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[公告] 博士論文口試 鄭佳揚 (2014/3/13)
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Mar 12, 2014, 10:21:27 AM3/12/14
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博士論文口試 鄭佳揚 (2014/3/13)
清華大學資訊工程學系博士論文口試
學 生：鄭佳揚
指導教授：唐傳義 教授
口試委員：
校內：唐傳義 教授、王雯靜 教授、韓永楷 教授
校外：許芳榮 教授、林俊淵 教授
時 間：103 年 3 月 13 日 (星期四) 15:00 - 17:00
地 點：台達館 613 會議室
題 目：Genome-wide analysis of SUMO-1 and SUMO-2/3 Binding Sites
Based on Next-generation ChIP-Seq Data
論文摘要：
SUMO (small ubiquitin-related modifier) was discovered to be a reversible
post-translational protein modifier. SUMOylation is a highly dynamic process
and its outcomes are extremely diverse. Chromatin immunoprecipitation (ChIP)
in combination with high-throughput sequencing (ChIP-seq) is being applied as
a gold standard when studying the genome-wide binding sites of transcription
factor (TFs). This has greatly improved our understanding of protein-DNA
interactions on a genomic-wide scale. However, current ChIP-seq peak calling
tools are not sufficiently sensitive and are unable to simultaneously
identify post-translational modified TFs based on ChIP-seq analysis; this is
largely due to the wide-spread presence of multiple modified TFs. Using SUMO
modification as an example; we propose a methodology that analyses SUMO
ChIP-seq patterns and predicts related TFs. Our analysis uses three peak
calling tools. The fusion of these different tools increases the precision of
the peak calling results. TFBS annotation method is able to predict potential
SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq data
analysis and allows the identification of multiple SUMOylated TF binding
sites simultaneously.
主要著作：
Journal Papers
1. Chia-Yang Cheng, Chia-Han Chu, Hung-Wei Hsu, Fang-Rong Hsu, Chung Yi Tang,
Wen-Ching Wang, Hsing-Jien Kung, Pei-Ching Chang: An improved ChIP-seq peak
detection system for simultaneously identifying post-translational modified
transcription factors by combinatorial fusion, using SUMOylation as an
example. BMC Genomics 2014, 15(Suppl 1):S1
2. Chia-Yang Cheng, Pei-Ching Chang, Mel Campbell, Yi-Cheng Yang, Hung-Wei
Hsu, Ting-Yu Chang, Chia-Han Chu, Yi-Wei Lee, Chiu-Lien Hung, Shi-Mei Lai,
Clifford G Tepper, Wen-Ping Hsieh, Hsei-Wei Wang, Chuan-Yi Tang, Wen-Ching
Wang and Hsing-Jien Kung: The chromatin modification by SUMO-2/3 but not
SUMO-1 mediates the epigenetic silencing of key immune-related genes during
Kaposi's sarcoma associated herpesvirus reactivation. (Chia-Yang Cheng is
co-first author)
BMC Genomics 2013, 14:824
--
[;32m※ Origin: 楓橋驛站<bbs.cs.nthu.edu.tw>
[;32m◆ From: cathi @ peton.bec.nthu.edu.tw [m
清華大學資訊工程學系博士論文口試
學 生：鄭佳揚
指導教授：唐傳義 教授
口試委員：
校內：唐傳義 教授、王雯靜 教授、韓永楷 教授
校外：許芳榮 教授、林俊淵 教授
時 間：103 年 3 月 13 日 (星期四) 15:00 - 17:00
地 點：台達館 613 會議室
題 目：Genome-wide analysis of SUMO-1 and SUMO-2/3 Binding Sites
Based on Next-generation ChIP-Seq Data
論文摘要：
SUMO (small ubiquitin-related modifier) was discovered to be a reversible
post-translational protein modifier. SUMOylation is a highly dynamic process
and its outcomes are extremely diverse. Chromatin immunoprecipitation (ChIP)
in combination with high-throughput sequencing (ChIP-seq) is being applied as
a gold standard when studying the genome-wide binding sites of transcription
factor (TFs). This has greatly improved our understanding of protein-DNA
interactions on a genomic-wide scale. However, current ChIP-seq peak calling
tools are not sufficiently sensitive and are unable to simultaneously
identify post-translational modified TFs based on ChIP-seq analysis; this is
largely due to the wide-spread presence of multiple modified TFs. Using SUMO
modification as an example; we propose a methodology that analyses SUMO
ChIP-seq patterns and predicts related TFs. Our analysis uses three peak
calling tools. The fusion of these different tools increases the precision of
the peak calling results. TFBS annotation method is able to predict potential
SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq data
analysis and allows the identification of multiple SUMOylated TF binding
sites simultaneously.
主要著作：
Journal Papers
1. Chia-Yang Cheng, Chia-Han Chu, Hung-Wei Hsu, Fang-Rong Hsu, Chung Yi Tang,
Wen-Ching Wang, Hsing-Jien Kung, Pei-Ching Chang: An improved ChIP-seq peak
detection system for simultaneously identifying post-translational modified
transcription factors by combinatorial fusion, using SUMOylation as an
example. BMC Genomics 2014, 15(Suppl 1):S1
2. Chia-Yang Cheng, Pei-Ching Chang, Mel Campbell, Yi-Cheng Yang, Hung-Wei
Hsu, Ting-Yu Chang, Chia-Han Chu, Yi-Wei Lee, Chiu-Lien Hung, Shi-Mei Lai,
Clifford G Tepper, Wen-Ping Hsieh, Hsei-Wei Wang, Chuan-Yi Tang, Wen-Ching
Wang and Hsing-Jien Kung: The chromatin modification by SUMO-2/3 but not
SUMO-1 mediates the epigenetic silencing of key immune-related genes during
Kaposi's sarcoma associated herpesvirus reactivation. (Chia-Yang Cheng is
co-first author)
BMC Genomics 2013, 14:824
--
[;32m※ Origin: 楓橋驛站<bbs.cs.nthu.edu.tw>
[;32m◆ From: cathi @ peton.bec.nthu.edu.tw [m
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