Search results for "Phylogenies"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
76	Alberto Apostolico, Andreas W. M. Dress, Laxmi Parida	10231 Abstracts Collection - Structure Discovery in Biology: Motifs, Networks & Phylogenies.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
59	Chris Whidden, Norbert Zeh	A Unifying View on Approximation and FPT of Agreement Forests.	WABI	2009	DBLP DOI BibTeX RDF
55	Alberto Apostolico, Andreas W. M. Dress, Laxmi Parida (eds.)	Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06. - 11.06.2010	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky	Estimation of alternative splicing isoform frequencies from RNA-Seq data.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Andreas W. M. Dress, Wim Hordijk, Lin Wei, Peter Serocka	The Ideal Storage Cellular Automaton Model.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Cinzia Pizzi	Efficient computation of statistics for words with mismatches.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Matteo Comin, Davide Verzotto	Remote Homology Detection of Protein Sequences.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, Filippo Utro	Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Anne Bergeron, Julia Mixtacki, Jens Stoye	A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
55	Matthias Gallé	A New Tree Distance Metric for Structural Comparison of Sequences.	Structure Discovery in Biology: Motifs, Networks & Phylogenies	2010	DBLP BibTeX RDF
50	Elchanan Mossel, Sébastien Roch	Learning nonsingular phylogenies and hidden Markov models.	STOC	2005	DBLP DOI BibTeX RDF	hidden Markov models, PAC learning, evolutionary trees, phylogenetic reconstruction
44	Daniel R. Brooks, Esra Erdem 0001, Selim T. Erdogan, James W. Minett, Donald Ringe	Inferring Phylogenetic Trees Using Answer Set Programming.	J. Autom. Reason.	2007	DBLP DOI BibTeX RDF	Cladistics, Answer set programming, Phylogeny
44	Daniel R. Brooks, Esra Erdem 0001, James W. Minett, Donald Ringe	Character-Based Cladistics and Answer Set Programming.	PADL	2005	DBLP DOI BibTeX RDF
44	Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue	Requirements of Phylogenetic Databases.	BIBE	2003	DBLP DOI BibTeX RDF
44	Wing-Kai Hon, Ming-Yang Kao, Tak Wah Lam	Improved Phylogeny Comparisons: Non-shared Edges, Nearest Neighbor Interchanges, and Subtree Transfers.	ISAAC	2000	DBLP DOI BibTeX RDF
44	Bhaskar DasGupta, Xin He, Tao Jiang 0001, Ming Li 0001, John Tromp	On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees.	Algorithmica	1999	DBLP DOI BibTeX RDF	Approximation algorithms, Lower bounds, Evolutionary trees
42	Vincent Ranwez	Méthodes efficaces pour reconstruire de grandes phylogénies suivant le principe du maximum de vraisemblance. (Efficient methods for reconstructing large phylogenies according to the maximum likelihood principle).		2002	RDF
36	Max H. Garzon, Tit-Yee Wong, Vinhthuy T. Phan	DNA Chips for Species Identification and Biological Phylogenies.	DNA	2009	DBLP DOI BibTeX RDF	DNA codeword design, noncrosshybridizing oligonucleotide bases, genomic signatures, DNA chips, 16S rRNA tree of life, phylogenetic analysis
36	Xiaoxu Han	Inferring Species Phylogenies: A Microarray Approach.	ICIC (3)	2006	DBLP DOI BibTeX RDF
31	Thomas Eiter, Esra Erdem 0001, Halit Erdogan, Michael Fink 0001	Finding Similar or Diverse Solutions in Answer Set Programming.	ICLP	2009	DBLP DOI BibTeX RDF	similar/diverse solutions, answer set programming, phylogenies
31	Zhi-Zhong Chen	Approximation Algorithms for Bounded Degree Phylogenetic Roots.	Algorithmica	2008	DBLP DOI BibTeX RDF	Phylogenetic roots, Approximation algorithms, Randomized algorithms, Graph algorithms, Computational biology, Phylogenies
31	Michael Elberfeld, Till Tantau	Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems.	MFCS	2008	DBLP DOI BibTeX RDF	circuit classes, computational complexity, bioinformatics, haplotyping, perfect phylogenies
30	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller	Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic.	IEEE ACM Trans. Comput. Biol. Bioinform.	2009	DBLP DOI BibTeX RDF	hardness and approximation, phylogenetic networks, Maximum parsimony, horizontal gene transfer
30	Travis J. Wheeler	Large-Scale Neighbor-Joining with NINJA.	WABI	2009	DBLP DOI BibTeX RDF	Phylogeny inference, external memory, Neighbor joining
30	Mariana Kant, Maurice LeBon, David Sankoff	Hierarchical Clustering Using Constraints.	ISBRA	2008	DBLP DOI BibTeX RDF
30	Daniel B. Goodman, Noah Ollikainen, Chris Sholley	Baculovirus Phylogeny Based on Genome Rearrangements.	RECOMB-CG	2007	DBLP DOI BibTeX RDF
30	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller	A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance.	ISBRA	2007	DBLP DOI BibTeX RDF
30	Md. Enamul Karim, Laxmi Parida, Arun Lakhotia	Using Permutation Patterns for Content-Based Phylogeny.	PRIB	2006	DBLP DOI BibTeX RDF
30	Guy E. Blelloch, Kedar Dhamdhere, Eran Halperin, R. Ravi 0001, Russell Schwartz, Srinath Sridhar 0001	Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction.	ICALP (1)	2006	DBLP DOI BibTeX RDF
30	Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey	Reconstructing Phylogenetic Networks Using Maximum Parsimony.	CSB	2005	DBLP DOI BibTeX RDF	phylogenetic networks, maximum parsimony, horizontal gene transfer
30	Dennis E. Shasha, Jason Tsong-Li Wang, Sen Zhang	Unordered Tree Mining with Applications to Phylogeny.	ICDE	2004	DBLP DOI BibTeX RDF
30	Jens Gramm, Till Nierhoff, Till Tantau	Perfect Path Phylogeny Haplotyping with Missing Data Is Fixed-Parameter Tractable.	IWPEC	2004	DBLP DOI BibTeX RDF
21	Ondrej Draganov, Steven Skiena	The Shape of Word Embeddings: Recognizing Language Phylogenies through Topological Data Analysis.	CoRR	2024	DBLP DOI BibTeX RDF
21	Wend Yam Donald Davy Ouedraogo, Aïda Ouangraoua	Inferring Transcript Phylogenies from Transcript Ortholog Clusters.	RECOMB-CG	2024	DBLP DOI BibTeX RDF
21	Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar 0001	Molecular timetrees using relaxed clocks and uncertain phylogenies.	Frontiers Bioinform.	2023	DBLP DOI BibTeX RDF
21	Alexander Kramer, Theo Sanderson, Russell Corbett-Detig	Treenome Browser: co-visualization of enormous phylogenies and millions of genomes.	Bioinform.	2023	DBLP DOI BibTeX RDF
21	E. Kulman, R. Kuang, Q. Morris	Orchard: building large cancer phylogenies using stochastic combinatorial search.	CoRR	2023	DBLP DOI BibTeX RDF
21	Rei Doko, Kevin Liu	Reconstructing Phylogenies Using Branch-Variable Substitution Models and Unaligned Biomolecular Sequences: A Performance Study and New Resampling Method.	BCB	2023	DBLP DOI BibTeX RDF
21	Ilya Plyusnin, Phuoc Thien Truong Nguyen, Tarja Sironen, Olli Vapalahti, Teemu Smura, Ravi Kant	ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
21	Diego Fuentes, Manuel Molina, Uciel Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón	PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.	Nucleic Acids Res.	2022	DBLP DOI BibTeX RDF
21	Stefano Pascarelli, Paola Laurino	Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.	PLoS Comput. Biol.	2022	DBLP DOI BibTeX RDF
21	Mattia Prosperi, Brittany Rife Magalis, Simone Marini, Marco Salemi	Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.	BIBM	2022	DBLP DOI BibTeX RDF
21	Sudip Sharma, Sudhir Kumar 0001	Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps.	Nat. Comput. Sci.	2021	DBLP DOI BibTeX RDF
21	Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar 0001	Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies.	Bioinform.	2021	DBLP DOI BibTeX RDF
21	Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza	VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.	Patterns	2021	DBLP DOI BibTeX RDF
21	Gabriel Nakamura, Aline Richter, Bruno E. Soares	FishPhyloMaker: An R package to generate phylogenies for ray-finned fishes.	Ecol. Informatics	2021	DBLP DOI BibTeX RDF
21	Shijia Wang, Shufei Ge, Caroline Colijn, Priscila Biller, Liangliang Wang, Lloyd T. Elliott	Estimating Genetic Similarity Matrices Using Phylogenies.	J. Comput. Biol.	2021	DBLP DOI BibTeX RDF
21	César Piñeiro, José Manuel Abuín, Juan Carlos Pichel	Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.	Bioinform.	2020	DBLP DOI BibTeX RDF
21	Uyen Mai, Siavash Mirarab	Log Transformation Improves Dating of Phylogenies.	RECOMB	2020	DBLP DOI BibTeX RDF
21	Simone Linz, Charles Semple	Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies.	Adv. Appl. Math.	2019	DBLP DOI BibTeX RDF
21	Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez	Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach.	IEEE ACM Trans. Comput. Biol. Bioinform.	2019	DBLP DOI BibTeX RDF
21	Charith B. Karunarathna, Jinko Graham	perfectphyloR: An R package for reconstructing perfect phylogenies.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
21	Fei Xiang, Bethany L. Dearlove, Simon D. W. Frost	genieR: An R package for inference of demographic history of phylogenies.	J. Open Source Softw.	2019	DBLP DOI BibTeX RDF
21	Rui Borges, João Paulo Machado, Cidália Gomes, Ana Paula Rocha 0002, Agostinho Antunes	Measuring phylogenetic signal between categorical traits and phylogenies.	Bioinform.	2019	DBLP DOI BibTeX RDF
21	Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu	MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP.	Bioinform.	2019	DBLP DOI BibTeX RDF
21	Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn	Phylogenies from dynamic networks.	PLoS Comput. Biol.	2019	DBLP DOI BibTeX RDF
21	Jucheol Moon, Oliver Eulenstein	The Cluster Affinity Distance for Phylogenies.	ISBRA	2019	DBLP DOI BibTeX RDF
21	Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma 0004, Russell Schwartz	Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases.	ISMCO	2019	DBLP DOI BibTeX RDF
21	Ademir Hujdurovic, Edin Husic, Martin Milanic, Romeo Rizzi, Alexandru I. Tomescu	Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth's Theorem.	ACM Trans. Algorithms	2018	DBLP DOI BibTeX RDF
21	Jiafan Zhu, Luay Nakhleh	Inference of species phylogenies from bi-allelic markers using pseudo-likelihood.	Bioinform.	2018	DBLP DOI BibTeX RDF
21	Taraka Rama, Søren Wichmann	Towards identifying the optimal datasize for lexically-based Bayesian inference of linguistic phylogenies.	COLING	2018	DBLP BibTeX RDF
21	Yun Deng, David Fernández-Baca	An efficient algorithm for testing the compatibility of phylogenies with nested taxa.	Algorithms Mol. Biol.	2017	DBLP DOI BibTeX RDF
21	Duo Xu, Yousef Jaber, Pavlos Pavlidis, Omer Gokcumen	VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.	BMC Bioinform.	2017	DBLP DOI BibTeX RDF
21	Emily Jane McTavish, James B. Pettengill, Steve Davis 0002, Hugh Rand, Errol Strain, Marc Allard, Ruth E. Timme	TreeToReads - a pipeline for simulating raw reads from phylogenies.	BMC Bioinform.	2017	DBLP DOI BibTeX RDF
21	Pieter Libin, Ewout Vanden Eynden, Francesca Incardona, Ann Nowé, Antonia Bezenchek, EucoHIV Study Group, Anders Sönnerborg, Anne-Mieke Vandamme, Kristof Theys, Guy Baele	PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context.	Bioinform.	2017	DBLP DOI BibTeX RDF
21	Sebastien Roch, Kun-Chieh Wang	Critical threshold for ancestral reconstruction by maximum parsimony on general phylogenies.	CoRR	2017	DBLP BibTeX RDF
21	Simone Linz, Charles Semple	Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies.	CoRR	2017	DBLP BibTeX RDF
21	Reem Alsrraj, Bassam AlKindy, Christophe Guyeux, Laurent Philippe 0001, Jean-François Couchot	Well-supported phylogenies using largest subsets of core-genes by discrete particle swarm optimization.	CoRR	2017	DBLP BibTeX RDF
21	Esaie Kuitche, Manuel Lafond, Aïda Ouangraoua	Reconstructing protein and gene phylogenies using reconciliation and soft-clustering.	J. Bioinform. Comput. Biol.	2017	DBLP DOI BibTeX RDF
21	Emma Saulnier, Olivier Gascuel, Samuel Alizon	Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study.	PLoS Comput. Biol.	2017	DBLP DOI BibTeX RDF
21	Pasan C. Fernando, Laura M. Jackson, Erliang Zeng, Paula M. Mabee, James P. Balhoff	A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies.	BIBM	2017	DBLP DOI BibTeX RDF
21	Po-Shen Lee, Sean T. Yang, Jevin D. West, Bill Howe	PhyloParser: A Hybrid Algorithm for Extracting Phylogenies from Dendrograms.	ICDAR	2017	DBLP DOI BibTeX RDF
21	Simon Dellicour, Rebecca Rose, Oliver G. Pybus	Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
21	Yun Deng, David Fernández-Baca	Fast Compatibility Testing for Phylogenies with Nested Taxa.	CoRR	2016	DBLP BibTeX RDF
21	Esaie Kuitche, Aïda Ouangraoua	Reconstructing protein and gene phylogenies by extending the framework of reconciliation.	CoRR	2016	DBLP BibTeX RDF
21	Eben Kenah, Tom Britton, M. Elizabeth Halloran, Ira M. Longini Jr.	Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.	PLoS Comput. Biol.	2016	DBLP DOI BibTeX RDF
21	Yun Deng, David Fernández-Baca	Fast Compatibility Testing for Phylogenies with Nested Taxa.	WABI	2016	DBLP DOI BibTeX RDF
21	Magali Semeria, Eric Tannier, Laurent Guéguen	Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
21	Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti	Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
21	Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez	Parallel Multiobjective Metaheuristicsfor Inferring Phylogenies on Multicore Clusters.	IEEE Trans. Parallel Distributed Syst.	2015	DBLP DOI BibTeX RDF
21	Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu	SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.	Bioinform.	2015	DBLP DOI BibTeX RDF
21	Samuel K. Handelman, Jacob M. Aaronson, Michal Seweryn, Igor Voronkin, Jesse J. Kwiek, Wolfgang Sadee, Joseph S. Verducci, Daniel A. Janies	Cladograms with Path to Event (ClaPTE): A novel algorithm to detect associations between genotypes or phenotypes using phylogenies.	Comput. Biol. Medicine	2015	DBLP DOI BibTeX RDF
21	Bethany L. Dearlove, Simon D. W. Frost	Measuring Asymmetry in Time-Stamped Phylogenies.	PLoS Comput. Biol.	2015	DBLP DOI BibTeX RDF
21	Ashok Rajaraman, Cédric Chauve, Yann Ponty	Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material.	ISBRA	2015	DBLP DOI BibTeX RDF
21	Michael J. Coulombe, Kristian Stevens, Dan Gusfield	Construction, enumeration, and optimization of perfect phylogenies on multi-state data.	ICCABS	2015	DBLP DOI BibTeX RDF
21	Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk, Markus Göker	Highly parallelized inference of large genome-based phylogenies.	Concurr. Comput. Pract. Exp.	2014	DBLP DOI BibTeX RDF
21	Michael J. Sanderson	Ceiba: scalable visualization of phylogenies and 2D/3D image collections.	Bioinform.	2014	DBLP DOI BibTeX RDF
21	Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis	PUmPER: phylogenies updated perpetually.	Bioinform.	2014	DBLP DOI BibTeX RDF
21	Alexandros Stamatakis	RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.	Bioinform.	2014	DBLP DOI BibTeX RDF
21	Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler	Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models.	PLoS Comput. Biol.	2014	DBLP DOI BibTeX RDF
21	Ayshwarya Subramanian, Russell Schwartz	Reference-free inference of tumor phylogenies from single-cell sequencing data.	ICCABS	2014	DBLP DOI BibTeX RDF
21	Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti	Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach.	BSB	2014	DBLP DOI BibTeX RDF
21	Fernando Izquierdo-Carrasco	Inference of Many-Taxon Phylogenies.		2014	RDF
21	Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz	A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion.	Algorithms Mol. Biol.	2013	DBLP DOI BibTeX RDF
21	Sebastian Höhna	Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes.	Bioinform.	2013	DBLP DOI BibTeX RDF
21	Peter J. Humphries, Simone Linz, Charles Semple	On the complexity of computing the temporal hybridization number for two phylogenies.	Discret. Appl. Math.	2013	DBLP DOI BibTeX RDF
21	Stephen A. Smith, Joseph W. Brown, Cody E. Hinchliff	Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs.	PLoS Comput. Biol.	2013	DBLP DOI BibTeX RDF
21	Katy Robinson, Nick Fyson, Ted Cohen, Christophe Fraser, Caroline Colijn	How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies.	PLoS Comput. Biol.	2013	DBLP DOI BibTeX RDF
21	Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou	Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery.	J. Comput. Biol.	2013	DBLP DOI BibTeX RDF
21	Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou	Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery.	RECOMB	2013	DBLP DOI BibTeX RDF