological research, the development of a similar toolbox for comparing biological networks is still in its infancy.  ...  As with biological sequence analysis, a comparative or evolutionary view provides a powerful base from which to address this challenge.  ...  ., by the David and Lucille Packard Foundation. This work was also supported by the National Center for Research Resources (RR018627) and the National Science Foundation (NSF 0425926).  ... 
doi:10.1038/nbt1196 pmid:16601728 fatcat:4dlkuaeapvcgfjlbaf2rie5jza

Predicting biological networks from genomic data

Eoghan D. Harrington, Lars J. Jensen, Peer Bork
2008 FEBS Letters  
Here, we review the computational methods available to predict biological networks from genomic sequence data and discuss how they relate to highthroughput experimental methods.  ...  The resulting challenge for bioinformatics is to interpret this deluge of data and place it back into its biological context.  ...  Early examples of such genes came from the comparison of bacterial and fungal genomes.  ... 
doi:10.1016/j.febslet.2008.02.033 pmid:18294967 fatcat:wxli4cdigzdj7iggbvlxtfkoya

Biological network analysis and comparison: mining new biological knowledge

Valeria Fionda
2011 Open Computer Science  
Within the plethora of applications devoted to the study of life mechanisms, tools for the analysis and comparison of biological networks are catching the attention of many researchers.  ...  Scientists all over the world are working very hard to clarify the processes regulating the cell life cycle and bioinformaticians try to support them by developing specialized automated tools.  ...  Giuseppe Pirrò for his valuable help and support. Many thanks also to the anonymous Reviewers for their precious comments.  ... 
doi:10.2478/s13537-011-0013-1 fatcat:v4y726hrrbgx5edu2dv3h6dfu4

Detecting Conserved Interaction Patterns in Biological Networks

Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
2006 Journal of Computational Biology  
conservation.  ...  Molecular interaction data plays an important role in understanding biological processes at a modular level by providing a framework for understanding cellular organization, functional hierarchy, and evolutionary  ...  Acknowledgements This research was supported in part by NIH Grant R01 GM068959-01 and NSF Grant CCR-0208709.  ... 
doi:10.1089/cmb.2006.13.1299 pmid:17037960 fatcat:qq3ei4c5qjbark2lyws7xwhvdy

The post-genomic era of biological network alignment

Fazle E Faisal, Lei Meng, Joseph Crawford, Tijana Milenković
2015 EURASIP Journal on Bioinformatics and Systems Biology  
Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species.  ...  Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable  ...  Acknowledgements This work has been supported by the National Science Foundation CAREER CCF-1452795 and CCF-1319469 grants.  ... 
doi:10.1186/s13637-015-0022-9 pmid:28194172 pmcid:PMC5270500 fatcat:3mee3vqx3zew7fslxmuqernft4

Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length

Benny Chor, Tamir Tuller
2007 Journal of Computational Biology  
We describe a new approach for comparing cellular-biological networks and finding conserved regions in two or more such networks.  ...  Our approach enables us to identify conserved regions among more than a dozen metabolic networks, and among two protein interaction networks.  ...  ACKNOWLEDGMENTS We would like to thank Nadir Ashkenazi, Nathan Nelson, Eytan Ruppin, Roded Sharan, and Tomer Shlomi for helpful discussions, and the anonymous referees for helpful comments on an earlier  ... 
doi:10.1089/cmb.2007.r018 pmid:17691896 fatcat:5lr3rlz64fa2th6gjnam7dpona

Challenges and Limitations of Biological Network Analysis

Marianna Milano, Giuseppe Agapito, Mario Cannataro
2022 BioTech  
databases in which they are stored and the alignment algorithms for the comparison of pathways and PPI networks of different organisms.  ...  Otherwise, biological networks such as Protein–Protein Interaction (PPI) Networks, represent the biochemical interactions among proteins by using nodes that model the proteins from a given organism, and  ...  LocalAli [66] is a local many-to-many algorithm that uses an evolutionary model to derive an evolutionary tree of networks nodes.  ... 
doi:10.3390/biotech11030024 pmid:35892929 pmcid:PMC9326688 fatcat:7f5zp3sczzfclbbz6ty3nyremu

PROTEIN INTERACTION NETWORKS [chapter]

Kai Tan, Trey Ideker
2007 Biological Networks  
The high degree of evolutionary conservation of motif constituents within the yeast protein interaction network (Wuchty et al. 2003 ) further indicate that motifs are indeed of direct biological relevance  ...  Network alignment and comparison A major emerging challenge of protein network biology is to systematically compare and contrast biological networks over different species, conditions, cell types, disease  ...  duplicate pair and of all its binding partners.  ... 
doi:10.1142/9789812772367_0005 fatcat:rsmpuyu6cbhd7idpickhsb5pha

Topological network alignment uncovers biological function and phylogeny [article]

Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes, Natasa Przulj
2009 arXiv   pre-print
Comparison and alignment of biological networks will likely have a similar impact.  ...  Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease.  ...  Comparison of the phylogenetic trees for protists obtained by genetic sequence alignments and by GRAAL's metabolic network alignments.  ... 
arXiv:0810.3280v4 fatcat:5vbxpym7g5g2hd47ipj2msgkj4

Integrative approaches for finding modular structure in biological networks

Koyel Mitra, Anne-Ruxandra Carvunis, Sanath Kumar Ramesh, Trey Ideker
2013 Nature reviews genetics  
biological function -that is, 'modules'.  ...  To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms.  ...  Acknowledgements We gratefully acknowledge US National Institutes of Health (NIH) grants P41 GM103504 and P50 GM085764 in support of this work.  ... 
doi:10.1038/nrg3552 pmid:24045689 pmcid:PMC3940161 fatcat:4b5rihmvyzefrm3om7vzanvqc4

Topological network alignment uncovers biological function and phylogeny

O. Kuchaiev, T. Milenkovic, V. Memisevic, W. Hayes, N. Przulj
2010 Journal of the Royal Society Interface  
Comparison and alignment of biological networks will likely have a similar impact.  ...  Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease.  ...  Left: The tree obtained from genetic sequence comparison. 57 Right: The tree obtained from GRAAL.  ... 
doi:10.1098/rsif.2010.0063 pmid:20236959 pmcid:PMC2894889 fatcat:3ontqvhmuncs3izvqcsov7nmx4

Topological network alignment uncovers biological function and phylogeny

Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes, Natasa Przulj
2009 Nature Precedings  
Comparison and alignment of biological networks will likely have a similar impact.  ...  Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease.  ...  Left: The tree obtained from genetic sequence comparison. 57 Right: The tree obtained from GRAAL.  ... 
doi:10.1038/npre.2009.4089.1 fatcat:a5yvanijpzd4zpooquisfdm7g4

A Novel Framework for the Comparative Analysis of Biological Networks

Roland A. Pache, Patrick Aloy, Philip M. Kim
2012 PLoS ONE  
Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast  ...  Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology.  ...  We are also thankful to Mike Smoot (UCSD) and Maxim Kalaev (Tel Aviv University) for NetworkBLAST support. Author Contributions Conceived and designed the experiments: RAP PA.  ... 
doi:10.1371/journal.pone.0031220 pmid:22363585 pmcid:PMC3283617 fatcat:uetdanizujf2pnog5gd237b3am
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