Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications

No abstract is available for this paper.

• Publication year

  2001

• Venue

  Pacific Symposium on Biocomputing

• Publication date

  2001-12-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1142/9789812799623_0050PMID 11928506
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Comparative Genomics: "Empirical And Analytical Approaches To Gene Order Dynamics, Map Alignment And The Evolution Of Gene Families"

  2000cited by this paper
• Proceedings of the 9th International Symposium on Algorithms and Computation

  1998cited by this paper
• Introduction to algorithms

  1996cited by this paper
• The phylogeny and classification of tetrapods

  1986cited by this paper

• A Probabilistic Algorithm for Gene–Species Reconciliation with Segmental Duplications

  2025cites this paper
• The path-label reconciliation (PLR) dissimilarity measure for gene trees

  2024cites this paper
• Unifying duplication episode clustering and gene-species mapping inference

  2024cites this paper
• Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings

  2023cites this paper
• Phylogenetic reconciliation

  2022cites this paper
• Predicting the Evolution of Syntenies - An Algorithmic Review

  2021cites this paper
• Novel genomic duplication models through integer linear programming

  2021cites this paper
• Minimizing genomic duplication episodes

  2020cites this paper
• Phylogenetic comparison measurements and their application towards the accurate inference of evolutionary histories

  2020cites this paper
• The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost

  2019cites this paper
• Reconciling multiple genes trees via segmental duplications and losses

  2018cites this paper
• Solving the Gene Duplication Feasibility Problem in Linear Time

  2018cites this paper
• Efficient Algorithms for Genomic Duplication Models

  2018influential citation
• Inferring duplication episodes from unrooted gene trees

  2018cites this paper
• Efficient network algorithms for two special cases of the weighted set cover problem

  2018cites this paper
• New Algorithms for the Genomic Duplication Problem

  2017cites this paper
• Genomic duplication problems for unrooted gene trees

  2016cites this paper
• Correcting Gene Trees by Leaf Insertions: Complexity and Approximation

  2016cites this paper
• Correcting gene tree by removal and modification: Tractability and approximability

  2015cites this paper
• Probabilistic Models for Species Tree Inference and Orthology Analysis

  2015cites this paper
• DrML: Probabilistic Modeling of Gene Duplications

  2014cites this paper
• Gene Tree Correction by Leaf Removal and Modification: Tractability and Approximability

  2014cites this paper
• The Inference of Gene Trees with Species Trees

  2013cites this paper
• Impact of Rates of Gene Duplication and Domain Shuffling on Species Tree Inference with Gene Tree Parsimony

  2013cites this paper
• Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony

  2013cites this paper
• Identifying the Phylogenetic Context of Whole-Genome Duplications in Plants

  2012cites this paper
• Large-scale tree parsimony

  2012cites this paper
• Analysis of gene order evolution beyond single-copy genes.

  2012cites this paper
• Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data

  2012cites this paper
• Inferring Optimal Species Trees Under Gene Duplication and Loss

  2012cites this paper
• Minimizing the number of episodes and Gallai's theorem on intervals

  2012cites this paper
• Minimum Leaf Removal for Reconciliation: Complexity and Algorithms

  2012cites this paper
• Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

  2011cites this paper
• Linear-Time Algorithms for the Multiple Gene Duplication Problems

  2011influential citation
• iGTP: A software package for large-scale gene tree parsimony analysis

  2010cites this paper
• Comparative analysis of vertebrate PEPT1 and PEPT2 genes

  2010cites this paper
• Inferring species trees from gene duplication episodes

  2010influential citation
• A scalable parallelization of the gene duplication problem

  2010cites this paper
• Algorithmes pour la réconciliation d’un arbre de gènes avec un arbre d’espèces

  2010cites this paper
• Evolutionary and Paleobiochemical Analyses of Heme Peroxidases

  2010cites this paper
• Dynamic evolution of bitter taste receptor genes in vertebrates

  2009cites this paper
• Algorithms for efficient phylogenetic tree construction

  2009influential citation
• The gene evolution model and computing its associated probabilities

  2009cites this paper
• A hierarchical model for incomplete alignments in phylogenetic inference

  2009cites this paper
• Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants

  2009influential citation
• Tangled Trees: Modelling Material Culture Evolution as Host-Associate Co-Speciation

  2009cites this paper
• Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

  2009cites this paper
• The multiple gene duplication problem revisited

  2008influential citation
• DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

  2008cites this paper
• The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

  2008cites this paper
• Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss

  2008cites this paper
• Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

  2008cites this paper
• The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches

  2008cites this paper
• Locating Multiple Gene Duplications through Reconciled Trees

  2008cites this paper
• Inferring angiosperm phylogeny from EST data with widespread gene duplication

  2007influential citation
• Heuristics for the Gene-duplication Problem : A Θ ( n ) Speed-up for the Local Search

  2007cites this paper
• A genome-scale approach to phylogeny of ray -finned fish (Actinopterygii) and molecular systematics of Clupeiformes

  2007cites this paper
• An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem

  2007cites this paper
• Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search

  2007cites this paper
• A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

  2007cites this paper
• Consensus Trees and Supertrees

  2006cites this paper
• Algorithms for minimum bipartite fill-in and the gene-duplication problem

  2006influential citation
• Exact algorithms and applications for Tree-like Weighted Set Cover

  2006cites this paper
• The shape of human gene family phylogenies

  2006cites this paper
• Algorithm design techniques for parameterized graph modification problems

  2006cites this paper
• Models and Methods in Comparative Genomics

  2006cites this paper
• Analytical methods for detecting paralogy in molecular datasets.

  2005cites this paper
• Reconciling a gene tree to a species tree under the duplication cost model

  2005cites this paper
• Species Identification of Collembola by Means of PCR-based Marker Systems

  2005cites this paper
• Rates and patterns of gene duplication and loss in the human genome

  2005cites this paper
• DRUIDS--detection of regions with unexpected internal deviation from stationarity.

  2005cites this paper
• ‘why polyploidy is rarer in animals than in plants’: myths and mechanisms

  2004cites this paper
• Tree decompositions of graphs: Saving memory in dynamic programming

  2004cites this paper
• Phylogenetic Analysis of Ciona intestinalis Gene Superfamilies Supports the Hypothesis of Successive Gene Expansions

  2004influential citation
• ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms

  2004cites this paper
• Reconciling Gene Trees to a Species Tree

  2003cites this paper
• Vertebrate phylogenomics and gene family evolution.

  2003influential citation
• Gene tree parsimony vs uninode coding for phylogenetic reconstruction.

  2003cites this paper
• Breaking down taxonomic barriers in polyploidy research.

  2003cites this paper
• MOLECULAR PHYLOGENETIC ANALYSES

  2002cites this paper
• Troubleshooting Molecular Phylogenetic Analyses

  2002cites this paper
• Check for Pre-Processing Errors : Alignment , Orthology / Paralogy

  2002cites this paper