Sheng Zhong

Department of Bioengineering, University of California San Diego

Affiliated withUniversity of California San Diego

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title	2017
Publication title Cited by 6	2022

Other Publications

Article	Year
Enabling interspecies epigenomic comparison with CEpBrowser. Bioinformatics (Oxford, England)\| PubMed ID: 23543396	2013
Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS computational biology\| PubMed ID: 24339764	2013
From genomes to societies: a holistic view of determinants of human health. Current opinion in biotechnology\| PubMed ID: 24686286	2014
Comparative epigenomics: defining and utilizing epigenomic variations across species, time-course, and individuals. Wiley interdisciplinary reviews. Systems biology and medicine\| PubMed ID: 25044241	2014
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome research\| PubMed ID: 25096407	2014
P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Molecular cell\| PubMed ID: 26365380	2015
GeNemo: a search engine for web-based functional genomic data. Nucleic acids research\| PubMed ID: 27098038	2016
Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC evolutionary biology\| PubMed ID: 28335721	2017
SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Cell reports\| PubMed ID: 28355564	2017
The 4D nucleome project. Nature\| PubMed ID: 28905911	2017
Trends in Cannabis Use Disorder among Pregnant Women in the U.S., 1993-2014. Journal of general internal medicine\| PubMed ID: 29030807	2018
GIVE: portable genome browsers for personal websites. Genome biology\| PubMed ID: 30016975	2018
RNA, Action through Interactions. Trends in genetics : TIG\| PubMed ID: 30177410	2018
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. iScience\| PubMed ID: 30240742	2018
Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience\| PubMed ID: 30267678
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Genomics, proteomics & bioinformatics\| PubMed ID: 30553884	2018
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. PLoS computational biology\| PubMed ID: 30586383	2018
EpiAlignment: alignment with both DNA sequence and epigenomic data. Nucleic acids research\| PubMed ID: 31114924	2019
Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 31481608	2019
Reply to Hartl and Gao: Lack of between-batch difference in the distributions of measured extracellular RNA levels. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 31964851
Reply to Verwilt et al.: Experimental evidence against DNA contamination in SILVER-seq. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 32788395
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction. Genome biology\| PubMed ID: 32907628
Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Nature communications\| PubMed ID: 33060583

Article	Year
Enabling interspecies epigenomic comparison with CEpBrowser. Bioinformatics (Oxford, England)\| PubMed ID: 23543396	2013
Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS computational biology\| PubMed ID: 24339764	2013
From genomes to societies: a holistic view of determinants of human health. Current opinion in biotechnology\| PubMed ID: 24686286	2014
Comparative epigenomics: defining and utilizing epigenomic variations across species, time-course, and individuals. Wiley interdisciplinary reviews. Systems biology and medicine\| PubMed ID: 25044241	2014
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome research\| PubMed ID: 25096407	2014
P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Molecular cell\| PubMed ID: 26365380	2015
GeNemo: a search engine for web-based functional genomic data. Nucleic acids research\| PubMed ID: 27098038	2016
Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC evolutionary biology\| PubMed ID: 28335721	2017
SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Cell reports\| PubMed ID: 28355564	2017
The 4D nucleome project. Nature\| PubMed ID: 28905911	2017
Trends in Cannabis Use Disorder among Pregnant Women in the U.S., 1993-2014. Journal of general internal medicine\| PubMed ID: 29030807	2018
GIVE: portable genome browsers for personal websites. Genome biology\| PubMed ID: 30016975	2018
RNA, Action through Interactions. Trends in genetics : TIG\| PubMed ID: 30177410	2018
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. iScience\| PubMed ID: 30240742	2018
Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience\| PubMed ID: 30267678
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Genomics, proteomics & bioinformatics\| PubMed ID: 30553884	2018
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. PLoS computational biology\| PubMed ID: 30586383	2018
EpiAlignment: alignment with both DNA sequence and epigenomic data. Nucleic acids research\| PubMed ID: 31114924	2019
Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 31481608	2019
Reply to Hartl and Gao: Lack of between-batch difference in the distributions of measured extracellular RNA levels. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 31964851
Reply to Verwilt et al.: Experimental evidence against DNA contamination in SILVER-seq. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 32788395
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction. Genome biology\| PubMed ID: 32907628
Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Nature communications\| PubMed ID: 33060583