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Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2012 Computer applications in the biosciences : CABIOS  
postulating speciation, gene duplication, horizontal gene transfer and gene loss events.  ...  This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature.  ...  ACKNOWLEDGEMENTS The authors thank Ali Tofigh for help with the tree simulation software, Lawrence David for providing the biological dataset, and Matt Rasmussen for helpful discussions.  ... 
doi:10.1093/bioinformatics/bts225 pmid:22689773 pmcid:PMC3371857 fatcat:ylxvi7ghoja2vjmewkhi7m2iza

Reconciliation problems for duplication, loss and horizontal gene transfer

Pawel Górecki
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
In the second the horizontal transfer is defined and a new polynomial reconciliation algorithm is presented.  ...  This paper presents a model of reconciling a species tree and a gene tree in an extended duplication-loss model. In the first part the definition of a model is introduced.  ...  We present an efficient polynomial time and space algorithm for reconciling gene and species trees under the assumption of a set of horizontal transfer hypothesis.  ... 
doi:10.1145/974614.974656 dblp:conf/recomb/Gorecki04 fatcat:zxlnionmp5eetjcyj5vx24yr5y

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation [article]

Misagh Kordi, Soumya Kundu, Mukul S. Bansal
2020 bioRxiv   pre-print
Specifically, we (1) introduce the DTRL reconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying  ...  Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation.  ...  Acknowledgements: The authors thank Abhijit Mondal for pointing out an error in an initial implementation of the heuristic.  ... 
doi:10.1101/2020.03.27.010785 fatcat:xpvtnhed2jdw7osnpobeufoiom

Improved gene tree error correction in the presence of horizontal gene transfer

Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis
2015 Computer applications in the biosciences : CABIOS  
Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira-Hasegawa (SH) test] to balance sequence likelihood  ...  Results: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer.  ...  , horizontal gene transfer (or simply transfer for short) and incomplete lineage sorting (ILS).  ... 
doi:10.1093/bioinformatics/btu806 pmid:25481006 pmcid:PMC4393519 fatcat:ur3e6f7vdnf6ldnmi3dnspg6ji

Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss [chapter]

Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2013 Lecture Notes in Computer Science  
Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular  ...  Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation.  ...  ., and National Science Foundation AToL grant 0936234 to E.J.A. and M.K.  ... 
doi:10.1007/978-3-642-37195-0_1 fatcat:554wa6v5cvhrrizhkkrr5urdii

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2013 Journal of Computational Biology  
Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular  ...  Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation.  ...  ., and National Science Foundation AToL grant 0936234 to E.J.A. and M.K.  ... 
doi:10.1089/cmb.2013.0073 pmid:24033262 pmcid:PMC3791060 fatcat:o77cbppk5jdufnzjlxqzgmishi

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1

Edwin Jacox, Cedric Chauve, Gergely J. Szöllősi, Yann Ponty, Celine Scornavacca
2016 Bioinformatics  
We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled  ...  The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees.  ...  We thank Jean-Francois Dufayard for providing the species tree for the HOG dataset. C.S. and E.J. benefited from the Montpellier Bioinformatics Biodiversity cluster computing platform.  ... 
doi:10.1093/bioinformatics/btw105 pmid:27153713 fatcat:2cpgorlqynhohner54q5j4e6lu

Reconciliation of Gene and Species Trees

L. Y. Rusin, E. V. Lyubetskaya, K. Y. Gorbunov, V. A. Lyubetsky
2014 BioMed Research International  
The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario.  ...  trees reconciliation into a single species tree when only gene duplications and losses are allowed.  ...  Acknowledgments The subsection "Coalescent approaches" in Section 1.7 is written together with S. A. Pirogov, whose help was precious.  ... 
doi:10.1155/2014/642089 pmid:24800245 pmcid:PMC3985182 fatcat:wsqo7d3pmbdkjnjxoymrk6w3x4

Predicting the Evolution of Syntenies—An Algorithmic Review

Nadia El-Mabrouk
2021 Algorithms  
However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another.  ...  Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization  ...  Accounting for Horizontal Gene Transfers Horizontal gene transfer, largely involved in shaping bacterial gene content, has been included later in the reconciliation analysis of gene families in the purpose  ... 
doi:10.3390/a14050152 fatcat:cqnfgv3st5a3dipcje7dcnk6wm

Models, algorithms and programs for phylogeny reconciliation

J.-P. Doyon, V. Ranwez, V. Daubin, V. Berry
2011 Briefings in Bioinformatics  
Among them, gene duplication, transfer and loss are especially important to identify and differentiate from speciation events.  ...  Existing models and algorithms of reconciliations are reviewed, and difficulties to model gene transfer are discussed.  ...  Acknowledgments This work was supported by the French Agence Nationale de la Recherche "Domaines Emergents" [ANR-08-EMER-011, "PhylAriane"] and by the Languedoc-Roussillon's "Chercheur d'Avenir" program  ... 
doi:10.1093/bib/bbr045 pmid:21949266 fatcat:p4227fxvjrdbfflum4gxz5e5bu

Maximum parsimony reconciliation in the DTLOR model

Jingyi Liu, Ross Mawhorter, Nuo Liu, Santi Santichaivekin, Eliot Bush, Ran Libeskind-Hadas
2021 BMC Bioinformatics  
However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family  ...  We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree  ...  Acknowledgements The authors thank Yi-Chieh Wu for valuable discussions and the anonymous reviewers for their comments and suggestions.  ... 
doi:10.1186/s12859-021-04290-6 fatcat:qg67s362qza3dc6h6srxbfbrca

A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation

Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
2020 Journal of Computational Biology  
An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss, and mobilization patterns of the gene within the  ...  The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given gene tree and species tree, and then interrogates this hypergraph for subtrees  ...  adaptation to animal and human host environment.  ... 
doi:10.1089/cmb.2019.0472 pmid:32250165 fatcat:xwj74bwdavbdnejnyg7r7mnapu

A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation [article]

Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
2019 arXiv   pre-print
An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the  ...  The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees  ...  Three major evolutionary processes, traditionally considered by reconciliation approaches, are horizontal gene transfer, gene duplication, and gene loss (Tofigh et al. (2011) ).  ... 
arXiv:1912.01934v1 fatcat:zq5vdk5z6nbfjabzizw6c6pwku

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees

Misagh Kordi, Mukul S. Bansal
2016 Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16  
Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer.  ...  DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events.  ...  BCB '16, October 2-5, 2016 primarily through gene duplication, gene loss, and horizontal gene transfer, and DTL reconciliation can infer these evolutionary events through the systematic comparison and  ... 
doi:10.1145/2975167.2975198 dblp:conf/bcb/KordiB16 fatcat:fw37clrj3jej7c2kjfetlblbcy

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees

Misagh Kordi, Mukul S. Bansal
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer.  ...  DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events.  ...  BCB '16, October 2-5, 2016 primarily through gene duplication, gene loss, and horizontal gene transfer, and DTL reconciliation can infer these evolutionary events through the systematic comparison and  ... 
doi:10.1109/tcbb.2017.2710342 pmid:28622673 fatcat:v5kodz6t2bc2hplmyfycewxg4u
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