Search results for "motif-finding"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
129	Sing-Hoi Sze, Songjian Lu, Jianer Chen	Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding.	WABI	2004	DBLP DOI BibTeX RDF
114	Francis Y. L. Chin, Henry C. M. Leung, Siu-Ming Yiu, Tak Wah Lam, Roni Rosenfeld, Wai Wan Tsang, David K. Smith 0001, Y. Jiang	Finding motifs for insufficient number of sequences with strong binding to transcription facto.	RECOMB	2004	DBLP DOI BibTeX RDF	binding energy, DNA microarray, transcription factor, motif finding
109	Giovanna Martínez-Arellano, Carlos A. Brizuela	Comparison of Simple Encoding Schemes in GA's for the Motif Finding Problem: Preliminary Results.	BSB	2007	DBLP DOI BibTeX RDF
105	Chengpeng Bi	A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences.	IEEE ACM Trans. Comput. Biol. Bioinform.	2009	DBLP DOI BibTeX RDF	Monte Carlo EM, multiple sequence alignment, motif discovery, transcriptional regulation, Expectation maximization (EM)
105	Yingren Liu, Karuturi R. Krishna Murthy, Wing-Kin Sung	ConstrainedMotif: A Periodicity Constraint Based Algorithm to Predict Cell-Cycle Associated Promoter Motifs Using Time-Course Gene Expression Data.	BIBE	2005	DBLP DOI BibTeX RDF	Motif prediction, Microarray, Constrained optimization, Cell-cycle
102	Chengpeng Bi	Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm.	ISBRA	2007	DBLP DOI BibTeX RDF	Monte Carlo EM, Multiple Sequence Local Alignment, Motif Discovery, Transcriptional Regulation, Expectation Maximization (EM)
83	Sing-Hoi Sze, Xiaoyan Zhao	Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences.	Systems Biology and Regulatory Genomics	2005	DBLP DOI BibTeX RDF
77	Vipin Narang, Wing-Kin Sung, Ankush Mittal	LocalMotif - An In-Silico Tool for Detecting Localized Motifs in Regulatory Sequences.	ICTAI	2006	DBLP DOI BibTeX RDF
76	Brona Brejová, Daniel G. Brown 0001, Ian M. Harrower, Tomás Vinar	New Bounds for Motif Finding in Strong Instances.	CPM	2006	DBLP DOI BibTeX RDF
71	Eleazar Eskin	From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles.	RECOMB	2004	DBLP DOI BibTeX RDF	patterns, profiles, transcription factor binding sites, motif-finding
63	Doaa Altarawy, Mohamed A. Ismail, Sahar Mohamed Ghanem	MProfiler: A Profile-Based Method for DNA Motif Discovery.	PRIB	2009	DBLP DOI BibTeX RDF	DNA Motif Finding, Clustering, Bioinformatics
56	Lifang Liu 0001, Licheng Jiao	Moitf GibbsGA: Sampling Transcription Factor Binding Sites Coupled with PSFM Optimization by GA.	ISICA	2009	DBLP DOI BibTeX RDF
54	Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli	An Interaction-Dependent Model for Transcription Factor Binding.	Systems Biology and Regulatory Genomics	2005	DBLP DOI BibTeX RDF
54	Saurabh Sinha, Martin Tompa	Performance Comparison of Algorithms for FindingTranscription Factor Binding Sites.	BIBE	2003	DBLP DOI BibTeX RDF
45	Carl Kingsford, Elena Zaslavsky, Mona Singh 0001	A Compact Mathematical Programming Formulation for DNA Motif Finding.	CPM	2006	DBLP DOI BibTeX RDF
43	Ya Zhang 0002, Yixin Chen 0002, Xiang Ji	Motif Discovery as a Multiple-Instance Problem.	ICTAI	2006	DBLP DOI BibTeX RDF
42	Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri	Identification of New Members of Hydrophobin Family Using Primary Structure Analysis.	IMSCCS (1)	2006	DBLP DOI BibTeX RDF	Hydrophobin, Batch BLAST, Motif finding, MEME
41	Yuh-Jyh Hu	Biological Sequence Data Mining.	PKDD	2001	DBLP DOI BibTeX RDF
36	Zheng Liu 0001, Jeffrey Xu Yu, Xuemin Lin 0001, Hongjun Lu, Wei Wang 0011	Locating Motifs in Time-Series Data.	PAKDD	2005	DBLP DOI BibTeX RDF
33	Guandong Wang, Weixiong Zhang	Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements.	Systems Biology and Regulatory Genomics	2005	DBLP DOI BibTeX RDF
33	Adnan Ferdous Ashrafi, A. K. M. Iqtidar Newaz, Rasif Ajwad, Moin Mahmud Tanvee, Md. A. Mottalib	A modified algorithm for DNA motif finding and ranking considering variable length motif and mutation.	ReTIS	2015	DBLP DOI BibTeX RDF
33	Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev	Motif discovery and motif finding from genome-mapped DNase footprint data.	Bioinform.	2009	DBLP DOI BibTeX RDF
30	Jan Schröder, Lars Wienbrandt, Gerd Pfeiffer, Manfred Schimmler	Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA.	PRIB	2008	DBLP DOI BibTeX RDF	DNA sequence analysis, High Performance Reconfigurable Computing (HPRC), FPGA, Motif finding
30	Mustafa Karabulut, Turgay Ibrikci	Fuzzy C-Means Based DNA Motif Discovery.	ICIC (1)	2008	DBLP DOI BibTeX RDF	Fuzzy Clustering, DNA Sequences, Motif Finding
30	Dongsheng Che, Yinglei Song, Khaled Rasheed	MDGA: motif discovery using a genetic algorithm.	GECCO	2005	DBLP DOI BibTeX RDF	genetic algorithms, transcription factor, motif finding
30	Mathieu Blanchette	Algorithms for phylogenetic footprinting.	RECOMB	2001	DBLP DOI BibTeX RDF	phylogenetic footprinting, regulatory elements, algorithm, phylogeny, motif finding
26	Uri Keich, Pavel A. Pevzner	Finding motifs in the twilight zone.	RECOMB	2002	DBLP DOI BibTeX RDF
23	Yue Fan, Mark A. Kon, Charles DeLisi	Ensemble Machine Methods for DNA Binding.	ICMLA	2008	DBLP DOI BibTeX RDF
23	Jin Chen 0012, Wynne Hsu, Mong-Li Lee, See-Kiong Ng	Labeling network motifs in protein interactomes for protein function prediction.	ICDE	2007	DBLP DOI BibTeX RDF
23	Cun-Quan Zhang, Yunkai Liu, Elaine M. Eschen, Keqiang Wu	Identifying Regulatory Signals in DNA-Sequences with a Non-statistical Approximation Approach.	CSB	2003	DBLP DOI BibTeX RDF
20	Jonathan Feldstein, Dominic Phillips, Efthymia Tsamoura	Principled and Efficient Motif Finding for Structure Learning in Lifted Graphical Models.	CoRR	2023	DBLP DOI BibTeX RDF
20	Jonathan Feldstein, Dominic Phillips, Efthymia Tsamoura	Principled and Efficient Motif Finding for Structure Learning of Lifted Graphical Models.	AAAI	2023	DBLP DOI BibTeX RDF
20	Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu 0002, Qin Ma 0003, Yan Wang 0028	Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
20	Kaijian Xia, Xiang Wu, Yaqing Mao, Huanhuan Wang	Secure DNA Motif-Finding Method Based on Sampling Candidate Pruning.	ACM Trans. Internet Techn.	2021	DBLP DOI BibTeX RDF
20	Weinan Wang, Yuhang Guo, Wei Ju, Xiao Luo 0001, Minghua Deng	An Interpretation of Convolutional Neural Networks for Motif Finding from the View of Probability.	ICTAI	2021	DBLP DOI BibTeX RDF
20	Xiang Wu, Huanhuan Wang, Minyu Shi, Aming Wang, Kaijian Xia	DNA Motif Finding Method Without Protection Can Leak User Privacy.	IEEE Access	2019	DBLP DOI BibTeX RDF
20	Bingqiang Liu, Ling Han, Xiangrong Liu, Jichang Wu, Qin Ma 0003	Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.	IEEE ACM Trans. Comput. Biol. Bioinform.	2019	DBLP DOI BibTeX RDF
20	Xiang Wu, Yuyang Wei, Yaqing Mao, Liang Wang	A differential privacy DNA motif finding method based on closed frequent patterns.	Clust. Comput.	2019	DBLP DOI BibTeX RDF
20	Abdelmenem S. Elgabry, Tahani M. Allam, Mahmoud M. Fahmy	An Identical String Motif Finding Algorithm Through Dynamic Programming.	PACBB	2019	DBLP DOI BibTeX RDF
20	Sanjay Soundarajan, Michelle Salomon, Jin H. Park	Efficient Branch and Bound Motif Finding with Maximum Accuracy based on Hashing.	CCWC	2019	DBLP DOI BibTeX RDF
20	Mai S. Mabrouk, Mohamed B. Abdelhalim, Ebtehal S. Elewa	A developed system based on nature-inspired algorithms for DNA motif finding process.	Neural Comput. Appl.	2018	DBLP DOI BibTeX RDF
20	Bingqiang Liu, Jinyu Yang, Yang Li 0089, Adam McDermaid, Qin Ma 0003	An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.	Briefings Bioinform.	2018	DBLP DOI BibTeX RDF
20	Josep Basha Gutierrez, Kenta Nakai	A study on the application of topic models to motif finding algorithms.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
20	Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna	PROJECTION Algorithm for Motif Finding on GPUs.	CoRR	2016	DBLP BibTeX RDF
20	Katrina B. Gapuz, Ephraim D. Mendoza, Richelle Ann B. Juayong, Nestine Hope S. Hernandez, Francis George C. Cabarle, Henry N. Adorna	Solution to Motif Finding Problem in Membranes.	Int. Conf. on Membrane Computing	2016	DBLP DOI BibTeX RDF
20	Josep Basha Gutierrez, Martin C. Frith, Kenta Nakai	A Genetic Algorithm for Motif Finding Based on Statistical Significance.	IWBBIO (1)	2015	DBLP DOI BibTeX RDF
20	Mostafa M. Abbas, Hazem M. Bahig, Mohamed Abouelhoda, Mustafa M. Mohie-Eldin	Parallelizing exact motif finding algorithms on multi-core.	J. Supercomput.	2014	DBLP DOI BibTeX RDF
20	C. J. Carstens	A uniform random graph model for directed acyclic networks and its effect on motif-finding.	J. Complex Networks	2014	DBLP DOI BibTeX RDF
20	P. Perera, Roshan G. Ragel	Accelerating motif finding in DNA sequences with multicore CPUs.	CoRR	2014	DBLP BibTeX RDF
20	Rui Chen 0012, Yun Peng, Byron Choi, Jianliang Xu, Haibo Hu 0001	A private DNA motif finding algorithm.	J. Biomed. Informatics	2014	DBLP DOI BibTeX RDF
20	Ziva Stepancic	Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences.	J. Comput. Biol.	2014	DBLP DOI BibTeX RDF
20	Mostafa M. Abbas, Qutaibah M. Malluhi, Ponnuraman Balakrishnan	Scalable Multi-core Implementation for Motif Finding Problem.	ISPDC	2014	DBLP DOI BibTeX RDF
20	Juho Kim, Seunghak Yu, Sungroh Yoon	Ensemble algorithms for DNA motif finding.	ICEIC	2014	DBLP DOI BibTeX RDF
20	Qiang Yu 0003, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey Scott Vitter, Jun Huan	An efficient motif finding algorithm for large DNA data sets.	BIBM	2014	DBLP DOI BibTeX RDF
20	Hoang X. Huan, Duong T. A. Tuyet, Doan T. T. Ha, Nguyen T. Hung	An Efficient Ant Colony Algorithm for DNA Motif Finding.	KSE	2014	DBLP DOI BibTeX RDF
20	Ali Gholami Rudi, Saeed Shahrivari, Saeed Jalili, Zahra Razaghi Moghadam Kashani	RANGI: A Fast List-Colored Graph Motif Finding Algorithm.	IEEE ACM Trans. Comput. Biol. Bioinform.	2013	DBLP DOI BibTeX RDF
20	Caiyan Jia, Matthew B. Carson, Jian Yu	A fast weak motif-finding algorithm based on community detection in graphs.	BMC Bioinform.	2013	DBLP DOI BibTeX RDF
20	Yaron Orenstein, Eran Mick, Ron Shamir	RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data.	J. Comput. Biol.	2013	DBLP DOI BibTeX RDF
20	David L. González-Álvarez, Miguel A. Vega-Rodríguez	Hybrid Multiobjective Artificial Bee Colony with Differential Evolution Applied to Motif Finding.	EvoBIO	2013	DBLP DOI BibTeX RDF
20	Sajid Hussain, Samuel Adeogun, Bright Dotu, Laurence T. Yang	Intelligent and Efficient Web-Based Middleware for Data Management in Motif Finding in Gene Regulation.	CSE	2013	DBLP DOI BibTeX RDF
20	Maria Federico, Mauro Leoncini, Manuela Montangero, Paolo Valente	Direct vs 2-Stage Approaches to Structured Motif Finding.	Algorithms Mol. Biol.	2012	DBLP DOI BibTeX RDF
20	Mostafa M. Abbas, Mohamed Abouelhoda, Hazem M. Bahig	A hybrid method for the exact planted (l, d) motif finding problem and its parallelization.	BMC Bioinform.	2012	DBLP DOI BibTeX RDF
20	Amin Zia, Alan M. Moses	Towards a theoretical understanding of false positives in DNA motif finding.	BMC Bioinform.	2012	DBLP DOI BibTeX RDF
20	Chengpeng Bi	Memetic algorithms for de novo motif-finding in biomedical sequences.	Artif. Intell. Medicine	2012	DBLP DOI BibTeX RDF
20	Thi Nhan Le, Tu Bao Ho	A Semi-Supervised Method for Discriminative Motif Finding and Its Application to Hepatitis C Virus Study.	ACIIDS (1)	2012	DBLP DOI BibTeX RDF
20	Sabine Pérès, François Vallée, Marie Beurton-Aimar, Jean-Pierre Mazat	ACoM: A classification method for elementary flux modes based on motif finding.	Biosyst.	2011	DBLP DOI BibTeX RDF
20	Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph	Discriminative Motif Finding for Predicting Protein Subcellular Localization.	IEEE ACM Trans. Comput. Biol. Bioinform.	2011	DBLP DOI BibTeX RDF
20	Hieu Dinh, Sanguthevar Rajasekaran, Vamsi Kundeti	PMS5: an efficient exact algorithm for the (l, d)-motif finding problem.	BMC Bioinform.	2011	DBLP DOI BibTeX RDF
20	Carl Kingsford, Elena Zaslavsky, Mona Singh 0001	A cost-aggregating integer linear program for motif finding.	J. Discrete Algorithms	2011	DBLP DOI BibTeX RDF
20	Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph	DECOD: fast and accurate discriminative DNA motif finding.	Bioinform.	2011	DBLP DOI BibTeX RDF
20	Xiaoyan Zhao, Sing-Hoi Sze	Motif Finding in DNA Sequences Based on Skipping Nonconserved Positions in Background Markov Chains.	J. Comput. Biol.	2011	DBLP DOI BibTeX RDF
20	Federico Zambelli, Giulio Pavesi	A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data.	CIBB	2011	DBLP DOI BibTeX RDF
20	Ke Mao, Jiawei Luo 0001	An immune network approach with directed information for motif finding.	ICNC	2011	DBLP DOI BibTeX RDF
20	Anjali Mohapatra, P. M. Mishra, S. Padhy	Planted (l, d) motif finding with allowable mismatches using kernel based approach.	ICCCS	2011	DBLP DOI BibTeX RDF
20	Pavel P. Kuksa, Vladimir Pavlovic 0001	Efficient motif finding algorithms for large-alphabet inputs.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
20	Sang Hyun Lee, Haris Vikalo, Sriram Vishwanath	Further results on message-passing algorithms for motif finding.	ICASSP	2010	DBLP DOI BibTeX RDF
20	Yazmín Magallanes-Velázquez, Iván Olmos, Mauricio Javier Osorio Galindo, Luis Oscar Peredo-Cholula, Christian Sarmiento-Vera	Motifs recognition in DNA sequences comparing the motif finding automaton algorithm against a traditional approach.	CONIELECOMP	2010	DBLP DOI BibTeX RDF
20	Salim Bouamama, Abdellah Boukerram, Amer F. Al-Badarneh	Motif Finding Using Ant Colony Optimization.	ANTS Conference	2010	DBLP DOI BibTeX RDF
20	Filippo Geraci, Marco Pellegrini 0001, M. Elena Renda	An Efficient Combinatorial Approach for Solving the DNA Motif Finding Problem.	ISDA	2009	DBLP DOI BibTeX RDF
20	Sang Hyun Lee, Haris Vikalo, Sriram Vishwanath	Message-passing for motif finding.	GENSiPS	2009	DBLP DOI BibTeX RDF
20	Shih-Yen Ku, Chih-Ying Wei, Yuh-Jyh Hu	Discovery of Structural Motifs in Metalloproteins Using Protein Structural Alphabets and 1D Motif-finding Methods.	BIOCOMP	2009	DBLP BibTeX RDF
20	Linbin Yu, Yun Xu	A Parallel Gibbs Sampling Algorithm for Motif Finding on GPU.	ISPA	2009	DBLP DOI BibTeX RDF	Moti, GPGPU, CUDA, Gibbs Sampling
20	Christina Boucher, Daniel G. Brown 0001	Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding.	BICoB	2009	DBLP DOI BibTeX RDF
20	Yong Chen, Guojun Li	An effective algorithm of motif finding problem.	Int. J. Bioinform. Res. Appl.	2008	DBLP DOI BibTeX RDF
20	Rahul Siddharthan	PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling.	PLoS Comput. Biol.	2008	DBLP DOI BibTeX RDF
20	Chen Chen, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig	GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences.	PRIB	2008	DBLP DOI BibTeX RDF
20	Modan K. Das, Ho-Kwok Dai	A survey of DNA motif finding algorithms.	BMC Bioinform.	2007	DBLP DOI BibTeX RDF
20	Chengpeng Bi	Seam: a Stochastic EM-Type Algorithm for Motif-Finding in Biopolymer Sequences.	J. Bioinform. Comput. Biol.	2007	DBLP DOI BibTeX RDF
20	Chengpeng Bi	A Genetic-Based EM Motif-Finding Algorithm for Biological Sequence Analysis.	CIBCB	2007	DBLP DOI BibTeX RDF
20	Elena Zaslavsky, Mona Singh 0001	A combinatorial optimization approach for diverse motif finding applications.	Algorithms Mol. Biol.	2006	DBLP DOI BibTeX RDF
20	Lawrence S. Hon, Ajay N. Jain	A deterministic motif finding algorithm with application to the human genome.	Bioinform.	2006	DBLP DOI BibTeX RDF
20	Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo	CMfinder - a covariance model based RNA motif finding algorithm.	Bioinform.	2006	DBLP DOI BibTeX RDF
20	Saurabh Sinha	On counting position weight matrix matches in a sequence, with application to discriminative motif finding.	ISMB (Supplement of Bioinformatics)	2006	DBLP DOI BibTeX RDF
20	Yan Qi 0003, Ping Ye, Joel S. Bader	Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality.	BMC Bioinform.	2005	DBLP DOI BibTeX RDF
20	Ben Wun, Jeremy Buhler, Patrick Crowley	Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor.	IEEE PACT	2005	DBLP DOI BibTeX RDF
20	Sündüz Keles, Mark J. van der Laan, Chris Vulpe	Regulatory motif finding by logic regression.	Bioinform.	2004	DBLP DOI BibTeX RDF
20	R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger	MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays.	Pacific Symposium on Biocomputing	2003	DBLP BibTeX RDF
20	Uri Keich, Pavel A. Pevzner	U Subtle motifs: defining the limits of motif finding algorithms.	Bioinform.	2002	DBLP DOI BibTeX RDF
15	Xiaolu Huang, Hesham H. Ali, Anguraj Sadanandam, Rakesh K. Singh	Protein Motif Searching Through Similar Enriched Parikh Vector Identification.	BIBE	2005	DBLP DOI BibTeX RDF
15	Bin Ma 0002, Kaizhong Zhang	On the Longest Common Rigid Subsequence Problem.	CPM	2005	DBLP DOI BibTeX RDF