**sequences**- Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of bio-resources such as knockout mutants, wild accessions and advanced breeding populations, there is a rising burden for gene functional annotation. (jove.com)
- Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. (wikipedia.org)
- At the core of HTM are learning algorithms that can store, learn, infer and recall high-order sequences. (wikipedia.org)
- There are two core components- a spatial pooling algorithm that creates sparse representations and a sequence memory algorithm that learns to represent and predict complex sequences. (wikipedia.org)
- Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. (wikipedia.org)
- In computational phylogenetics, tree alignment is the problem of producing a multiple sequence alignment, which can be used to analyse a set of sequences with evolutionary relationship using a fixed tree. (wikipedia.org)

**parallel**- CALL FOR PAPERS* *3rd International Workshop on* *Biological **Knowledge Discovery and Data Mining** **(BIOKDD'12)* Held in parallel with *23rd International Conference on Database and * *Expert Systems Applications **(**DEXA'12**)* www.dexa.org Vienna, Austria *September 3 - 7, 2012* With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. (bio.net)
- His main interests are genetic algorithms and genetic programming, including theoretical issues (parallel GA/GP) and application issues (design, layout, scheduling, etc. (msu.edu)
- Landau's research interests focus on string algorithms, data structures, computational biology, and parallel computation. (wikipedia.org)
- However, all the cost values can be computed in parallel, and the algorithm can be adapted to perform the minimum function in phases to eliminate dependencies. (wikipedia.org)
- He is best known for his research contributions in parallel algorithms and applications, interdisciplinary research in bioinformatics and computational biology, and particularly the intersection of these two fields. (wikipedia.org)
- Aluru's research focus has centered around contributions to parallel algorithms and bioinformatics, particularly genomics. (wikipedia.org)
- He pioneered the development of parallel methods in computational biology, and development of algorithms and software for high-throughput DNA sequencing analysis and its applications. (wikipedia.org)

**bioinformatics**- He has served on numerous program committees for international conferences, most recently, International Conference on Language and Automata Theory and Applications (LATA), International Symposium on String Processing and Information Retrieval (SPIRE), International Symposium on Algorithms and Computation (ISAAC), Annual Symposium on Combinatorial Pattern Matching (CPM), Workshop on Algorithms in Bioinformatics (WABI), International Workshop on Combinatorial Algorithms (IWOCA), and Brazilian Symposium on Bioinformatics (BSB). (wikipedia.org)
- Boguski's interest in computational biology started in graduate school in the early 1980s (more than ten years before the term bioinformatics first appeared in the literature). (wikipedia.org)
- His main areas of research are high performance computing, data science, bioinformatics and systems biology, combinatorial methods in scientific computing, and string algorithms. (wikipedia.org)
- Therefore, to design a rational and efficient sequence alignment algorithm becomes a very important branch of research in the field of bioinformatics. (wikipedia.org)

**2001**- the Distinguished Service Prize, ACM Special Interest Group on Algorithms and Computation Theory, 2001. (wikipedia.org)

**1995**- Algorithms for constructing a GST include Ukkonen's algorithm (1995) and McCreight's algorithm (1976). (wikipedia.org)

**Strings**- CS 5343 Algorithm Analysis & Data Structures (3 semester hours) Formal specifications and representation of lists, arrays, trees, graphs, multilinked structures, strings and recursive pattern structures. (utdallas.edu)
- In computer science, the Wagner-Fischer algorithm is a dynamic programming algorithm that computes the edit distance between two strings of characters. (wikipedia.org)

**Suffix Arrays**- In this context, some of his group's work led to the development of fundamental string algorithms, particularly for constructing suffix arrays and algorithms for approximate sequence matching. (wikipedia.org)

**Alignments**- In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. (wikipedia.org)

**combinatorial methods**- Original papers are solicited that describe research on combinatorial methods for problems arising from the following areas (nonexhaustive) of molecular biology: -- DNA sequencing -- DNA mapping -- recognition of genes and regulatory elements -- RNA/protein structure prediction -- molecular evolution -- combinatorial libraries and drug design -- bio-sequence analysis and comparison -- computing with biomolecules. (bio.net)

**data**- Discussions focused on computing research challenges in data center efficiency and sustainability as well as computational issues related to reducing our carbon footprint. (microsoft.com)
- When hits are evaluated after a search, global positions are mapped into documents and local positions with some algorithm and/or data structure, such as a binary search in the starting/ending positions of the documents. (wikipedia.org)
- An alternate representation is a suffix array, which is considered to require less virtual memory and supports data compression such as the BWT algorithm. (wikipedia.org)
- This algorithm parallelizes poorly, due to a large number of data dependencies. (wikipedia.org)
- Srinivas Aluru is a professor in the School of Computational Science and Engineering at Georgia Institute of Technology, and co-Executive Director for the Georgia Tech Interdisciplinary Research Institute in Data Engineering and Science. (wikipedia.org)

**approaches**- Computational approaches provide a powerful means for addressing previously unsolvable problems. (microsoft.com)
- the relevant biological and computational concepts are presented along with the advantages and limitations of individual approaches. (springer.com)

**molecular**- SM] J. Setubal and J. Meidanis, Introduction to Computational Molecular Biology , PWS Publishing Co., 1997, 296 pages. (univ-mlv.fr)
- SECOND CALL FOR PAPERS ====================== Journal of Combinatorial Optimization Special Issue on Computational Molecular Biology Guest Editors: Ying Xu, Satoru Miyano, Tom Head. (bio.net)
- The past ten years have witnessed the rapid development of a new discipline, computational molecular biology. (bio.net)
- The partnership between mathematics, in particular combinatorial optimization and algorithms, and molecular biology has greatly enriched both fields, leading to new ways of thinking and greater challenges to meet. (bio.net)
- The scope of this Special Issue includes all aspects of combinatorial optimization and algorithms in computational molecular biology. (bio.net)
- While in school, he worked as a research assistant for the Laboratory of Molecular Biology, National Cancer Institute, Baltimore Cancer Research Center from 1974-1978. (wikipedia.org)

**genetic**- William F. Punch is director of the MSU High Performance Computing Center and co-director of the Genetic Algorithms Research and Applications Group or GARAGe. (msu.edu)

**Sequence Alignment**- The footprints of Landau's research can be found in almost every subarea of string algorithms, including his foundational work on dynamic programming algorithms for the edit distance problem, his numerous papers on modeling digitized images and 2D matching, incremental sequence alignment, and recently, his work on jumbled pattern matching and compressed text algorithms. (wikipedia.org)

**Wagner**- The Wagner-Fischer algorithm has a history of multiple invention. (wikipedia.org)
- Early algorithms for on-line approximate matching were suggested by Wagner and Fisher and by Sellers. (wikipedia.org)
- Sellers' algorithm searches approximately for a substring in a text while the algorithm of Wagner and Fisher calculates Levenshtein distance, being appropriate for dictionary fuzzy search only. (wikipedia.org)

**statistical**- Recorded Future's linguistic and statistical algorithms extract time-related information and through temporal reasoning we structure the unstructured. (chalmers.se)
- The methods of identification of tribes relied heavily on algorithms and techniques from statistical physics, computational biology and network science. (wikipedia.org)

**research**- Stein's research interests include the design and analysis of algorithms, combinatorial optimization, operations research, network algorithms, scheduling, algorithm engineering and computational biology. (wikipedia.org)
- Stein has published many influential papers in the leading conferences and journals in his fields of research, and has occupied a variety of editorial positions including in the journals ACM Transactions on Algorithms, Mathematical Programming, Journal of Algorithms, SIAM Journal on Discrete Mathematics and Operations Research Letters. (wikipedia.org)

**displaystyle**- i]} else L[i,j] := 0 return ret This algorithm runs in O ( n r ) {\displaystyle O(nr)} time. (wikipedia.org)

**analysis**- Analysis of associated algorithms. (utdallas.edu)

**textbooks**- He is also the co-author of two textbooks: Introduction to Algorithms, with T. Cormen, C. Leiserson and R. Rivest, which is currently the best-selling textbook in algorithms and has been translated into 8 languages. (wikipedia.org)

**approximate**- Traditionally, approximate string matching algorithms are classified into two categories: on-line and off-line. (wikipedia.org)

**Techniques**- He was instrumental in the application of pattern matching techniques to the area of computational biology, working on problems in several diverse areas such as DNA and RNA comparison, clustering, haplotype inference, protein secondary structure prediction, and tandem repeats. (wikipedia.org)

**Computer Science**- Gad Menahem Landau (born 1954) is an Israeli computer scientist noted for his contributions to combinatorial pattern matching and string algorithms and is the founding department chair of the Computer Science Department at the University of Haifa. (wikipedia.org)

**problems**- Approximation algorithms for multicommodity flow and shop scheduling problems. (wikipedia.org)
- Both algorithms are based on dynamic programming but solve different problems. (wikipedia.org)

**Machine Learning**- Some mathematical maturity is expected, and a basic course in linear algebra and machine learning (equivalend to TDA 231 Algorithms for Machine Learning & Inference or FFR135 Artificial Neural Networks ) are required before taking this course. (chalmers.se)

**edit distance**- T[yis a substring of T with the minimal edit distance to the pattern P. Computing the E(x, y) array takes O(mn) time with the dynamic programming algorithm, while the backwards-working phase takes O(n + m) time. (wikipedia.org)
- Essentially, tree alignment is an algorithm for optimizing phylogenetic tree by calculating the edit distance to achieve the minimum value. (wikipedia.org)

**development**- Boguski's subsequent work in computational biology has, over the years, involved algorithm development (e.g. (wikipedia.org)

**include**- Possible modifications to this algorithm include: We can adapt the algorithm to use less space, O(m) instead of O(mn), since it only requires that the previous row and current row be stored at any one time. (wikipedia.org)

**Introduction**- Introduction to Algorithms (second ed. (wikipedia.org)

**text**- With on-line algorithms the pattern can be processed before searching but the text cannot. (wikipedia.org)

**Journal**- He serves on the editorial board of Journal of Discrete Algorithms, and served as a guest editor for TCS and Discrete Applied Mathematics. (wikipedia.org)

**Georgia Institute**- In 2013, he shifted to the School of Computational Science and Engineering at Georgia Institute of Technology. (wikipedia.org)

**time**- In this way, the algorithm can be run in O(kl) time, where l is the length of the shortest string. (wikipedia.org)
- However, this algorithm would have the running time O(n3 m). (wikipedia.org)
- Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. (wikipedia.org)

**different**- The second generation of HTM learning algorithms was drastically different from Zeta 1. (wikipedia.org)

**School**- Boguski earned his M.D., Ph.D. from Washington University School of Medicine and Division of Biology and Biomedical Sciences. (wikipedia.org)

**uses**- Tree alignment problem is a NP-hard problem when we restrict its scoring mode and alphabet size, and it can be found an algorithm, which uses to find the optimized solution. (wikipedia.org)

**index**- Search engine index merging is similar in concept to the SQL Merge command and other merge algorithms. (wikipedia.org)

**several**- There have been several generations of HTM algorithms. (wikipedia.org)

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