Search results for "Ortholog"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
161	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Ortholog Clustering on a Multipartite Graph.	WABI	2005	DBLP DOI BibTeX RDF
122	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Ortholog Clustering on a Multipartite Graph.	IEEE ACM Trans. Comput. Biol. Bioinform.	2007	DBLP DOI BibTeX RDF	clustering algorithms, genetics, biology, Graph-theoretic methods
122	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Screening for Ortholog Clusters Using Multipartite Graph Clustering by Quasi-Concave Set Function Optimization.	RSFDGrC (2)	2005	DBLP DOI BibTeX RDF
103	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization.	RECOMB	2006	DBLP DOI BibTeX RDF
84	Tao Jiang 0001	A Combinatorial Approach to Genome-Wide Ortholog Assignment: Beyond Sequence Similarity Search.	CPM	2007	DBLP DOI BibTeX RDF
84	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Automatic Protein Function Annotation through Candidate Ortholog Clusters from Incomplete Genomes.	CSB Workshops	2005	DBLP DOI BibTeX RDF
75	Xin Chen 0037, Jie Zheng 0002, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang 0001	Assignment of Orthologous Genes via Genome Rearrangement.	IEEE ACM Trans. Comput. Biol. Bioinform.	2005	DBLP DOI BibTeX RDF	Ortholog, paralog, reversal, comparative genomics, genome rearrangement, gene duplication
65	Zheng Fu, Xin Chen 0037, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang 0001	A Parsimony Approach to Genome-Wide Ortholog Assignment.	RECOMB	2006	DBLP DOI BibTeX RDF
58	Xiao Liu, Neil D. Clarke	Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets.	RECOMB-CG	2009	DBLP DOI BibTeX RDF
58	Ming Ouyang, John Case, Joan Burnside	Divide and Conquer Machine Learning for a Genomics Analogy Problem (Progress Report).	Discovery Science	2001	DBLP DOI BibTeX RDF
26	J. Ludwig, Jan Mrázek	OrthoRefine: automated enhancement of prior ortholog identification via synteny.	BMC Bioinform.	2024	DBLP DOI BibTeX RDF
26	Wend Yam Donald Davy Ouedraogo, Aïda Ouangraoua	Inferring Transcript Phylogenies from Transcript Ortholog Clusters.	RECOMB-CG	2024	DBLP DOI BibTeX RDF
26	Wenkang Wang, Xiangmao Meng, Ju Xiang, Yunyan Shuai, Hayat Dino Bedru, Min Li 0007	CACO: A Core-Attachment Method With Cross-Species Functional Ortholog Information to Detect Human Protein Complexes.	IEEE J. Biomed. Health Informatics	2023	DBLP DOI BibTeX RDF
26	Takuya Aramaki, Romain Blanc-Mathieu, Hisashi Endo, Koichi Ohkubo, Minoru Kanehisa, Susumu Goto, Hiroyuki Ogata	KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold.	Bioinform.	2020	DBLP DOI BibTeX RDF
26	Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac	The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction.	Bioinform.	2020	DBLP DOI BibTeX RDF
26	Kevin Correia, Shi M. Yu, Radhakrishnan Mahadevan	AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution.	Database J. Biol. Databases Curation	2019	DBLP DOI BibTeX RDF
26	Justin Miller, Brandon D. Pickett, Perry G. Ridge	JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.	Bioinform.	2019	DBLP DOI BibTeX RDF
26	Deborah Galpert, Alberto Fernández 0001, Francisco Herrera, Agostinho Antunes, Reinaldo Molina Ruiz, Guillermín Agüero-Chapín	Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.	BMC Bioinform.	2018	DBLP DOI BibTeX RDF
26	Jean-David Aguilar, Safa Jammali, Esaie Kuitche, Aïda Ouangraoua	Improving spliced alignment for identification of ortholog groups and multiple CDS alignment.	CoRR	2017	DBLP BibTeX RDF
26	George L. Sutphin, J. Matthew Mahoney, Keith S. Sheppard, David O. Walton, Ron Korstanje	WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.	PLoS Comput. Biol.	2016	DBLP DOI BibTeX RDF
26	Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl J. Schmidt, Jinglong Fang, Jian Chen 0006	PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
26	Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba	MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.	Nucleic Acids Res.	2015	DBLP DOI BibTeX RDF
26	Hirokazu Chiba, Ikuo Uchiyama	Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score.	BMC Bioinform.	2014	DBLP DOI BibTeX RDF
26	Kun Gao, Jonathan Miller 0002	Human-chimpanzee alignment: Ortholog exponentials and paralog power laws.	Comput. Biol. Chem.	2014	DBLP DOI BibTeX RDF
26	Deborah Galpert Cañizares, Reinier Millo Sánchez, María Matilde García Lorenzo, Gladys Casas Cardoso, Ricardo Grau Ábalo, Leticia Arco García	Rough Sets in Ortholog Gene Detection - Selection of Feature Subsets and Case Reduction Considering Imbalance.	RSEISP	2014	DBLP DOI BibTeX RDF
26	Cyrus Afrasiabi, Bushra Samad, David Dineen, Christopher Meacham, Kimmen Sjölander	The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.	Nucleic Acids Res.	2013	DBLP DOI BibTeX RDF
26	Akihiro Nakaya, Toshiaki Katayama, Masumi Itoh, Kazushi Hiranuka, Shuichi Kawashima, Yuki Moriya, Shujiro Okuda, Michihiro Tanaka, Toshiaki Tokimatsu, Yoshihiro Yamanishi, Akiyasu C. Yoshizawa, Minoru Kanehisa, Susumu Goto	KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.	Nucleic Acids Res.	2013	DBLP DOI BibTeX RDF
26	Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz	Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs.	PLoS Comput. Biol.	2012	DBLP DOI BibTeX RDF
26	Xiaoshu Chen, Jianzhi Zhang	The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data.	PLoS Comput. Biol.	2012	DBLP DOI BibTeX RDF
26	Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E. Mohr	An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies.	BMC Bioinform.	2011	DBLP DOI BibTeX RDF
26	Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner	Ortholog identification in the presence of domain architecture rearrangement.	Briefings Bioinform.	2011	DBLP DOI BibTeX RDF
26	Luis Sánchez-Pulido, Chris P. Ponting	Cdc45: the missing RecJ ortholog in eukaryotes?	Bioinform.	2011	DBLP DOI BibTeX RDF
26	Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn	Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals.	PLoS Comput. Biol.	2011	DBLP DOI BibTeX RDF
26	Yu Lin, Zuoshuang Xiang, Yongqun He	Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis.	ICBO	2011	DBLP BibTeX RDF
26	Ting-Wen Chen, Timothy H. Wu, Wailap V. Ng, Wen-Chang Lin	DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
26	Guanqun Shi, Liqing Zhang 0002, Tao Jiang 0001	MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
26	Meng-Ru Ho, Chun-Houh Chen, Wen-Chang Lin	Gene-oriented ortholog database: a functional comparison platform for orthologous loci.	Database J. Biol. Databases Curation	2010	DBLP DOI BibTeX RDF
26	Chandra Sekhar Pedamallu, Janos Posfai	Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information.	Source Code Biol. Medicine	2010	DBLP DOI BibTeX RDF
26	Tao Jiang 0001	Some Algorithmic Challenges in Genome-Wide Ortholog Assignment.	J. Comput. Sci. Technol.	2009	DBLP DOI BibTeX RDF
26	Sheng-An Lee, Chen-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang	Ortholog-based protein-protein interaction prediction and its application to inter-species interactions.	BMC Bioinform.	2008	DBLP DOI BibTeX RDF
26	Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Kaori Yamaguchi, Toshinori Endo, Satoshi Ota, Wojciech Makalowski, Kazuho Ikeo, Yoshiyuki Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lihua Jin, Yayoi Kaneko, Masako Kanno, Katsuhiko Murakami, Akiko Ogura Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun-ichi Takeda, Masayuki Tanaka 0009, Takashi Gojobori, Tadashi Imanishi, Takeshi Itoh	Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.	Nucleic Acids Res.	2008	DBLP DOI BibTeX RDF
26	Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer	InParanoid 6: eukaryotic ortholog clusters with inparalogs.	Nucleic Acids Res.	2008	DBLP DOI BibTeX RDF
26	Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones	THOR: targeted high-throughput ortholog reconstructor.	Bioinform.	2007	DBLP DOI BibTeX RDF
26	Zheng Fu, Xin Chen 0037, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang 0001	MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement.	J. Comput. Biol.	2007	DBLP DOI BibTeX RDF
26	Aijazuddin Syed, Chris Upton	Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis.	BMC Bioinform.	2006	DBLP DOI BibTeX RDF
26	Debra L. Fulton, Yvonne Y. Li, Matthew R. Laird, Benjamin G. S. Horsman, Fiona M. Roche, Fiona S. L. Brinkman	Improving the specificity of high-throughput ortholog prediction.	BMC Bioinform.	2006	DBLP DOI BibTeX RDF
26	Chunguang Liang, Thomas Dandekar	inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons.	BMC Bioinform.	2006	DBLP DOI BibTeX RDF
26	Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr., David S. Roos	OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.	Nucleic Acids Res.	2006	DBLP DOI BibTeX RDF
26	Joanna C. Chiu, Ernest K. Lee, Mary G. Egan, Indra Neil Sarkar, Gloria M. Coruzzi, Robert DeSalle	OrthologID: automation of genome-scale ortholog identification within a parsimony framework.	Bioinform.	2006	DBLP DOI BibTeX RDF
26	Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, Bruce J. Aronow	CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes.	Nucleic Acids Res.	2005	DBLP DOI BibTeX RDF
26	Natalia Grabar, Magali Sillam, Marie-Christine Jaulent, Céline Lefebvre, Édouard Henrion, Christian Néri	From likelihoodness between words to the finding of functional profile for ortholog genes.	RANLP Text Mining Workshop	2005	DBLP BibTeX RDF
26	Hsing-Kuo Pao, John Case	Computing Entropy for Ortholog Detection.	International Conference on Computational Intelligence	2004	DBLP BibTeX RDF
26	Christian E. V. Storm, Erik L. L. Sonnhammer	Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.	Bioinform.	2002	DBLP DOI BibTeX RDF
19	Freddy Cliquet, Guillaume Fertin, Irena Rusu, Dominique Tessier	Comparison of Spectra in Unsequenced Species.	BSB	2009	DBLP DOI BibTeX RDF
19	Xin Chen 0037, Lan Liu 0001, Zheng Liu, Tao Jiang 0001	On the minimum common integer partition problem.	ACM Trans. Algorithms	2008	DBLP DOI BibTeX RDF	approximation algorithm, combinatorial optimization, NP-hard, computational biology, Subset sum, integer partition
19	Li Tang, Sheng-Jun Wang, Chao-Ming Mao, Jun Chen, Zheng-Jun Hu, Jun-Feng Bao, Qi-Xiang Shao, Hua-Xi Xu	Human GITRLaa50-177 Expressed in Bac-to-Bac Baculovirus Expression System.	BMEI (1)	2008	DBLP DOI BibTeX RDF	GITRL, recombinant protein
19	Peter Damaschke	Minimum Common String Partition Parameterized.	WABI	2008	DBLP DOI BibTeX RDF
19	Rohit Singh 0001, Jinbo Xu, Bonnie Berger	Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology.	RECOMB	2007	DBLP DOI BibTeX RDF
19	Gaëlle Brevier, Romeo Rizzi, Stéphane Vialette	Pattern Matching in Protein-Protein Interaction Graphs.	FCT	2007	DBLP DOI BibTeX RDF
19	Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Björn Olsson, Olof Olsson	Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets.	BIRD	2007	DBLP DOI BibTeX RDF
19	Steinar Thorvaldsen, Elinor Ytterstad, Tor Flå	Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices.	ISBRA	2007	DBLP DOI BibTeX RDF	Stratified data, Two-way ANOVA, Mantel-Haenszel test, cold adaptation
19	Xin Chen 0037, Lan Liu 0001, Zheng Liu, Tao Jiang 0001	On the Minimum Common Integer Partition Problem.	CIAC	2006	DBLP DOI BibTeX RDF
19	Tae-Kyung Kim, Kyoung-Ran Kim, Sang-Keun Oh, Jong-Hak Lee, Wan-Sup Cho	A Hybrid Grid and Its Application to Orthologous Groups Clustering.	CompLife	2006	DBLP DOI BibTeX RDF
19	David P. Woodruff	Better Approximations for the Minimum Common Integer Partition Problem.	APPROX-RANDOM	2006	DBLP DOI BibTeX RDF
19	David Sankoff, Chunfang Zheng, Aleksander Lenert	Reversals of Fortune.	Comparative Genomics	2005	DBLP DOI BibTeX RDF
19	David Sankoff, Phil Trinh	Chromosomal breakpoint re-use in the inference of genome sequence rearrangement.	RECOMB	2004	DBLP DOI BibTeX RDF	Hannenhalli-Pevzner algorithm, synteny blocks, evolution, inversion, comparative genomics, breakpoints, rearrangements