Using Deep Learning to Predict Transcription Factor Binding Sites Combining Raw DNA Sequence, Evolutionary Information and Epigenomic Data

[1]  De-Shuang Huang,et al.  Modeling in-vivo protein-DNA binding by combining multiple-instance learning with a hybrid deep neural network , 2019, Scientific Reports.

[2]  Klaudia Walter,et al.  Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2004, PLoS biology.

[3]  De-Shuang Huang,et al.  Recurrent Neural Network for Predicting Transcription Factor Binding Sites , 2018, Scientific Reports.

[4]  B. Frey,et al.  Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.

[5]  Li Shang,et al.  Hierarchical Attention Network for Predicting DNA-Protein Binding Sites , 2019, ICIC.

[6]  Zhen Cao,et al.  Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning , 2018, ISBRA.

[7]  R. Young,et al.  Transcriptional Regulation and Its Misregulation in Disease , 2013, Cell.

[8]  Dongwon Lee,et al.  kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets , 2013, Nucleic Acids Res..

[9]  Hong-Bo Zhang,et al.  LMMO: A Large Margin Approach for Refining Regulatory Motifs , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[10]  Li Shang,et al.  Motif Discovery via Convolutional Networks with K-mer Embedding , 2019, ICIC.

[11]  M. Bulyk,et al.  Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. , 2013, Cell reports.

[12]  De-Shuang Huang,et al.  ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[13]  G. Church,et al.  Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. , 2000, Genome research.

[14]  Hai-Cheng Yi,et al.  Prediction of Drug–Target Interactions From Multi-Molecular Network Based on Deep Walk Embedding Model , 2020, Frontiers in Bioengineering and Biotechnology.

[15]  Eric D Siggia,et al.  Identification of the binding sites of regulatory proteins in bacterial genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[16]  De-Shuang Huang,et al.  High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites , 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[17]  Alexander J. Stewart,et al.  Why Transcription Factor Binding Sites Are Ten Nucleotides Long , 2012, Genetics.

[18]  De-Shuang Huang,et al.  DCDE: An Efficient Deep Convolutional Divergence Encoding Method for Human Promoter Recognition , 2019, IEEE Transactions on NanoBioscience.

[19]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[20]  M. Nóbrega,et al.  Comparative genomics at the vertebrate extremes , 2004, Nature Reviews Genetics.

[21]  G. Stormo,et al.  Determining the specificity of protein–DNA interactions , 2010, Nature Reviews Genetics.

[22]  Hongbo Zhang,et al.  DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[23]  R. Mann,et al.  Quantitative modeling of transcription factor binding specificities using DNA shape , 2015, Proceedings of the National Academy of Sciences.

[24]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[25]  A. Philippakis,et al.  Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.

[26]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[27]  De-Shuang Huang,et al.  An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency. , 2017, Molecular bioSystems.

[28]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[29]  Jon D. McAuliffe,et al.  Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.

[30]  Atina G. Coté,et al.  Evaluation of methods for modeling transcription factor sequence specificity , 2013, Nature Biotechnology.