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522 results on '"Pan, Zhicheng"'

13. Assessing the Condition of Copper Conductors Using Deep Learning

Author

Pan, Zhicheng, Wilson, David, Stommel, Martin, Castellanos, Alex, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Yan, Wei Qi, editor, Nguyen, Minh, editor, and Stommel, Martin, editor

Published
2023
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22. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring

Author

Yeom, Kyu-Hyeon, Pan, Zhicheng, Lin, Chia-Ho, Lim, Han Young, Xiao, Wen, Xing, Yi, and Black, Douglas L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Neurosciences, Stem Cell Research, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Cell Nucleus, Genes, Developmental, Introns, Mice, RNA Precursors, RNA Splicing, Medical and Health Sciences, Bioinformatics
Abstract

Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 (Gabbr1) are highly expressed in mESCs but are absent from the cytoplasm. Instead, incompletely spliced Gabbr1 RNA remains sequestered on chromatin, where it is bound by PTBP1, similar to certain long noncoding RNAs. Upon neuronal differentiation, Gabbr1 RNA becomes fully processed and exported for translation. Thus, splicing repression and chromatin anchoring of RNA combine to allow posttranscriptional regulation of Gabbr1 over development. For this and other genes, polyadenylated RNA abundance does not indicate functional gene expression. Our data sets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.

Published
2021

34. Misty: Microservice-Based Streaming Trajectory Similarity Search

Author

Tao, Jiachun, Pan, Zhicheng, Fang, Junhua, Chao, Pingfu, Zhao, Pengpeng, Xu, Jiajie, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Troya, Javier, editor, Medjahed, Brahim, editor, Piattini, Mario, editor, Yao, Lina, editor, Fernández, Pablo, editor, and Ruiz-Cortés, Antonio, editor

Published
2022
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35. A Learning-Based Approach for Multi-scenario Trajectory Similarity Search

Author

Feng, Chunhui, Pan, Zhicheng, Fang, Junhua, Chao, Pingfu, Liu, An, Zhao, Lei, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Chbeir, Richard, editor, Huang, Helen, editor, Silvestri, Fabrizio, editor, Manolopoulos, Yannis, editor, and Zhang, Yanchun, editor

Published
2022
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36. Lunatory: A Real-Time Distributed Trajectory Clustering Framework for Web Big Data

Author

Wu, Yang, Pan, Zhicheng, Chao, Pingfu, Fang, Junhua, Chen, Wei, Zhao, Lei, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Di Noia, Tommaso, editor, Ko, In-Young, editor, Schedl, Markus, editor, and Ardito, Carmelo, editor

Published
2022
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46. Deep-learning augmented RNA-seq analysis of transcript splicing

Author

Zhang, Zijun, Pan, Zhicheng, Ying, Yi, Xie, Zhijie, Adhikari, Samir, Phillips, John, Carstens, Russ P, Black, Douglas L, Wu, Yingnian, and Xing, Yi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Algorithms, Alternative Splicing, Bayes Theorem, Deep Learning, Epigenomics, Exons, Gene Expression Profiling, Gene Expression Regulation, Hep G2 Cells, High-Throughput Nucleotide Sequencing, Humans, K562 Cells, Models, Statistical, RNA, RNA Splicing, Reproducibility of Results, Sequence Analysis, RNA, Signal Processing, Computer-Assisted, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions with empirical RNA-seq evidence to infer differential alternative splicing between biological samples. DARTS leverages public RNA-seq big data to provide a knowledge base of splicing regulation via deep learning, thereby helping researchers better characterize alternative splicing using RNA-seq datasets even with modest coverage.

Published
2019

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