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1
July 2010
GECCO '10: Proceedings of the 12th annual conference companion on Genetic and evolutionary computation
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 2, Downloads (12 Months): 30, Downloads (Overall): 166
Full text available:
PDF
Keywords:
bioinformatics, computational biology
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
2
February 2016
SIGCSE '16: Proceedings of the 47th ACM Technical Symposium on Computing Science Education
Publisher: ACM
An ultimate goal of traditional textual criticism is the reconstruction of the archetype of a given work. By comparing differences and similarities among multiple versions of the work, the interrelations among existing and hypothetical ancestral versions can be naturally presented as a tree, in which a branch represents derivation of ...
Keywords:
stemmatics, phylogenetics, computational biology
CCS:
Computational biology
Keywords:
computational biology
3
August 2000
ACM SIGBIO Newsletter: Volume 20 Issue 2, Aug. 2000
Publisher: ACM
Bibliometrics:
Citation Count: 11
Downloads (6 Weeks): 2, Downloads (12 Months): 53, Downloads (Overall): 896
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The Biopython project was formed in August 1999 as a collaboration to collect and produce open source bioinformatics tools written in Python, an object-oriented scripting language. It is modeled on the highly successful Bioperl project, but has the goal of making libraries available for people doing computations in Python. The ...
Keywords:
Python, bioinformatics, computational biology
CCS:
Computational biology
Keywords:
computational biology
Title:
Biopython: Python tools for computational biology
Primary CCS:
Computational biology
Full Text:
Biopython: Python Tools for Computational Biology Brad Chapman University of Georgia Rm 162, Riverbend Research Lab ... problems, and describes plans for future development. Keywords Python, bioinformatics, computational biology 1. INTRODUCTION Development of software tools is one of the ...
4
July 2009
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 6 Issue 3, July 2009
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 0, Downloads (12 Months): 3, Downloads (Overall): 120
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Some genetic diseases in human beings are dominated by short sequences repeated consecutively called tandem repeats. Once a region containing tandem repeats is found, it is of great interest to study the history of creating the repeats. The computational problem of reconstructing the duplication history of tandem repeats has been ...
Keywords:
Computational biology, approximation algorithms.
CCS:
Computational biology
Keywords:
Computational biology, approximation algorithms.
References:
M. Tang, M.S. Waterman, and S. Yooseph, "Zinc Finger Gene Clusters and Tandem Gene Duplication," J. Computational Biology, vol. 9, pp. 429-446, 2002.
Full Text:
... ? for any constant ? > 0 but runs slower.Index Terms?Computational biology, , approximation algorithms. 1 INTRODUCTIONTHE genomes of many species are dominated ... of a tandem repeated region is a very importantproblem in computational biology [3], [5], [9]. A number ofpapers related to this problem ... v2; . . . ; vk appear438 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009. Z.-Z. Chen ...
... or how two nonleaves becomeunrelated in M.440 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009Lemma 2.5. Let ...
... we can define Mr the right root-marked442 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009multiroot semimodel obtained ...
... vertex in the witness block for the444 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009 x2; x3 -crossing in ...
... ? is a 0.75-separator of M. tu446 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009For example, if ...
... S is the string list of ?.448 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009We next detail ...
... 2.5and runs in O n9 n2m time.450 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009Unfortunately, it seems ...
... forMolecular Biology (ISMB ?99), pp. 44-53, 1999.452 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 6, NO. 3, JULY-SEPTEMBER 2009[2] Z.-Z. Chen, ... S. Yooseph, ?Zinc Finger GeneClusters and Tandem Gene Duplication,? J. Computational Biology, ,vol. 9, pp. 429-446, 2002.[10] L. Wang, T. Jiang, and ...
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January 1999
Journal of the ACM (JACM): Volume 46 Issue 1, Jan. 1999
Publisher: ACM
Bibliometrics:
Citation Count: 130
Downloads (6 Weeks): 10, Downloads (12 Months): 69, Downloads (Overall): 1,671
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Genomes frequently evolve by reversals &rgr;( i,j ) that transform a gene order &pgr; 1 … &pgr; i &pgr; i +1 … &pgr; j -1 &pgr; j … &pgr; n into &pgr; 1 … &pgr; i &pgr; j -1 … &pgr; i +1 &pgr; j … &pgr; n . Reversal ...
Keywords:
computational biology, genetics
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
Full Text:
... Sciences]: biology andgeneticsGeneral Terms: Algorithms, PerformanceAdditional Key Words and Phrases: Computational biology, , geneticsA preliminary version of this paper appeared in Proceedings ...
6
August 2011
BCB '11: Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 4, Downloads (12 Months): 9, Downloads (Overall): 74
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With the increase of the number of available prokaryotic genomes, studies focusing on the higher level evolutionary events, including the evolution of whole genomes, are now possible. Simulated datasets are essential components in both the development and evaluation stages for all evolutionary studies. In this paper, we implemented the first ...
Keywords:
evolution, bioinformatics, computational biology, genomics, simulation
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
References:
Yang, K. and J. C. Setubal. Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes, in ACM International Conference on Bioinformatics and Computational Biology. 2010. Niagara Falls, New York, U. S. A.
Full Text:
... and order of ancestral bacterial genomes??LQ?ACMInternational Conference on Bioinformatics and Computational Biology?
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March 2004
ACM SIGCSE Bulletin: Volume 36 Issue 1, March 2004
Publisher: ACM
Bibliometrics:
Citation Count: 2
Downloads (6 Weeks): 1, Downloads (12 Months): 9, Downloads (Overall): 407
Full text available:
PDF
Keywords:
interdisciplinary education, bioinformatics, computational biology, genomics
Also published in:
March 2004
SIGCSE '04: Proceedings of the 35th SIGCSE technical symposium on Computer science education
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
Full Text:
... Biology and genetics. General Terms: Human Factors, Standardization. Keywords: Bioinformatics, Computational Biology, , Genomics, Interdisciplinary Education 1. Debra Burhans There are a ...
8
October 2008
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 5 Issue 4, October 2008
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 6
Downloads (6 Weeks): 1, Downloads (12 Months): 2, Downloads (Overall): 100
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The gene-duplication problem is to infer a species supertree from gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact ...
Keywords:
Algorithms, Phylogenetics, Computational Biology, Gene Duplication, Supertrees
CCS:
Computational biology
Keywords:
Algorithms, Phylogenetics, Computational Biology, Gene Duplication, Supertrees
Primary CCS:
Computational biology
References:
B. Mirkin, I. Muchnik, and T.F. Smith, "A Biologically Consistent Model for Comparing Molecular Phylogenies," J. Computational Biology, vol. 2, no. 4, pp. 493-507, 1995.
L. Zhang, "On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies," J. Computational Biology, vol. 4, no. 2, pp. 177-187, 1997.
K. Chen, D. Durand, and M. Farach-Colton, "NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees," J. Computational Biology, vol. 7, no. 3/4, 2000.
Full Text:
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 5, NO. 4, OCTOBER-DECEMBER 2008. The authors ...
... that? G; T ? minT2TBRS? G; T :516 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 5, NO. 4, OCTOBER-DECEMBER 20082. A gene ...
... t butdS P 0 g f (Lemma 4.5).518 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 5, NO. 4, OCTOBER-DECEMBER 2008Lemma 4.1. If ...
... if we are moving out of subtree520 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 5, NO. 4, OCTOBER-DECEMBER 2008Fig. 5. Here, ...
... of P . In this case, when522 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 5, NO. 4, OCTOBER-DECEMBER 2008we enter the ...
... Zhang, ?On a Mirkin-Muchnik-Smith Conjecture for Compar-ing Molecular Phylogenies,? J. Computational Biology, , vol. 4, no. 2,pp. 177-187, 1997.[17] K. Chen, D. ... AProgram for Dating Gene Duplications and Optimizing GeneFamily Trees,? J. Computational Biology, , vol. 7, no. 3/4, 2000.[18] P. Bonizzoni, G.D. Vedova, ... candidate in the Department ofComputer Science, ISU. His research interestsinclude computational biology and phyloge-netics, graph theory, combinatorial optimization,approximation algorithms, and algorithms in ... of Computer Science, Iowa StateUniversity, Ames, USA. His research focuseson computational biology, , particularly on com-putational phylogenetics.. For more information on this ... topic,please visit our Digital Library at www.computer.org/publications/dlib.524 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY
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April 2014
HSCC '14: Proceedings of the 17th international conference on Hybrid systems: computation and control
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 4, Downloads (12 Months): 15, Downloads (Overall): 78
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Real-time control has been recently applied to drive actual intracellular processes with unprecedented accuracy. Here we introduce the motivations for the development of these approaches and then present a platform for the real-time control of gene expression in yeast cells. We conclude by surveying related works and discussing possible future ...
Keywords:
yeast, computational biology, gene expression, systems biology, synthetic biology
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
10
September 2015
BCB '15: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 8, Downloads (12 Months): 24, Downloads (Overall): 57
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Background. Next Generation Sequencing (NGS) data has been extensively exploited in the last decade to analyse genome variations and to understand the role of genome variations in complex diseases. Copy number variations (CNVs) are genomic structural variants estimated to account for about 1.2% of the total variation in humans. CNVs ...
Keywords:
computational biology, copy number variation, next generation sequencing
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
11
May 2011
ICS '11: Proceedings of the international conference on Supercomputing
Publisher: ACM
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 2, Downloads (12 Months): 18, Downloads (Overall): 148
Full text available:
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Interactions among proteins are essential to many biological functions in living cells but experimentally detected interactions represent only a small fraction of the real interaction network. Computational protein interaction prediction methods have become important to augment the experimental methods; in particular sequence based prediction methods that do not require additional ...
Keywords:
high throughput, protein interaction prediction, computational biology, massively parallel application
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
Full Text:
... Sciences andEngineering Research Council of Canada.General TermsParallel ComputingKeywordsMassively Parallel Application, Computational Biology, , Pro-tein Interaction Prediction, High Throughput.1. INTRODUCTION1.1 BackgroundInteractions among proteins ...
... WORKDue to the high computational complexity of many prob-lems in Computational Biology, , parallel systems have beendesigned for numerous bioinformatics tools (see ...
12
April 2003
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biology
Publisher: ACM
Bibliometrics:
Citation Count: 4
Downloads (6 Weeks): 1, Downloads (12 Months): 1, Downloads (Overall): 875
Full text available:
Pdf
In [13] we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae . Genome-wide comparative analysis allowed the identification of functionally important sequences, both coding and non-coding. In this companion paper we describe the mathematical ...
Keywords:
comparative genomics, computational biology, genome annotation, regulatory motif discovery
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
Full Text:
... and medical sciences]: Biology and Genetics General Terms: Algorithms. Keywords: Computational biology, , Comparative genomics, Genome annotation, Regulatory motif discovery. 1. INTRODUCTION ...
13
March 2008
ACM SIGMETRICS Performance Evaluation Review: Volume 35 Issue 4, March 2008
Publisher: ACM
Bibliometrics:
Citation Count: 11
Downloads (6 Weeks): 1, Downloads (12 Months): 5, Downloads (Overall): 354
Full text available:
Pdf
We introduce a scalable framework built upon the BlenX language and inspired by the Beta-binders process calculus to model, simulate and analyse biological systems. We show the features of the Beta Workbench framework on a running example based on the mitogen-activated kinase pathway. We also discuss an incremental modelling process ...
Keywords:
process calculi, computational biology, systems biology, modelling and simulation
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
References:
Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., and Kitano, H. 2002. The erato systems biology workbench: Enabling interaction and exchange between software tools for computational biology.
Ramsey, S., Orrell, D., and Bolouri, H. 2005. Dizzy: Stochastic simulation of large-scale genetic regulatory networks (supplementary material). J. Bioinformatics and Computational Biology 3, 2, 437--454.
14
May 2014
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 11 Issue 3, May/June 2014
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 1, Downloads (12 Months): 4, Downloads (Overall): 21
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Information theory has been used for quite some time in the area of computational biology. In this paper we present a pattern discovery method, named Fast Entropic Profiler, that is based on a local entropy function that captures the importance of a region with respect to the whole genome. The ...
Keywords:
local entropy, computational biology, information theory, pattern discovery
CCS:
Computational biology
Keywords:
computational biology
Abstract:
... been used for quite some time in the area of computational biology. . In this paper we present a pattern discovery method, ...
Primary CCS:
Computational biology
References:
A. Apostolico, M. Comin, and L. Parida, "Varun: Discovering Extensible Motifs Under Saturation Constraints," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 4, pp. 752-762, Oct.-Dec. 2010.
M. Comin and D. Verzotto, "The Irredundant Class Method for Remote Homology Detection of Protein Sequences," J. Computational Biology, vol. 18, no. 12, pp. 1819-1829, 2011.
Y. Gene and C. Burge, "Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals," J. Computional Biology, vol. 11, no. 23, pp. 377-394, 2004.
G. Menconi and R. Marangoni, "A Compression-Based Approach for Coding Sequences Identification. I. Application to Prokaryotic Genomes," J. Computational Biology, vol. 13, no. 8, pp. 1477-1488, 2006.
M.S. Waterman, An Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman Hall, 1995.
Full Text:
... been used for quite some time in the area of computational biology. . In this paper we present apattern discovery method, named ... and noncoding DNA. These are just a fewexamples of the computational biology applicationsinspired by information theory.The increasing availability of biological sequences, fromproteins ...
... Object Identifier below.Digital Object Identifier no. 10.1109/TCBB.2013.2297924500 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 3, MAY/JUNE 20141545-5963? 2013 IEEE. ...
... as implemented in the original entropic profiler.502 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 3, MAY/JUNE 2014there are at ...
... entropy v c v ? 1? ?XLk h v 14kfk:504 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 3, MAY/JUNE 2014The maximum potential ...
... position 14165 for various values of L.506 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 3, MAY/JUNE 2014L 12 ...
... and L. Parida, ?Varun: DiscoveringExtensible Motifs Under Saturation Constraints,? IEEE/ACMTrans. Computational Biology and Bioinformatics, vol. 7, no. 4,pp. 752-762, Oct.-Dec. 2010.[3] A. ... Times in Seconds for EP and FastEP508 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 3, MAY/JUNE 2014[7] M. Comin ... Modeling of ShortSequence Motifs with Applications to RNA Splicing Signals,?J. Computional Biology, , vol. 11, no. 23, pp. 377-394, 2004.[15] J. Hagenauer, ... Compression-Based Approachfor Coding Sequences Identification. I. Application to ProkaryoticGenomes,? J. Computational Biology, , vol. 13, no. 8, pp. 1477-1488,2006.[22] G. Menconi, G. ...
... no. 1, pp. 105-123, 2000.[31] M.S. Waterman, An Introduction to Computational Biology: : Maps,Sequences and Genomes. Chapman Hall, 1995.[32] J. Ziv and ...
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March 2002
SAC '02: Proceedings of the 2002 ACM symposium on Applied computing
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 1, Downloads (12 Months): 1, Downloads (Overall): 126
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This paper describes ongoing work on a project to simulate the behaviour of epidermal growth factor receptors. These are structures which can be found on the surface of cells in the body, which receive and process chemical signals concerned with cell growth. We describe the implementation of a program which ...
Keywords:
receptor biology, computational biology, individual-based models, modelling, simulation
CCS:
Computational biology
Keywords:
computational biology
Full Text:
... results from experiments. Keywords receptor biology, simulation, modelling, individual-based models, computational biology 1. B IOLOGICAL BACKGROUND. In order for the body to ...
16
April 2001
RECOMB '01: Proceedings of the fifth annual international conference on Computational biology
Publisher: ACM
Bibliometrics:
Citation Count: 6
Downloads (6 Weeks): 0, Downloads (12 Months): 6, Downloads (Overall): 312
Full text available:
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The problem of fast searching of a pattern that contains Classes of characters and Bounded size Gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site is associated with the CBG [ RK ...
Keywords:
PROSITE, information retrieval, bit-parallelism, computational biology, pattern matching
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
References:
E. Myers. Approximate matching of network expressions with spacers. Journal of Computational Biology, 3(1):33-51, 1996.]]
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January 1997
RECOMB '97: Proceedings of the first annual international conference on Computational molecular biology
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 2, Downloads (12 Months): 2, Downloads (Overall): 362
Full text available:
PDF
Keywords:
approximation algorithm, computational biology, evolutionary tree, multiple sequence alignment, phylogeny
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
References:
L. Wang and T. Jiang, On the complexity of multiple sequence alignment, Journal of Computational Biology 1, pp. 337-348, 1994.
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July 2012
GECCO '12: Proceedings of the 14th annual conference on Genetic and evolutionary computation
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 2, Downloads (12 Months): 9, Downloads (Overall): 103
Full text available:
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While development plays a critical role in the emergence of diversity, its mechanical and chemical actions are considered to be inextricably correlated with genetic control . Since in most extant species the complex growth from zygote to adult organism is orchestrated by a complex gene regulatory network (GRN), the prevalent ...
Keywords:
evolutionary development, morphogenesis, computational biology, tensegrity, indirect encoding
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
19
April 2001
RECOMB '01: Proceedings of the fifth annual international conference on Computational biology
Publisher: ACM
Bibliometrics:
Citation Count: 2
Downloads (6 Weeks): 2, Downloads (12 Months): 6, Downloads (Overall): 516
Full text available:
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One of the key open problems in large-scale DNA sequence assembly is the correct reconstruction of sequences that contain repeats. A long repeat can confound a sequence assembler into falsely overlaying fragments that sample its copies, effectively compressing out the repeat in the reconstructed sequence. We call the task of ...
Keywords:
disambiguating repeats, k-median problem, computational biology, shotgun sequencing
CCS:
Computational biology
Keywords:
computational biology
Primary CCS:
Computational biology
References:
Idury, R.M. and M.S. Waterman. "A new algorithm for DNA sequence assembly." Journal of Computational Biology 2:2, 291-306, 1995.
Myers, E.W. "Toward simplifying and accurately formulating fragment assembly." Journal of Computational Biology 2:2, 275-290, 1995.
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January 2016
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 13 Issue 1, January/February 2016
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 4, Downloads (12 Months): 20, Downloads (Overall): 21
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Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the ( l, d ) motif search problem of identifying one or more motifs of length l present in at least q of the n given ...
Keywords:
graph algorithms, hardware acceleration, finite automaton, computational biology, motif detection
CCS:
Computational biology
Keywords:
computational biology
Abstract:
... multiple DNA or protein sequences is an important problem in computational biology. . In this paper, we consider the (<i>l, d</i>) motif ...
Full Text:
... across multiple DNA or protein sequences is an importantproblem in computational biology. . In this paper, we consider the l; d motif search ... useful guide to solving problems using this new accelerator technology.Index Terms?Computational biology, , finite automaton, graph algorithms, hardware acceleration, motif detection 1 INTRODUCTIONLARGE ...
... Digital Object Identifier below.Digital Object Identifier no. 10.1109/TCBB.2015.2430313IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016 991545-5963? 2015 ...
... Example of mapping ?-transitions to the AP.100 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016are loaded onto ...
... STEs, and d start-of-data STEs and reporting STEs.102 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016u is connected ...
... to identify neighboring cliques of a node.104 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016Each term in ...
... from the j? r -length prefix of Ti.106 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016from layer j ...
... layer j ?, i.e., actual motif(s).108 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 2016Algorithm 5: Find ...
... 17 2,285 48.67 22.9254 0.3317 4.03950 2.3128110 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 13, NO. 1, JANUARY/FEBRUARY 20168 CONCLUSIONThe micron ...
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