Search results for "homologs"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
73	Maricel Kann, Richard A. Goldstein	Optimizing for success: a new score function for distantly related protein sequence comparison.	RECOMB	2000	DBLP DOI BibTeX RDF
55	Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna	Structural Alignment of Pseudoknotted RNA.	RECOMB	2006	DBLP DOI BibTeX RDF
49	Arvind K. Bansal, Christopher Woolverton	Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways.	IEEE Trans. Knowl. Data Eng.	2003	DBLP DOI BibTeX RDF	enzymes, gene-groups, microbes, operons, orthologs, pathogenicity, Automation, homologs, drug-discovery, pathway, metabolic pathway, bacteria
44	Guillaume Blin, Annie Chateau, Cédric Chauve, Yannick Gingras	Inferring Positional Homologs with Common Intervals of Sequences.	Comparative Genomics	2006	DBLP DOI BibTeX RDF
44	Guillaume Bourque, Yasmine Yacef, Nadia El-Mabrouk	Maximizing Synteny Blocks to Identify Ancestral Homologs.	Comparative Genomics	2005	DBLP DOI BibTeX RDF
44	Yuheng Li, Mario Lauria, Ralf Bundschuh	Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches.	BIBE	2005	DBLP DOI BibTeX RDF	PSI-BLAST, suboptimal alignment, sequence alignment, hybrid algorithm, forward-backward algorithm
37	Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna	Searching Genomes for Noncoding RNA Using FastR.	IEEE ACM Trans. Comput. Biol. Bioinform.	2005	DBLP DOI BibTeX RDF	Noncoding RNA, riboswitch, bacterial genome, filtration, database search
37	Rose Hoberman, David Sankoff, Dannie Durand	The Statistical Significance of Max-Gap Clusters.	Comparative Genomics	2004	DBLP DOI BibTeX RDF
37	Vineet Bafna, Shaojie Zhang	FastR: Fast Database Search Tool for Non-Coding RNA.	CSB	2004	DBLP DOI BibTeX RDF	non-coding RNA genes, dynamic programming, sequence alignment, RNA, filtration, database search
37	Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Cheng-Yan Kao, Jorng-Tzong Horng	A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome.	BIBE	2003	DBLP DOI BibTeX RDF	regulatory site, data mining gene expression, transcription factor
37	Parvin Mousavi, Sidney S. Fels, Rabab Kreidieh Ward, Peter M. Lansdorp	Classification of homologous human chromosomes using mutual information maximization.	ICIP (2)	2001	DBLP DOI BibTeX RDF
31	Ankit Agrawal 0001, Xiaoqiu Huang 0001	Pairwise statistical significance of local sequence alignment using multiple parameter sets.	DTMBIO	2008	DBLP DOI BibTeX RDF	database statistical significance, pairwise statistical significance, sequence alignment, homologs, parameter set
31	Ankit Agrawal 0001, Volker Brendel, Xiaoqiu Huang 0001	Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences.	ISBRA	2008	DBLP DOI BibTeX RDF	Database statistical significance, Pairwise local alignment, Pairwise statistical significance, Homologs
26	Kenneth J. Bures	Cracking PURPLE: the identification of homologs in the cryptanalysis of the Angooki Taipu B cipher machine.	Cryptologia	2023	DBLP DOI BibTeX RDF
26	Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash	A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
26	Sizhen Li, Ning Dai, He Zhang, Apoorv Malik, David H. Mathews, Liang Huang 0001	LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs.	CoRR	2023	DBLP DOI BibTeX RDF
26	Tatsuya Yoshizawa, Shoichi Ishida, Tomohiro Sato, Masateru Ohta, Teruki Honma, Kei Terayama	Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
26	Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo	Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
26	Jayanta Kumar Das, Christian Heryakusuma, Dwi Susanti, Pabitra Pal Choudhury, Biswarup Mukhopadhyay	Reduced protein sequence patterns in identifying key structural elements of dissimilatory sulfite reductase homologs.	Comput. Biol. Chem.	2022	DBLP DOI BibTeX RDF
26	Chloé Quignot, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, Raphaël Guérois	InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.	Nucleic Acids Res.	2021	DBLP DOI BibTeX RDF
26	Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang 0001	LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.	Proc. Natl. Acad. Sci. USA	2021	DBLP DOI BibTeX RDF
26	Adrian C. D. Fuchs, Vikram Alva, Andrei N. Lupas	An astonishing wealth of new proteasome homologs.	Bioinform.	2021	DBLP DOI BibTeX RDF
26	Richard A. Schäfer, Steffen Lott, Jens Georg, Björn A. Grüning, Wolfgang R. Hess, Björn Voß	GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs.	Bioinform.	2020	DBLP DOI BibTeX RDF
26	Archana Pal Negi, Ratnesh Singh, Anupma Sharma, Vishal Singh Negi	Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs.	Comput. Biol. Chem.	2020	DBLP DOI BibTeX RDF
26	William R. Pearson	Identification of Homologs.	Encyclopedia of Bioinformatics and Computational Biology (3)	2019	DBLP DOI BibTeX RDF
26	David Sankoff, Chunfang Zheng, Yue Zhang, Joao Meidanis, Eric Lyons 0002, Haibao Tang	Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics.	IEEE ACM Trans. Comput. Biol. Bioinform.	2019	DBLP DOI BibTeX RDF
26	P. Chellapandi, R. Prathiviraj, A. Prisilla	Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints.	J. Comput. Aided Mol. Des.	2019	DBLP DOI BibTeX RDF
26	Nelson Gil, András Fiser	The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.	Bioinform.	2019	DBLP DOI BibTeX RDF
26	Siavash Sheikhizadeh, Dick de Ridder, M. Eric Schranz, Sandra Smit	Efficient inference of homologs in large eukaryotic pan-proteomes.	BMC Bioinform.	2018	DBLP DOI BibTeX RDF
26	Pablo Mier, Antonio J. Pérez-Pulido, Miguel A. Andrade-Navarro	Automated selection of homologs to track the evolutionary history of proteins.	BMC Bioinform.	2018	DBLP DOI BibTeX RDF
26	Christian D. Schenkelberg, Christopher Bystroff	Protein backbone ensemble generation explores the local structural space of unseen natural homologs.	Bioinform.	2016	DBLP DOI BibTeX RDF
26	Beibei Wang, Joshua Francis, Monika Sharma, Sean M. Law, Alexander V. Predeus, Michael Feig	Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways.	PLoS Comput. Biol.	2016	DBLP DOI BibTeX RDF
26	Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra	Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
26	Svenja Alter, Kai Christian Bader, Manuel Spannagl, Yu Wang 0008, Eva Bauer, Chris-Carolin Schön, Klaus F. X. Mayer	DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species.	Database J. Biol. Databases Curation	2015	DBLP DOI BibTeX RDF
26	Simone Zorzan, Erika Lorenzetto, Michele Ettorre, Valeria Pontelli, Carlo Laudanna, Mario Buffelli	HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration.	Bioinform.	2013	DBLP DOI BibTeX RDF
26	Melvin Zhang, Hon Wai Leong	BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity.	BMC Syst. Biol.	2012	DBLP DOI BibTeX RDF
26	Maria D. Chikina, Olga G. Troyanskaya	Accurate Quantification of Functional Analogy among Close Homologs.	PLoS Comput. Biol.	2011	DBLP DOI BibTeX RDF
26	Andrew Kuziemko, Barry Honig, Donald Petrey	Using Structure to Explore the Sequence Alignment Space of Remote Homologs.	PLoS Comput. Biol.	2011	DBLP DOI BibTeX RDF
26	Gaurav Sharma 0001, Arif Ozgun Harmanci, David H. Mathews	Iterative estimation of structures of multiple RNA homologs: Turbofold.	ICASSP	2011	DBLP DOI BibTeX RDF
26	Weilong Hao	OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
26	Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst, Berend Snel	Enrichment of homologs in insignificant BLAST hits by co-complex network alignment.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
26	Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Saikat Chakrabarti 0001	Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble.	Bioinform.	2009	DBLP DOI BibTeX RDF
26	Anoop Kumar, Lenore Cowen	Augmented training of hidden Markov models to recognize remote homologs via simulated evolution.	Bioinform.	2009	DBLP DOI BibTeX RDF
26	Vesselin Baev, Evelina Daskalova, Ivan Nikiforov Minkov	Computational identification of novel microRNA homologs in the chimpanzee genome.	Comput. Biol. Chem.	2009	DBLP DOI BibTeX RDF
26	Gérard Ramstein, Nicolas Beaume, Yannick Jacques	Detection of Remote Protein Homologs Using Social Programming.	Foundations of Computational Intelligence (4)	2009	DBLP DOI BibTeX RDF
26	Usman Roshan, Satish Chikkagoudar, Dennis R. Livesay	Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.	BMC Bioinform.	2008	DBLP DOI BibTeX RDF
26	Jos Boekhorst, Berend Snel	Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.	BMC Bioinform.	2007	DBLP DOI BibTeX RDF
26	Masako Ogura, J. Christian Perez, Peer R. E. Mittl, Hae-Kyung Lee, Geidrius Dailide, Shumin Tan, Yoshiyuki Ito, Ousman Secka, Daiva Dailidiene, Kalyani Putty, Douglas E. Berg, Awdhesh Kalia	Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes.	PLoS Comput. Biol.	2007	DBLP DOI BibTeX RDF
26	Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng	RNAMST: efficient and flexible approach for identifying RNA structural homologs.	Nucleic Acids Res.	2006	DBLP DOI BibTeX RDF
26	Tobias Dezulian, Michael Remmert, Javier F. Palatnik, Detlef Weigel, Daniel H. Huson	Identification of plant microRNA homologs.	Bioinform.	2006	DBLP DOI BibTeX RDF
26	Jakob Fredslund, Leif Schauser, Lene H. Madsen, Niels Sandal, Jens Stougaard	PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.	Nucleic Acids Res.	2005	DBLP DOI BibTeX RDF
26	Ruslan Sadreyev, Nick V. Grishin	Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.	Bioinform.	2004	DBLP DOI BibTeX RDF
26	Robert J. Klein, Sean R. Eddy	RSEARCH: Finding homologs of single structured RNA sequences.	BMC Bioinform.	2003	DBLP DOI BibTeX RDF
26	Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek	Bioinformatics classification and functional analysis of PhoH homologs.	Silico Biol.	2003	DBLP BibTeX RDF
26	Maricel Kann, Richard A. Goldstein	OPTIMA: A New Score Function for the Detection of Remote Homologs.	Mathematical Methods for Protein Structure Analysis and Design	2003	DBLP DOI BibTeX RDF
26	Janusz M. Bujnicki, Leszek Rychlewski	RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.	BMC Bioinform.	2002	DBLP DOI BibTeX RDF
26	Wei Zhu 0001, Volker Brendel	Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions.	Bioinform.	2002	DBLP DOI BibTeX RDF
26	Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy	Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.	Bioinform.	2000	DBLP DOI BibTeX RDF
26	Miguel A. Andrade	Position-Specific Annotation of Protein Function Based on Multiple Homologs.	ISMB	1999	DBLP BibTeX RDF
26	Azat Ya. Badretdinov, Alexei V. Finkelstein	How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences.	J. Comput. Biol.	1998	DBLP DOI BibTeX RDF
26	Peter J. van der Spek, André Eker, Suzanne Rademakers, Cécile Visser, Kaoru Sugasawa, Chikahide Masutani, Fumio Hanaoka, Dirk Bootsma, Jan H. J. Hoeijmakers	XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes.	Nucleic Acids Res.	1996	DBLP DOI BibTeX RDF
18	Server Kasap, Khaled Benkrid, Ying Liu 0003	A high performance fpga-based implementation of position specific iterated blast.	FPGA	2009	DBLP DOI BibTeX RDF	psi-blast, fpga, blast, handel c
18	Olivier Perriquet, Pedro Barahona	Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction.	EPIA	2009	DBLP DOI BibTeX RDF
18	Nazar Zaki	Protein-Protein Interaction Prediction Using Homology and Inter-domain Linker Region Information.	World Congress on Engineering (Selected Papers)	2008	DBLP DOI BibTeX RDF	Inter-domain Linker Region, yeast protein, Prediction, Protein-Protein Interaction, Homology
18	Yue Lu, Sing-Hoi Sze	Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences.	RECOMB	2007	DBLP DOI BibTeX RDF
18	Viktor Martyanov, Larkin Elderon, Amy Gladfelter, Dhanalakshmi R. Nair, Robert H. Gross	Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder.	BIBE	2007	DBLP DOI BibTeX RDF
18	David A. Lightfoot, Mengxia Michelle Zhu	Using The Soybean Genome Database (SoyGD) To Display and Analyze a 1 Gbp Genome Sequence.	BIBE	2007	DBLP DOI BibTeX RDF
18	Deepak Perumal, Chu Sing Lim, Meena K. Sakharkar	In silico Identification of Putative Drug Targets in Pseudomonas aeruginosa Through Metabolic Pathway Analysis.	PRIB	2007	DBLP DOI BibTeX RDF	Pseudomonas aeruginosa, Homo sapiens, Comparative microbial genomics, KEGG, kdsA, kdsB, waaG, lpxC, Potential drug targets, MODELLER, Homology
18	Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai	Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment.	IEEE ACM Trans. Comput. Biol. Bioinform.	2006	DBLP DOI BibTeX RDF	Structure-sequence alignment, RNA structure homology search, dynamic programming, tree decomposition, parameterized algorithm, protein threading
18	Nan Song, R. D. Sedgewick, Dannie Durand	Domain Architecture in Homolog Identification.	Comparative Genomics	2006	DBLP DOI BibTeX RDF
18	Fa Zhang 0001, Lin Xu, Bo Yuan	A method to improve structural modeling based on conserved domain clusters.	IPDPS	2006	DBLP DOI BibTeX RDF
18	Xiaoxu Han	Inferring Species Phylogenies: A Microarray Approach.	ICIC (3)	2006	DBLP DOI BibTeX RDF
18	Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai	Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.	WABI	2005	DBLP DOI BibTeX RDF
18	Walter L. Ruzzo	Searching for Non-coding RNA.	BSB	2005	DBLP DOI BibTeX RDF
18	Zasha Weinberg, Walter L. Ruzzo	Faster genome annotation of non-coding RNA families without loss of accuracy.	RECOMB	2004	DBLP DOI BibTeX RDF	covariance models, gene families, genome annotation, histone downstream element, hyperthermophile archaea snoRNA, iron response element, rigorous filter, profile hidden Markov models, non-coding RNA
18	Yonghua Han, Bin Ma 0002, Kaizhong Zhang	SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error.	CSB	2004	DBLP DOI BibTeX RDF	de novo sequencing, sequence tags, database search, protein identification
18	Kyungsook Han, Byungkyu Park	A Database Server for Predicting Protein-Protein Interactions.	International Conference on Computational Science	2004	DBLP DOI BibTeX RDF
18	Gaurav Narale, Jacques Beaumont, Philip A. Rice, Mark E. Schmitt	Computational Identification of RNA Motifs in Genome Sequences.	IEA/AIE	2004	DBLP DOI BibTeX RDF
18	Ying Xu 0001, Dong Xu 0002, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu	Protein structure determination using protein threading and sparse NMR data (extended abstract).	RECOMB	2000	DBLP DOI BibTeX RDF	fold recognition, protein structure determination, energy minimization, protein threading, NMR