Pan-cancer identification of the relationship of metabolism-related differentially expressed transcription regulation with non-differentially expressed target genes via a gated recurrent unit network
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Fengfeng Zhou | Lan Huang | Xingyuan Pan | Yueying Wang | Meiyu Duan | Yusi Fan | Ya Qiao | Yangyang Wang | Zhuyu Hu | Yanyue Ran | Xian Fu | Z. Hu
[1] J. Chai,et al. Conservative analysis of Synaptopodin‐2 intron sense‐overlapping lncRNA reveals its novel function in promoting muscle atrophy , 2022, Journal of cachexia, sarcopenia and muscle.
[2] Shaoping Shi,et al. Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking , 2021, Bioinform..
[3] J. Burnham,et al. TNF-inhibition in vasculitis management in adenosine deaminase 2 deficiency (DADA2). , 2021, The Journal of allergy and clinical immunology.
[4] Q. Kong,et al. A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression , 2021, BMC biology.
[5] T. Wada,et al. Sense-overlapping lncRNA as a decoy of translational repressor protein for dimorphic gene expression , 2021, PLoS genetics.
[6] L. Deng,et al. DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence , 2021, International journal of molecular sciences.
[7] K. Cornetta,et al. Autologous Ex Vivo Lentiviral Gene Therapy for Adenosine Deaminase Deficiency. , 2021, The New England journal of medicine.
[8] F. Westermann,et al. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma , 2021, Nature Genetics.
[9] B. A. Kotsias,et al. Functional relationship between CFTR and RAC3 expression for maintaining cancer cell stemness in human colorectal cancer , 2021, Cellular Oncology.
[10] Sagar,et al. Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection , 2021, Nature Immunology.
[11] Rui Zhang,et al. LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events , 2020, Briefings Bioinform..
[12] Brian Craft,et al. Visualizing and interpreting cancer genomics data via the Xena platform , 2020, Nature Biotechnology.
[13] Di Zhang,et al. Somatic synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma , 2020, BMC Medical Genomics.
[14] Xin Qi,et al. Decoding competing endogenous RNA networks for cancer biomarker discovery , 2020, Briefings Bioinform..
[15] Peng Huang,et al. Development and validation of hub genes for lymph node metastasis in patients with prostate cancer , 2020, Journal of cellular and molecular medicine.
[16] Simeon E. Spasov,et al. Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer’s Disease , 2019, Front. Genet..
[17] 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.
[18] Fu Zhang,et al. PC-3-Derived Exosomes Inhibit Osteoclast Differentiation by Downregulating miR-214 and Blocking NF-κB Signaling Pathway , 2019, BioMed research international.
[19] Yu-Dong Cai,et al. Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network , 2018, Computational and structural biotechnology journal.
[20] Wenqiang Shi,et al. Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants , 2018, Bioinform..
[21] De-Shuang Huang,et al. Recurrent Neural Network for Predicting Transcription Factor Binding Sites , 2018, Scientific Reports.
[22] Hui Hu,et al. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors , 2018, Nucleic Acids Res..
[23] Chandra L. Theesfeld,et al. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk , 2018, Nature Genetics.
[24] Abdullah M. Khamis,et al. A novel method for improved accuracy of transcription factor binding site prediction , 2018, Nucleic acids research.
[25] Lincoln Stein,et al. Reactome diagram viewer: data structures and strategies to boost performance , 2017, Bioinform..
[26] Julien Mairal,et al. Biological Sequence Modeling with Convolutional Kernel Networks , 2017, bioRxiv.
[27] Hyojin Kim,et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions , 2017, Nucleic Acids Res..
[28] Zhen Gao,et al. Computational modeling of in vivo and in vitro protein‐DNA interactions by multiple instance learning , 2017, Bioinform..
[29] Cory Y. McLean,et al. Sequential regulatory activity prediction across chromosomes with convolutional neural networks , 2017, bioRxiv.
[30] Wen Jin,et al. Predicting gene expression level by the transcription factor binding signals in human embryonic stem cells , 2016, Biosyst..
[31] Marek Kretowski,et al. The role of decision tree representation in regression problems - An evolutionary perspective , 2016, Appl. Soft Comput..
[32] Ilias Tagkopoulos,et al. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli , 2016, Nature Communications.
[33] M. Gerstein,et al. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals , 2016, Nature Communications.
[34] H. Xi,et al. Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap , 2015, BMC Genomics.
[35] Yoshua Bengio,et al. Learning Phrase Representations using RNN Encoder–Decoder for Statistical Machine Translation , 2014, EMNLP.
[36] Henning Hermjakob,et al. The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..
[37] Ellen T. Gelfand,et al. The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.
[38] R. Young,et al. Transcriptional Regulation and Its Misregulation in Disease , 2013, Cell.
[39] Kevin Y. Yip,et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data , 2012, Genome research.
[40] M. Gerstein,et al. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells , 2011, Nucleic acids research.
[41] D. Hanahan,et al. Hallmarks of Cancer: The Next Generation , 2011, Cell.
[42] Trevor Hastie,et al. Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.
[43] Qing Zhou,et al. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells , 2009, Proceedings of the National Academy of Sciences.
[44] Hong Yan,et al. An Improved Position Weight Matrix Method Based on an Entropy Measure for the Recognition of Prokaryotic Promoters , 2009, 2009 3rd International Conference on Bioinformatics and Biomedical Engineering.
[45] Mikael Bodén,et al. MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..
[46] R. Kageyama,et al. Regulation of retinal cell fate specification by multiple transcription factors , 2008, Brain Research.
[47] Georgia Chenevix-Trench,et al. BCoR-L1 variation and breast cancer , 2007, Breast Cancer Research.
[48] C. Lawrence,et al. The Gibbs Centroid Sampler , 2007, Nucleic Acids Res..
[49] D. Ernst,et al. Extremely randomized trees , 2006, Machine Learning.
[50] G. Stormo,et al. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites , 2005, Nucleic acids research.
[51] Yi Zhao,et al. NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..
[52] Michael A. Beer,et al. Predicting Gene Expression from Sequence , 2004, Cell.
[53] R. J. Roberts. PubMed Central: The GenBank of the published literature. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[54] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.
[55] Naixue Xiong,et al. An intelligent scheme for big data recovery in Internet of Things based on Multi-Attribute assistance and Extremely randomized trees , 2021, Inf. Sci..