nucleosome hongde liu

Common genetic variants associated with Parkinson s

 · Liu H Duan X Yu S Sun X. Analysis of nucleosome positioning determined by DNA helix curvature in the human genome. BMC Genomics. 2011 12 72. doi 10.1186/.

Frontiers Effect for Human Genomic Variation During the

 · Role of genomic variation in differentiation has not been well understood yet. Here the genomic variations were determined with the whole-genome sequencing for three pairs of pluripotent stem cell lines and their corresponding BMP4-induced trophoblast cell lines. We identified 3 500 single nucleotide variations and 4 500 indels by comparing the genome sequenced data between the stem

Nucleosome Positioning and Its Role in Gene Regulation in

 · Nucleosome composed of a 147-bp segment of DNA helix wrapped around a histone protein octamer serves as the basic unit of chromatin. Nucleosome

A deconvolution method and its application in analyzing

 · The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions primarily from the gene expression data of a bulk sample. However the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of gene expression across multiple conditions.

Southeast University

Hongde Liu (Xiao Sun) Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions Biophysical J. (In press) 4.75 SCI 7. Yang Xinan Meta-analysis of several gene lists for distinct types of cancer A simple way

Chromatin structure is distinct between coding and non

 · Hongde LX Sun Analysis of Nucleosome Positioning in The Vicinity of Sites of Nucleotide Polymorphism in Human Genome. Progress Biochem Biophysics. 2011 38 5-10.3724/SP.J.1206.2010.00083. 10.3724/SP.J.1206.2010.00083. Hongde Liu Jinchen Zhai Lingjie Liu. Department of Neurosurgery Xinjiang Evidence-Based Medicine Research Institute

Issue Biophysical Journal

 · Characteristics of Nucleosome Core DNA and Their Applications in Predicting Nucleosome Positions. Hongde Liu Jiansheng Wu Jianming Xie Xi nan Yang Zuhong Lu Xiao Sun By analyzing dinucleotide position-frequency data of yeast nucleosome-bound DNA sequences dinucleotide periodicities of core DNA sequences were investigated. Within

Connecting Chromatin Modifying Factors to DNA

 · Weiwei Lai 1 2 3 Hongde Li 1 2 3 Shuang Liu 4 5 and Yongguang Tao 1 2 3 1 Cancer Research Institute Central South University Changsha 410078 Hunan China The nucleosome sliding factors chromatin accessibility complex (CHRAC) and ATP-dependent chromatin assembly and remodeling factor (ACF) are required for a

Nucleosomes Are Well Positioned at Both Ends of Exons

 · The results indicate nucleosomes are well positioned at both ends of exons. Nucleosome at 5 end is more conserved than that at 3 end which probably has a link with alternative splicing. The distance between nucleosome centre and splice site varies among specieses suggesting an evolution selection. Our analysis reveals that nucleosomes

Histone chaperone Chz1 facilitates the disfavouring

 · Abstract < Language=VBScript > < Option Explicit > Biochemical Journal (2014) 460 H. Liu and othersRegulation of the distribution of Spt16 by Chz1" < PageType = "Art_FullHTML" > < SectionNo="4" strYear="2014" strMonth="06" strDay="15" Arttype="bjfull" volshort="460" vol="460" Issue="3" fpageshort="387" fpage="0387" lpageshort="397" lpage=""

Chromatin structure is distinct between coding and non

 · Hongde LX Sun Analysis of Nucleosome Positioning in The Vicinity of Sites of Nucleotide Polymorphism in Human Genome. Progress Biochem Biophysics. 2011 38 5-10.3724/SP.J.1206.2010.00083. 10.3724/SP.J.1206.2010.00083. Hongde Liu Jinchen Zhai Lingjie Liu. Department of Neurosurgery Xinjiang Evidence-Based Medicine Research Institute

Jansen Woo LAMDA Group at NJU

 · Hongde Liu Jiansheng Wu Jianming Xie Xi nan Yang Zuhong Lu and Xiao Sun. Characteristics of Nucleosome Core DNA and Their Applications in Predicting Nucleosome Positions. Biophysical Journal 2008 94 1–8.

Nucleosomes Are Well Positioned at Both Ends of Exons

 · The results indicate nucleosomes are well positioned at both ends of exons. Nucleosome at 5 end is more conserved than that at 3 end which probably has a link with alternative splicing. The distance between nucleosome centre and splice site varies among specieses suggesting an evolution selection. Our analysis reveals that nucleosomes

Pervasive Transcription Represses Coding Gene Expression

 · Pervasive Transcription Represses Coding Gene Expression by Closing Their Nucleosome‐Depleted Regions

Distinct roles for histone chaperones in the deposition of

 · This article is from Bioscience Reports volume 34.AbstractHistone variant Htz1 substitution for H2A plays important roles in diverse DNA transactions. Histone

Nucleosomes Are Well Positioned at Both Ends of Exons

 · The results indicate nucleosomes are well positioned at both ends of exons. Nucleosome at 5 end is more conserved than that at 3 end which probably has a link with alternative splicing. The distance between nucleosome centre and splice site varies among specieses suggesting an evolution selection. Our analysis reveals that nucleosomes

A dynamic program ming algorithm for nucleosome

 · Yiru Zhang Changchang Cao Hongde Liu Xiao Sun State Key Laboratory of Bioelectronics School of Biological Science Medical Engineering Southeast University Nanjing China E -mail zhan gyiru_seu 163 Abstract ² Nucleosome s are the basic units of eukaryotic chromatin. The nucleosome positioning is dynamic for various

2014 8th International Conference on Systems Biology

 · A dynamic programming algorithm for nucleosome positions alignment 7 Yiru Zhang Changchang Cao Hongde Liu Xiao Sun A Class-Information-based SNMF Method for Selecting Characteristic Genes 11 Jin-Xing Liu Chun-Xia Ma Ying-Lian Gao Jian Liu Chun-Hou Zheng Global analysis of a delay virus dynamics model with Beddington-DeAngelis incidence

Chromatin structure is distinct between coding and non

 · Taken together the results indicated that nucleosome organization is distinct between coding-SNPs and noncoding SNPs. It was observed that the patterns of nucleosome occupancy were almost consistent between in vivo (Figure 1A-B) and in vitro (Figure 1C) conditions suggesting that the DNA sequence has a role in patterns of SNPs relative to nucleosomes.

Distinct roles for histone chaperones in the deposition of

 · This article is from Bioscience Reports volume 34.AbstractHistone variant Htz1 substitution for H2A plays important roles in diverse DNA transactions. Histone

The application of next-generation sequencing techniques

Liu Yajun Zhang Feng Liu Hongde Sun Xiao. The application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells J . Hereditas(Beijing) 2017 39(8) .

2014 8th International Conference on Systems Biology

 · A dynamic programming algorithm for nucleosome positions alignment 7 Yiru Zhang Changchang Cao Hongde Liu Xiao Sun A Class-Information-based SNMF Method for Selecting Characteristic Genes 11 Jin-Xing Liu Chun-Xia Ma Ying-Lian Gao Jian Liu Chun-Hou Zheng Global analysis of a delay virus dynamics model with Beddington-DeAngelis incidence

Huan HUANG Hongde L and Xiao SUN y

 · nucleosome occupancy near key point sites including splicing sites16) and transcription factor binding sites 17) that suggests nucleosome-regulated gene expression and the processing of pre-mRNA. We have also studied nucleosome regulation of the use of polyadenylation sites (Huan Huang Hongde Liu and Xiao Sun unpublished results).

Histone chaperone Chz1 facilitates the disfavouring

The results of the present study revealed that Spt16 and Pol II are associated bind at nucleosome-depleted regions and are positively correlated with the transcription rate. Importantly Spt16 disfavours the Htz1-bound genes and this discrimination is impaired upon the deletion of chz1. The negative correlation between the binding profiles of Spt16 and Htz1 at promoters is not an intrinsic repulsion

Common genetic variants associated with Parkinson s

 · Liu H Duan X Yu S Sun X. Analysis of nucleosome positioning determined by DNA helix curvature in the human genome. BMC Genomics. 2011 12 72. doi 10.1186/.

Frontiers Effect for Human Genomic Variation During the

 · Role of genomic variation in differentiation has not been well understood yet. Here the genomic variations were determined with the whole-genome sequencing for three pairs of pluripotent stem cell lines and their corresponding BMP4-induced trophoblast cell lines. We identified 3 500 single nucleotide variations and 4 500 indels by comparing the genome sequenced data between the stem

Nucleosome alterations caused by mutations at modifiable

 · Liu M. J. et al. Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res. 25 1182–1195 doi 10.1101/gr.188680.114 (2015). Liu Hongde

RESEARCH ARTICLE Open Access Chromatin structure is

 · RESEARCH ARTICLE Open Access Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms Hongde Liu1 Jinchen Zhai1 Kun Luo2 and Lingjie Liu1 Abstract Background Previous studies suggested that nucleosomes are

Pervasive Transcription Represses Coding Gene Expression

 · Pervasive Transcription Represses Coding Gene Expression by Closing Their Nucleosome‐Depleted Regions

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Functional role of histone variant Htz1 in the stress

 · Nucleosome occupancy Htz1 Pol II H3K4me2 and H3K79me3 profiles for up-regulated genes in nitrogen depletion and heat shock are shown in Supplementary Figures S5(B) and S5(D). Hongde Liu and Yakun Wan designed the study and wrote the paper. Guanglin Li performed the experiments. Hongde Liu Lingjie Liu and Yakun Wan analysed the data.

Jansen Woo LAMDA Group at NJU

 · Hongde Liu Jiansheng Wu Jianming Xie Xi nan Yang Zuhong Lu and Xiao Sun. Characteristics of Nucleosome Core DNA and Their Applications in Predicting Nucleosome Positions. Biophysical Journal 2008 94 1–8.