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
Finding motifs in the twilight zone
Proceedings of the sixth annual international conference on Computational biology
Biological Sequence Data Mining
PKDD '01 Proceedings of the 5th European Conference on Principles of Data Mining and Knowledge Discovery
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
On the Parameterized Intractability of CLOSEST SUBSTRINGsize and Related Problems
STACS '02 Proceedings of the 19th Annual Symposium on Theoretical Aspects of Computer Science
Pattern discovery in sequences under a Markov assumption
Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Finding Higher Order Motifs under the Levenshtein Measure
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Cooperative Metaheuristics for Exploring Proteomic Data
Artificial Intelligence Review
On the complexity of finding common approximate substrings
Theoretical Computer Science
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
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
PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences
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)
Tight lower bounds for certain parameterized NP-hard problems
Information and Computation
Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences
Artificial Intelligence Review
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
Self-organizing neural networks to support the discovery of DNA-binding motifs
Neural Networks - 2006 Special issue: Advances in self-organizing maps--WSOM'05
Motif discovery by monotone scores
Discrete Applied Mathematics
An Exact Data Mining Method for Finding Center Strings and All Their Instances
IEEE Transactions on Knowledge and Data Engineering
A leader-based parallel cross entropy algorithm for MCP
Proceedings of the 9th annual conference companion on Genetic and evolutionary computation
Detecting time series motifs under uniform scaling
Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
DNA Motif Representation with Nucleotide Dependency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximating the maximum vertex/edge weighted clique using local search
Journal of Heuristics
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
An effective algorithm of motif finding problem
International Journal of Bioinformatics Research and Applications
Detection of subtle variations as consensus motifs
Theoretical Computer Science
MOGAMOD: Multi-objective genetic algorithm for motif discovery
Expert Systems with Applications: An International Journal
On the Structure of Small Motif Recognition Instances
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
An efficient algorithm for planted structured motif extraction
Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology
Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Swarm optimized organizing map (SWOM): A swarm intelligence basedoptimization of self-organizing map
Expert Systems with Applications: An International Journal
Efficient discovery of unusual patterns in time series
New Generation Computing
Clustering sequences by overlap
International Journal of Data Mining and Bioinformatics
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
An Efficient Fixed-Parameter Enumeration Algorithm for Weighted Edge Dominating Set
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Faster Algorithms for Sampling and Counting Biological Sequences
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Dynamic local search for the maximum clique problem
Journal of Artificial Intelligence Research
A simple algorithm for (l, d) motif search
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Tight lower bounds for certain parameterized NP-hard problems
Information and Computation
Learning Approximate Sequential Patterns for Classification
The Journal of Machine Learning Research
Efficient selection of unique and popular oligos for large EST databases
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Improved pattern-driven algorithms for motif finding in DNA sequences
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
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
Protein sequence motif discovery on distributed supercomputer
GPC'08 Proceedings of the 3rd international conference on Advances in grid and pervasive computing
A Max-SAT inference-based pre-processing for Max-clique
SAT'08 Proceedings of the 11th international conference on Theory and applications of satisfiability testing
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Efficient algorithms for model-based motif discovery from multiple sequences
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
Accelerating motif finding problem using grid computing with enhanced brute force
ICACT'10 Proceedings of the 12th international conference on Advanced communication technology
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
Motif finding using ant colony optimization
ANTS'10 Proceedings of the 7th international conference on Swarm intelligence
A Cluster Refinement Algorithm for Motif Discovery
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
VARUN: Discovering Extensible Motifs under Saturation Constraints
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Discovering almost any hidden motif from multiple sequences
ACM Transactions on Algorithms (TALG)
Generalised Sequence Signatures through symbolic clustering
International Journal of Data Mining and Bioinformatics
Why large CLOSEST STRING instances are easy to solve in practice
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
On the hardness of counting and sampling center strings
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
A frequent pattern mining method for finding planted (l, d)-motifs of unknown length
RSKT'10 Proceedings of the 5th international conference on Rough set and knowledge technology
Planted (l,d) motif finding with allowable mismatches using kernel based approach
Proceedings of the 2011 International Conference on Communication, Computing & Security
Probabilistic Analysis of a Motif Discovery Algorithm for Multiple Sequences
SIAM Journal on Discrete Mathematics
Cooperating local search for the maximum clique problem
Journal of Heuristics
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Unsupervised discovery of motifs under amplitude scaling and shifting in time series databases
MLDM'11 Proceedings of the 7th international conference on Machine learning and data mining in pattern recognition
The bounded search tree algorithm for the closest string problem has quadratic smoothed complexity
MFCS'11 Proceedings of the 36th international conference on Mathematical foundations of computer science
A cost-aggregating integer linear program for motif finding
Journal of Discrete Algorithms
Discovering consensus patterns in biological databases
VDMB'06 Proceedings of the First international conference on Data Mining and Bioinformatics
PAKDD'06 Proceedings of the 10th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining
New bounds for motif finding in strong instances
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Common substrings in random strings
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
A compact mathematical programming formulation for DNA motif finding
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Computational biology – the new frontier of computer science
IWDC'04 Proceedings of the 6th international conference on Distributed Computing
Identifying transcription factor binding sites based on a neural network
ISNN'06 Proceedings of the Third international conference on Advances in Neural Networks - Volume Part III
Structural alphabet motif discovery and a structural motif database
Computers in Biology and Medicine
A new algorithm for fast all-against-all substring matching
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Finding gapped motifs by a novel evolutionary algorithm
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Sharper upper and lower bounds for an approximation scheme for consensus-pattern
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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
On the effective enumerability of NP problems
IWPEC'06 Proceedings of the Second international conference on Parameterized and Exact Computation
Graphical approach to weak motif recognition in noisy data sets
PRIB'06 Proceedings of the 2006 international conference on Pattern Recognition in Bioinformatics
Space and time efficient algorithms for planted motif search
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Application of kernel method to reveal subtypes of TF binding motifs
RRG'04 Proceedings of the 2004 RECOMB international conference on Regulatory Genomics
Parameter landscape analysis for common motif discovery programs
RRG'04 Proceedings of the 2004 RECOMB international conference on Regulatory Genomics
RISOTTO: fast extraction of motifs with mismatches
LATIN'06 Proceedings of the 7th Latin American conference on Theoretical Informatics
MoDEL: an efficient strategy for ungapped local multiple alignment
Computational Biology and Chemistry
Optimizing genetic algorithm for motif discovery
Mathematical and Computer Modelling: An International Journal
Trie-based apriori motif discovery approach
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
A graph clustering approach to weak motif recognition
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Identification of distinguishing motifs
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
On the Hardness of Counting and Sampling Center Strings
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parameterized top-K algorithms
Theoretical Computer Science
An improved voting algorithm for planted (l,d) motif search
Information Sciences: an International Journal
Finding recurrent patterns from continuous sign language sentences for automated extraction of signs
The Journal of Machine Learning Research
Decomposing combinatorial auctions and set packing problems
Journal of the ACM (JACM)
On approximating string selection problems with outliers
Theoretical Computer Science
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