Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
出版年份 2016 全文链接
标题
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
作者
关键词
-
出版物
NUCLEIC ACIDS RESEARCH
Volume 44, Issue 13, Pages 6055-6069
出版商
Oxford University Press (OUP)
发表日期
2016-06-11
DOI
10.1093/nar/gkw521
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Combinatorial Cis -regulation in Saccharomyces Species
- (2016) Aaron T. Spivak et al. G3-Genes Genomes Genetics
- Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness
- (2015) Justin Crocker et al. CELL
- Unraveling determinants of transcription factor binding outside the core binding site
- (2015) Michal Levo et al. GENOME RESEARCH
- DNA-dependent formation of transcription factor pairs alters their binding specificity
- (2015) Arttu Jolma et al. NATURE
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon
- (2015) Hamed S Najafabadi et al. NATURE BIOTECHNOLOGY
- Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
- (2015) Babak Alipanahi et al. NATURE BIOTECHNOLOGY
- Specificity and nonspecificity in RNA–protein interactions
- (2015) Eckhard Jankowsky et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Varying levels of complexity in transcription factor binding motifs
- (2015) Jens Keilwagen et al. NUCLEIC ACIDS RESEARCH
- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
- (2015) Ivan V. Kulakovskiy et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
- (2015) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- Quantitative modeling of transcription factor binding specificities using DNA shape
- (2015) Tianyin Zhou et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data
- (2014) Victor G Levitsky et al. BMC GENOMICS
- High-Resolution Specificity from DNA Sequencing Highlights Alternative Modes of Lac Repressor Binding
- (2014) Z. Zuo et al. GENETICS
- Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition
- (2014) Carlo Baejen et al. MOLECULAR CELL
- Diversity and dynamics of the Drosophila transcriptome
- (2014) James B. Brown et al. NATURE
- CTCF: an architectural protein bridging genome topology and function
- (2014) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models
- (2014) Jonas Maaskola et al. NUCLEIC ACIDS RESEARCH
- A pause sequence enriched at translation start sites drives transcription dynamics in vivo
- (2014) M. H. Larson et al. SCIENCE
- Stability selection for regression-based models of transcription factor-DNA binding specificity
- (2013) F. Mordelet et al. BIOINFORMATICS
- DNA-Binding Specificities of Human Transcription Factors
- (2013) Arttu Jolma et al. CELL
- Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis
- (2013) Daniel Schulz et al. CELL
- Extensive transcriptional heterogeneity revealed by isoform profiling
- (2013) Vicent Pelechano et al. NATURE
- Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
- (2013) Silvi Rouskin et al. NATURE
- Evaluation of methods for modeling transcription factor sequence specificity
- (2013) Matthew T Weirauch et al. NATURE BIOTECHNOLOGY
- TherMos: Estimating protein–DNA binding energies from in vivo binding profiles
- (2013) Wenjie Sun et al. NUCLEIC ACIDS RESEARCH
- Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1
- (2013) J. M. Edwards et al. NUCLEIC ACIDS RESEARCH
- Unravelling the hidden DNA structural/physical code provides novel insights on promoter location
- (2013) Elisa Durán et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
- (2013) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
- (2013) Hirotaka Nakahashi et al. Cell Reports
- Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape
- (2013) Raluca Gordân et al. Cell Reports
- The Next Generation of Transcription Factor Binding Site Prediction
- (2013) Anthony Mathelier et al. PLoS Computational Biology
- FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES
- (2013) IVAN KULAKOVSKIY et al. Journal of Bioinformatics and Computational Biology
- Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
- (2012) Yue Zhao et al. GENETICS
- P-value-based regulatory motif discovery using positional weight matrices
- (2012) H. Hartmann et al. GENOME RESEARCH
- Sequence and chromatin determinants of cell-type-specific transcription factor binding
- (2012) A. Arvey et al. GENOME RESEARCH
- SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates
- (2012) Mikhail Pachkov et al. NUCLEIC ACIDS RESEARCH
- Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses
- (2012) P. M. Fordyce et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Quantitative analysis demonstrates most transcription factors require only simple models of specificity
- (2011) Yue Zhao et al. NATURE BIOTECHNOLOGY
- Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
- (2011) Tyler J. Creamer et al. PLoS Genetics
- Signals for pre-mRNA cleavage and polyadenylation
- (2011) Bin Tian et al. Wiley Interdisciplinary Reviews-RNA
- Origins of Specificity in Protein-DNA Recognition
- (2010) Remo Rohs et al. Annual Review of Biochemistry
- Structural Basis of Alternative DNA Recognition by Maf Transcription Factors
- (2009) H. Kurokawa et al. MOLECULAR AND CELLULAR BIOLOGY
- The role of DNA shape in protein–DNA recognition
- (2009) Remo Rohs et al. NATURE
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- Diversity and Complexity in DNA Recognition by Transcription Factors
- (2009) G. Badis et al. SCIENCE
- DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity
- (2009) S. H. Meijsing et al. SCIENCE
- Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
- (2009) Elizabeth A Rach et al. GENOME BIOLOGY
- Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
- (2008) Xi Chen et al. CELL
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