Algorithms for phylogenetic footprinting
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Finding motifs using random projections
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Proceedings of the 2002 ACM symposium on Applied computing
Finding motifs in the twilight zone
Proceedings of the sixth annual international conference on Computational biology
Proceedings of the sixth annual international conference on Computational biology
A comparative analysis method for detecting binding sites in coding regions
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Biological Sequence Data Mining
PKDD '01 Proceedings of the 5th European Conference on Principles of Data Mining and Knowledge Discovery
Pattern discovery in sequences under a Markov assumption
Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining
Mining biomolecular data using background knowledge and artificial neural networks
Handbook of massive data sets
LOGOS: a modular Bayesian model for de novo motif detection
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Identifying Regulatory Signals in DNA-Sequences with a Non-statistical Approximation Approach
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Probabilistic discovery of time series motifs
Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Finding motifs for insufficient number of sequences with strong binding to transcription facto
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
A combined model and a varied Gibbs sampling algorithm used for motif discovery
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Particle Swarm Optimisation for Protein Motif Discovery
Genetic Programming and Evolvable Machines
Verbumculus and the discovery of unusual words
Journal of Computer Science and Technology - Special issue on bioinformatics
MISAE: A New Approach for Regulatory Motif Extraction
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
A Uniform Projection Method for Motif Discovery in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Combining Sequence and Time Series Expression Data to Learn Transcriptional Modules
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Neural Networks - 2005 Special issue: IJCNN 2005
Identification of weak motifs in multiple biological sequences using genetic algorithm
Proceedings of the 8th annual conference on Genetic and evolutionary computation
PDC: pattern discovery with confidence in DNA sequences
ACST'06 Proceedings of the 2nd IASTED international conference on Advances in computer science and technology
Motif discovery by monotone scores
Discrete Applied Mathematics
An upper bound on the hardness of exact matrix based motif discovery
Journal of Discrete Algorithms
DNA Motif Representation with Nucleotide Dependency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient composite pattern finding from monad patterns
International Journal of Bioinformatics Research and Applications
UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery
International Journal of Bioinformatics Research and Applications
An efficient motif discovery algorithm with unknown motif length and number of binding sites
International Journal of Data Mining and Bioinformatics
A graph approach to the threshold all-against-all substring matching problem
Journal of Experimental Algorithmics (JEA)
An effective algorithm of motif finding problem
International Journal of Bioinformatics Research and Applications
Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
MOGAMOD: Multi-objective genetic algorithm for motif discovery
Expert Systems with Applications: An International Journal
Efficient automatic exact motif discovery algorithms for biological sequences
Expert Systems with Applications: An International Journal
Learning structural SVMs with latent variables
ICML '09 Proceedings of the 26th Annual International Conference on Machine Learning
Efficient discovery of unusual patterns in time series
New Generation Computing
A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
MProfiler: A Profile-Based Method for DNA Motif Discovery
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Computational Biology and Chemistry
Detection of over-represented motifs corresponding to known TFBSs via motif clustering and matching
Computers & Mathematics with Applications
Moitf GibbsGA: Sampling Transcription Factor Binding Sites Coupled with PSFM Optimization by GA
ISICA '09 Proceedings of the 4th International Symposium on Advances in Computation and Intelligence
Improving motif refinement using hybrid expectation maximization and random projection
ISB '10 Proceedings of the International Symposium on Biocomputing
A Gibbs sampling algorithm for motif discovery using a linear mixed model
ISB '10 Proceedings of the International Symposium on Biocomputing
Efficient selection of unique and popular oligos for large EST databases
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Build a dictionary, learn a grammar, decipher stegoscripts, and discover genomic regulatory elements
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
Multiple sequence local alignment using monte carlo EM algorithm
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Comparison of simple encoding schemes in GA's for the motif finding problem: preliminary results
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
MotifMiner: a table driven greedy algorithm for DNA motif mining
ICIC'09 Proceedings of the Intelligent computing 5th international conference on Emerging intelligent computing technology and applications
A parallel combinatorial algorithm for subtle motifs
International Journal of Bioinformatics Research and Applications
Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood
Pattern Recognition Letters
Pattern Recognition Letters
Discovery of non-induced patterns from sequences
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
iGAPK: improved GAPK algorithm for regulatory DNA motif discovery
ICONIP'10 Proceedings of the 17th international conference on Neural information processing: models and applications - Volume Part II
SOMIX: motifs discovery in gene regulatory sequences using self-organizing maps
ICONIP'10 Proceedings of the 17th international conference on Neural information processing: models and applications - Volume Part II
Planted (l,d) motif finding with allowable mismatches using kernel based approach
Proceedings of the 2011 International Conference on Communication, Computing & Security
Theory and Use of the EM Algorithm
Foundations and Trends in Signal Processing
Predicting MHC-II Binding Affinity Using Multiple Instance Regression
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Finding motifs in DNA sequences applying a multiobjective artificial bee colony (MOABC) algorithm
EvoBIO'11 Proceedings of the 9th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
A method for mixed states texture segmentation with simultaneous parameter estimation
Pattern Recognition Letters
A cost-aggregating integer linear program for motif finding
Journal of Discrete Algorithms
Computational identification of regulatory factors involved in MicroRNA transcription
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
A mixture model based markov random field for discovering patterns in sequences
SETN'06 Proceedings of the 4th Helenic conference on Advances in Artificial Intelligence
A compact mathematical programming formulation for DNA motif finding
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
An upper bound on the hardness of exact matrix based motif discovery
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Flexible pattern discovery with (extended) disjunctive logic programming
ISMIS'05 Proceedings of the 15th international conference on Foundations of Intelligent Systems
Generalized planted (l,d)-motif problem with negative set
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Randomized algorithms for motif detection
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Parameter landscape analysis for common motif discovery programs
RRG'04 Proceedings of the 2004 RECOMB international conference on Regulatory Genomics
MoDEL: an efficient strategy for ungapped local multiple alignment
Computational Biology and Chemistry
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Memetic algorithms for de novo motif-finding in biomedical sequences
Artificial Intelligence in Medicine
Identification of distinguishing motifs
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Comparing multiobjective swarm intelligence metaheuristics for DNA motif discovery
Engineering Applications of Artificial Intelligence
Aligning discovered patterns from protein family sequences
PRIB'12 Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
An improved voting algorithm for planted (l,d) motif search
Information Sciences: an International Journal
Parallelizing a hybrid multiobjective differential evolution for identifying cis-regulatory elements
Proceedings of the 20th European MPI Users' Group Meeting
Finding recurrent patterns from continuous sign language sentences for automated extraction of signs
The Journal of Machine Learning Research
Journal of Global Optimization
A parallel cooperative team of multiobjective evolutionary algorithms for motif discovery
The Journal of Supercomputing
Hi-index | 0.00 |
The MEME algorithm extends the expectation maximization (EM) algorithm for identifying motifs in unaligned biopolymer sequences. The aim of MEME is to discover new motifs in a set of biopolymer sequences where little or nothing is known in advance about any motifs that may be present. MEME innovations expand the range of problems which can be solved using EM and increase the chance of finding good solutions. First, subsequences which actually occur in the biopolymer sequences are used as starting points for the EM algorithm to increase the probability of finding globally optimal motifs. Second, the assumption that each sequence contains exactly one occurrence of the shared motif is removed. This allows multiple appearances of a motif to occur in any sequence and permits the algorithm to ignore sequences with no appearance of the shared motif, increasing its resistance to noisy data. Third, a method for probabilistically erasing shared motifs after they are found is incorporated so that several distinct motifs can be found in the same set of sequences, both when different motifs appear in different sequences and when a single sequence may contain multiple motifs. Experiments show that MEME can discover both the CRP and LexA binding sites from a set of sequences which contain one or both sites, and that MEME can discover both the −10 and −35 promoter regions in a set of E. coli sequences.