Search results for "phylogeny"

Hits ?▲	Authors	Title	Venue	Year	Link
16	Chao Zhou, Hongyu Zhao 0003, Tao Wang 0067	Transformation and differential abundance analysis of microbiome data incorporating phylogeny.	Bioinform.	2021	DBLP DOI BibTeX RDF
16	Maya Gupta, Paul Zaharias, Tandy J. Warnow	Accurate large-scale phylogeny-aware alignment using BAli-Phy.	Bioinform.	2021	DBLP DOI BibTeX RDF
16	Benjamin D. Redelings	Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny.	Bioinform.	2021	DBLP DOI BibTeX RDF
16	Benjamin D. Redelings	Bali-Phy version 3: model-based co-estimation of alignment and phylogeny.	Bioinform.	2021	DBLP DOI BibTeX RDF
16	Miklós Csürös	Gain-loss-duplication models on a phylogeny: exact algorithms for computing the likelihood and its gradient.	CoRR	2021	DBLP BibTeX RDF
16	Muhammad Anaz K, Sasidharan N., Remakanthan A., Dilsha M. V.	ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp.	Comput. Biol. Chem.	2021	DBLP DOI BibTeX RDF
16	Qiaoji Xu, Xiaomeng Zhang, Yue Zhang, Chunfang Zheng, James H. Leebens-Mack, Lingling Jin, David Sankoff	The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny.	J. Bioinform. Comput. Biol.	2021	DBLP DOI BibTeX RDF
16	Soogang Eoh, Suh-Ryung Kim	On chordal phylogeny graphs.	Discret. Appl. Math.	2021	DBLP DOI BibTeX RDF
16	Thomas K. F. Wong, Teng Li, Louis Ranjard, Steven H. Wu, Jeet Sukumaran, Allen G. Rodrigo	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
16	Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky	Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations.	J. Comput. Biol.	2021	DBLP DOI BibTeX RDF
16	Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson	Simpler and Faster Development of Tumor Phylogeny Pipelines.	J. Comput. Biol.	2021	DBLP DOI BibTeX RDF
16	Giulia Bernardini 0001, Paola Bonizzoni, Pawel Gawrychowski	Incomplete Directed Perfect Phylogeny in Linear Time.	WADS	2021	DBLP DOI BibTeX RDF
16	Vladimir Smirnov	Large-scale methods for multiple sequence alignment and phylogeny estimation		2021	RDF
16	Changchuan Yin, Stephen S.-T. Yau	Whole-genome phylogeny of giant viruses by Fourier transform.	Commun. Inf. Syst.	2020	DBLP DOI BibTeX RDF
16	Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan, Srinivas Aluru	An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.	BMC Bioinform.	2020	DBLP DOI BibTeX RDF
16	Uciel Chorostecki, Manuel Molina, Leszek P. Pryszcz, Toni Gabaldón	MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.	Nucleic Acids Res.	2020	DBLP DOI BibTeX RDF
16	Camir Ricketts, Daniel Seidman, Victoria Popic, Fereydoun Hormozdiari, Serafim Batzoglou, Iman Hajirasouliha	Meltos: multi-sample tumor phylogeny reconstruction for structural variants.	Bioinform.	2020	DBLP DOI BibTeX RDF
16	Yufeng Wu	Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach.	Bioinform.	2020	DBLP DOI BibTeX RDF
16	Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikic, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, E. Michael Gertz, Chi-Ping Day, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergün, Süleyman Cenk Sahinalp	PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem.	Bioinform.	2020	DBLP DOI BibTeX RDF
16	Kevin McDonnell, Nicholas Waters, Enda Howley, Florence Abram	Chordomics: a visualization tool for linking function to phylogeny in microbiomes.	Bioinform.	2020	DBLP DOI BibTeX RDF
16	Patrick H. Bradley, Katherine S. Pollard	phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.	Bioinform.	2020	DBLP DOI BibTeX RDF
16	Sudipta Banerjee, Arun Ross	Face Phylogeny Tree Using Basis Functions.	CoRR	2020	DBLP BibTeX RDF
16	Wai-Tong Louis Fan, Brandon Legried, Sebastien Roch	Impossibility of phylogeny reconstruction from k-mer counts.	CoRR	2020	DBLP BibTeX RDF
16	Giulia Bernardini 0001, Paola Bonizzoni, Pawel Gawrychowski	Incomplete Directed Perfect Phylogeny in Linear Time.	CoRR	2020	DBLP BibTeX RDF
16	Sudipta Banerjee, Arun Ross	Face Phylogeny Tree Using Basis Functions.	IEEE Trans. Biom. Behav. Identity Sci.	2020	DBLP DOI BibTeX RDF
16	Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter	Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases.	PLoS Comput. Biol.	2020	DBLP DOI BibTeX RDF
16	Zhi-Zhong Chen, Shohei Ueta, Jingyu Li, Lusheng Wang 0001	Computing a Consensus Phylogeny via Leaf Removal.	J. Comput. Biol.	2020	DBLP DOI BibTeX RDF
16	Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael	Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses.	RECOMB	2020	DBLP DOI BibTeX RDF
16	Lamis Sharawy, Maha Tantawy, Yara Ahmed, Ahmed Taha, Omar Soliman, Tamer M. Ibrahim, Mohamed El-Hadidi	In-Silico Comparative Analysis of Egyptian SARS CoV-2 with Other Populations: a Phylogeny and Mutation Analysis.	NILES	2020	DBLP DOI BibTeX RDF
16	Pavlos Malakonakis, Andreas Brokalakis, Nikolaos Alachiotis 0001, Euripides Sotiriades, Apostolos Dollas	Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML.	BIBE	2020	DBLP DOI BibTeX RDF
16	Michael Zhou, Yongsheng Bai	Bioinf-PHP: Bioinformatics Pipeline for Protein Homology and Phylogeny.	CLOUD	2020	DBLP DOI BibTeX RDF
16	Pasquale Ardimento, Mario Luca Bernardi, Marta Cimitile	Malware Phylogeny Analysis using Data-Aware Declarative Process Mining.	EAIS	2020	DBLP DOI BibTeX RDF
16	Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal	TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity.	ISBRA	2020	DBLP DOI BibTeX RDF
16	Leah L. Weber, Mohammed El-Kebir	Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors.	WABI	2020	DBLP DOI BibTeX RDF
16	Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow	Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees.	WABI	2020	DBLP DOI BibTeX RDF
16	Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi	Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection.	ISMCO	2020	DBLP DOI BibTeX RDF
16	Phanucheep Chotnithi	Efficient Similarity Measures in NGS Genome Data Comparison for Phylogeny Reconstruction.		2020	RDF
16	Gryte Satas	Tumor Phylogeny Reconstruction from DNA Sequencing Data.		2020	RDF
16	Mario Luca Bernardi, Marta Cimitile, Damiano Distante, Fabio Martinelli, Francesco Mercaldo	Dynamic malware detection and phylogeny analysis using process mining.	Int. J. Inf. Sec.	2019	DBLP DOI BibTeX RDF
16	Phanucheep Chotnithi, Hong Van Le, Atsuhiro Takasu	An Effective Parameter-free Comparison of NGS Short Reads for Phylogeny Reconstruction.	J. Inf. Process.	2019	DBLP DOI BibTeX RDF
16	Erin K. Molloy, Tandy J. Warnow	Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge.	Algorithms Mol. Biol.	2019	DBLP DOI BibTeX RDF
16	Qiuyi Zhang 0001, Satish Rao, Tandy J. Warnow	Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy.	Algorithms Mol. Biol.	2019	DBLP DOI BibTeX RDF
16	Nan Zhu, Junge Shen	Image phylogeny tree construction based on local inheritance relationship correction.	Multim. Tools Appl.	2019	DBLP DOI BibTeX RDF
16	Hosein Toosi, Ali Moeini, Iman Hajirasouliha	BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
16	Emanuel Maldonado, Agostinho Antunes	LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
16	Carlos J. Rivera-Rivera, Juan I. Montoya-Burgos	LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
16	Nikola Jovanovic 0002, Alexander S. Mikheyev	Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO.	Nucleic Acids Res.	2019	DBLP DOI BibTeX RDF
16	Yaokun Wu, Yanzhen Xiong, Soesoe Zaw	Competition Numbers and Phylogeny Numbers: Uniform Complete Multipartite Graphs.	Graphs Comb.	2019	DBLP DOI BibTeX RDF
16	He-Chuan Yang, Bingxin Lu, Lan Huong Lai, Abner Herbert Lim, Jacob Josiah Santiago Alvarez, Weiwei Zhai	PSiTE: a Phylogeny guided Simulator for Tumor Evolution.	Bioinform.	2019	DBLP DOI BibTeX RDF
16	Nuraini Aguse, Yuanyuan Qi, Mohammed El-Kebir	Summarizing the solution space in tumor phylogeny inference by multiple consensus trees.	Bioinform.	2019	DBLP DOI BibTeX RDF
16	Surjyendu Ray, Bei Jia, Sam Safavi, Tim van Opijnen, Ralph Isberg, Jason Rosch, José Bento 0001	Exact inference under the perfect phylogeny model.	CoRR	2019	DBLP BibTeX RDF
16	Chad Clark, Attila Egri-Nagy, Andrew R. Francis, Volker Gebhardt	Bacterial phylogeny in the Cayley graph.	Discret. Math. Algorithms Appl.	2019	DBLP DOI BibTeX RDF
16	David Fernández-Baca, Lei Liu	Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study.	Algorithms	2019	DBLP DOI BibTeX RDF
16	Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow	Using INC Within Divide-and-Conquer Phylogeny Estimation.	AlCoB	2019	DBLP DOI BibTeX RDF
16	Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Atif Hasan Rahman 0001, Rifat Shahriyar, M. Sohel Rahman	A 'phylogeny-aware' multi-objective optimization approach for computing MSA.	GECCO	2019	DBLP DOI BibTeX RDF
16	Zhi-Zhong Chen, Shohei Ueta, Jingyu Li, Lusheng Wang 0001	Computing a Consensus Phylogeny via Leaf Removal.	ISBRA	2019	DBLP DOI BibTeX RDF
16	Jyotsna Talreja Wassan, Huiru Zheng, Haiying Wang 0001, Fiona Browne, Paul Walsh, Timmy Manning, Richard J. Dewhurst, Rainer Roehe	A Phylogeny-aware Feature Ranking for Classification of Cattle Rumen Microbiome.	BIBM	2019	DBLP DOI BibTeX RDF
16	Stéphane Chrétien, Christophe Guyeux	Efficient Online Laplacian Eigenmap Computation for Dimensionality Reduction in Molecular Phylogeny via Optimisation on the Sphere.	IWBBIO (1)	2019	DBLP DOI BibTeX RDF
16	Sudipta Banerjee, Arun Ross	Face Phylogeny Tree: Deducing Relationships Between Near-Duplicate Face Images Using Legendre Polynomials and Radial Basis Functions.	BTAS	2019	DBLP DOI BibTeX RDF
16	Bingyu Shen 0001, Christopher W. Forstall, Anderson de Rezende Rocha, Walter J. Scheirer	Practical Text Phylogeny for Real-World Settings.	IEEE Access	2018	DBLP DOI BibTeX RDF
16	Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu	Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples.	IEEE ACM Trans. Comput. Biol. Bioinform.	2018	DBLP DOI BibTeX RDF
16	Mohammed El-Kebir	SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.	Bioinform.	2018	DBLP DOI BibTeX RDF
16	Christopher Monit, Richard A. Goldstein	SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny.	Bioinform.	2018	DBLP DOI BibTeX RDF
16	Eugene Urrutia, Hao Chen 0064, Zilu Zhou, Nancy Ruonan Zhang, Yuchao Jiang	Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.	Bioinform.	2018	DBLP DOI BibTeX RDF
16	Jesse Eaton, Jingyi Wang, Russell Schwartz	Deconvolution and phylogeny inference of structural variations in tumor genomic samples.	Bioinform.	2018	DBLP DOI BibTeX RDF
16	Leo van Iersel, Mark Jones 0001, Steven Kelk	A third strike against perfect phylogeny.	CoRR	2018	DBLP BibTeX RDF
16	Bei Jia, Surjyendu Ray, Sam Safavi, José Bento 0001	Efficient Projection onto the Perfect Phylogeny Model.	CoRR	2018	DBLP BibTeX RDF
16	Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard	Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.	PLoS Comput. Biol.	2018	DBLP DOI BibTeX RDF
16	Erin K. Molloy, Tandy J. Warnow	NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees.	RECOMB-CG	2018	DBLP DOI BibTeX RDF
16	Dikshant Pradhan, Mohammed El-Kebir	On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem.	RECOMB-CG	2018	DBLP DOI BibTeX RDF
16	Thomas Dencker, Chris-André Leimeister, Michael Gerth, Christoph Bleidorn, Sagi Snir, Burkhard Morgenstern	Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees.	RECOMB-CG	2018	DBLP DOI BibTeX RDF
16	Giovanni Acampora, Mario Luca Bernardi, Marta Cimitile, Genoveffa Tortora, Autilia Vitiello	A Fuzzy Clustering-based Approach to study Malware Phylogeny.	FUZZ-IEEE	2018	DBLP DOI BibTeX RDF
16	Kiran Tomlinson, Layla Oesper	Examining Tumor Phylogeny Inference in Noisy Sequencing Data.	BIBM	2018	DBLP DOI BibTeX RDF
16	Timmy Manning, Jyotsna Talreja Wassan, Cintia C. Palu, Haiying Wang 0001, Fiona Browne, Huiru Zheng, Brian Kelly, Paul Walsh	Phylogeny-Aware Deep 1-Dimensional Convolutional Neural Network for the Classification of Metagenomes.	BIBM	2018	DBLP DOI BibTeX RDF
16	Jyotsna Talreja Wassan, Haiying Wang 0001, Fiona Browne, Huiru Zheng	PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification.	BIBM	2018	DBLP DOI BibTeX RDF
16	Bei Jia, Surjyendu Ray, Sam Safavi, José Bento 0001	Efficient Projection onto the Perfect Phylogeny Model.	NeurIPS	2018	DBLP BibTeX RDF
16	Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow	New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy.	WABI	2018	DBLP DOI BibTeX RDF
16	Rafael L. Fernandes, Rogério Güths, Guilherme P. Telles, Nalvo F. Almeida, Maria Emília M. T. Walter	A Genetic Algorithm for Character State Live Phylogeny.	BSB	2018	DBLP DOI BibTeX RDF
16	Jodh Pannu, Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru	An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction.	BCB	2018	DBLP DOI BibTeX RDF
16	Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco	Species-Driven Persistent Phylogeny.	Fundam. Informaticae	2017	DBLP DOI BibTeX RDF
16	Manuel Bodirsky, Peter Jonsson, Van Trung Pham	The Complexity of Phylogeny Constraint Satisfaction Problems.	ACM Trans. Comput. Log.	2017	DBLP DOI BibTeX RDF
16	Burkhard Morgenstern, Svenja Schöbel, Chris-André Leimeister	Phylogeny reconstruction based on the length distribution of k-mismatch common substrings.	Algorithms Mol. Biol.	2017	DBLP DOI BibTeX RDF
16	Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco	A colored graph approach to perfect phylogeny with persistent characters.	Theor. Comput. Sci.	2017	DBLP DOI BibTeX RDF
16	Stephen A. Smith, James Pease	Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny.	Briefings Bioinform.	2017	DBLP DOI BibTeX RDF
16	Luyang Huo, Han Zhang 0017, Xueting Huo, Yasong Yang, Xueqiong Li	pHMM-tree: phylogeny of profile hidden Markov models.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Qi Wu 0016, Zu-Guo Yu, Jianyi Yang	DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Chris-André Leimeister, Salma Sohrabi-Jahromi, Burkhard Morgenstern	Fast and accurate phylogeny reconstruction using filtered spaced-word matches.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Xingjian Xu, Zhaohua Ji, Zhang Zhang 0002	CloudPhylo: a fast and scalable tool for phylogeny reconstruction.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Jan P. Meier-Kolthoff, Markus Göker	VICTOR: genome-based phylogeny and classification of prokaryotic viruses.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Gryte Satas, Benjamin J. Raphael	Tumor phylogeny inference using tree-constrained importance sampling.	Bioinform.	2017	DBLP DOI BibTeX RDF
16	Cédric Chauve, Mark Jones 0001, Manuel Lafond, Céline Scornavacca, Mathias Weller	Constructing a Consensus Phylogeny from a Leaf-Removal Distance.	CoRR	2017	DBLP BibTeX RDF
16	Allan da Silva Pinto, Daniel Moreira, Aparna Bharati, Joel Brogan, Kevin W. Bowyer, Patrick J. Flynn, Walter J. Scheirer, Anderson Rocha 0001	Provenance Filtering for Multimedia Phylogeny.	CoRR	2017	DBLP BibTeX RDF
16	Aparna Bharati, Daniel Moreira, Allan da Silva Pinto, Joel Brogan, Kevin W. Bowyer, Patrick J. Flynn, Walter J. Scheirer, Anderson Rocha 0001	U-Phylogeny: Undirected Provenance Graph Construction in the Wild.	CoRR	2017	DBLP BibTeX RDF
16	Dimitris P. Papamichail, Angela Huang, Edward Kennedy, Jan-Lucas Ott, Andrew Miller, Georgios Papamichail	Live phylogeny with polytomies: Finding the most compact parsimonious trees.	Comput. Biol. Chem.	2017	DBLP DOI BibTeX RDF
16	Filipe de Oliveira Costa, Alberto A. de Oliveira, Pasquale Ferrara, Zanoni Dias, Siome Goldenstein, Anderson Rocha 0001	New dissimilarity measures for image phylogeny reconstruction.	Pattern Anal. Appl.	2017	DBLP DOI BibTeX RDF
16	Seung Chul Lee, Jihoon Choi, Suh-Ryung Kim, Yoshio Sano	On the phylogeny graphs of degree-bounded digraphs.	Discret. Appl. Math.	2017	DBLP DOI BibTeX RDF
16	Olga K. Kamneva	Genome composition and phylogeny of microbes predict their co-occurrence in the environment.	PLoS Comput. Biol.	2017	DBLP DOI BibTeX RDF
16	Diane Oyen, Blake Anderson, Kari Sentz, Christine M. Anderson-Cook	Order priors for Bayesian network discovery with an application to malware phylogeny.	Stat. Anal. Data Min.	2017	DBLP DOI BibTeX RDF
16	Allan da Silva Pinto, Daniel Moreira, Aparna Bharati, Joel Brogan, Kevin W. Bowyer, Patrick J. Flynn, Walter J. Scheirer, Anderson Rocha 0001	Provenance filtering for multimedia phylogeny.	ICIP	2017	DBLP DOI BibTeX RDF
16	Aparna Bharati, Daniel Moreira, Allan da Silva Pinto, Joel Brogan, Kevin W. Bowyer, Patrick J. Flynn, Walter J. Scheirer, Anderson Rocha 0001	U-Phylogeny: Undirected provenance graph construction in the wild.	ICIP	2017	DBLP DOI BibTeX RDF