Cargando…

Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models

Messenger RNA sequences possess specific nucleotide patterns distinguishing them from non-coding genomic sequences. In this study, we explore the utilization of modified Markov models to analyze sequences up to 44 bp, far beyond the 8-bp limit of conventional Markov models, for exon/intron discrimin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shepard, Samuel S., McSweeny, Andrew, Serpen, Gursel, Fedorov, Alexei
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2012
Materias:	Computational Biology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367190/ https://www.ncbi.nlm.nih.gov/pubmed/22344692 http://dx.doi.org/10.1093/nar/gks154

Ejemplares similares

Critical association of ncRNA with introns
por: Rearick, David, et al.
Publicado: (2011)

Genome Evolution by Matrix Algorithms: Cellular Automata Approach to Population Genetics
por: Qiu, Shuhao, et al.
Publicado: (2014)

Evolution of genomic sequence inhomogeneity at mid-range scales
por: Prakash, Ashwin, et al.
Publicado: (2009)

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures
por: Bechtel, Jason M, et al.
Publicado: (2008)

Mid-Range Inhomogeneity of Eukaryotic Genomes
por: Fedorova, Larisa, et al.
Publicado: (2011)

MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection
por: Wang, Zhenyi, et al.
Publicado: (2021)

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
por: Siebert, Matthias, et al.
Publicado: (2016)

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison
por: Kazemian, Majid, et al.
Publicado: (2011)

Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base
por: Wang, Shu-dong, et al.
Publicado: (2022)

Extracting binary signals from microarray time-course data
por: Sahoo, Debashis, et al.
Publicado: (2007)

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
por: Pei, Jimin, et al.
Publicado: (2006)

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models
por: Maaskola, Jonas, et al.
Publicado: (2014)

Markov processes for stochastic modeling
por: Ibe, Oliver C
Publicado: (2013)

The Binary Cascade
por: Folger, G, et al.
Publicado: (2005)

One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses
por: Narlikar, Leelavati, et al.
Publicado: (2013)

Markov logic: an interface layer for artificial intelligence
por: Domingos, Pedro, et al.
Publicado: (2009)

Performance Modeling of Communication Networks with Markov Chains
por: Mo, Jeonghoon
Publicado: (2010)

Binary analysis cookbook: actionable recipes for disassembling and analyzing binaries for security risks
por: Born, Michael
Publicado: (2019)

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
por: Colella, Stefano, et al.
Publicado: (2007)

Learning Linux binary analysis: uncover the secrets of Linux binary analysis with this handy guide
por: O'Neill, Ryan
Publicado: (2016)

Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors
por: Nandi, Soumyadeep, et al.
Publicado: (2013)

Hacking: the art of exploitation
por: Erickson, Jon
Publicado: (2003)

Hacking: the art of exploitation
por: Erickson, Jon
Publicado: (2004)

Hacking: the art of exploitation
por: Erickson, Jon
Publicado: (2008)

Digital circuits for binary arithmetic
por: Oberman, Roelof Maarten Marie
Publicado: (1979)

Practical binary analysis: build your own Linux tools for binary instrumentation, analysis, and disassembly
por: Andriesse, Dennis
Publicado: (2019)

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
por: Li, Ao, et al.
Publicado: (2011)

Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference
por: Gamerman, Dani, et al.
Publicado: (2006)

Algorithms for random generation and counting: a Markov chain approach
por: Sinclair, Alistair
Publicado: (1993)

Association testing for binary trees—A Markov branching process approach
por: Wu, Xiaowei, et al.
Publicado: (2022)

Bayesian Analysis of First-Order Markov Models for Autocorrelated Binary Responses
por: Lee, Dasom, et al.
Publicado: (2022)

Functional Consequences of Poor Binaural Hearing in Development: Evidence From Children With Unilateral Hearing Loss and Children Receiving Bilateral Cochlear Implants
por: McSweeny, Claire, et al.
Publicado: (2021)

Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
por: Bergh, Cathrine, et al.
Publicado: (2021)

Learning from the unknown: exploring the range of bacterial functionality
por: Mahlich, Yannick, et al.
Publicado: (2023)

Scalable Bayesian Inference for Coupled Hidden Markov and Semi-Markov Models
por: Touloupou, Panayiota, et al.
Publicado: (2019)

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions
por: Huang, Yiran, et al.
Publicado: (2016)

Exploiting the power of group differences: using patterns to solve data analysis problems
por: Dong, Guozhu, et al.
Publicado: (2019)

Dynamic Binary Modification: Tools, Techniques and Applications
por: Hazelwood, Kim
Publicado: (2011)

Linking BASIC variables to binary data world
por: Nguyen-Ngoc, Hoan
Publicado: (1981)

Network attacks and exploitation: a framework
por: Monte, Matthew
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_lndkef6c344so1nuhjtl0ki9n3