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<?xml version="1.0" encoding="utf-8"?>
<feed xmlns="http://www.w3.org/2005/Atom">
<title>Zhanglab</title>
<link href="https://phoenixr-zhanglab.github.io/atom.xml" rel="self"/>
<link href="https://phoenixr-zhanglab.github.io/"/>
<updated>2023-09-25T12:32:11.602Z</updated>
<id>https://phoenixr-zhanglab.github.io/</id>
<author>
<name>Zihan Rong</name>
</author>
<generator uri="https://hexo.io/">Hexo</generator>
<entry>
<title>ZHANG Lab @ TMU</title>
<link href="https://phoenixr-zhanglab.github.io/2023/09/25/ZHANG-Lab-TMU/"/>
<id>https://phoenixr-zhanglab.github.io/2023/09/25/ZHANG-Lab-TMU/</id>
<published>2023-09-25T12:19:13.000Z</published>
<updated>2023-09-25T12:32:11.602Z</updated>
<content type="html"><![CDATA[<h3 id="Laboratory-of-RNA-structural-functions"><a href="#Laboratory-of-RNA-structural-functions" class="headerlink" title="Laboratory of RNA structural functions"></a>Laboratory of RNA structural functions</h3><p>RNA typically is a single-stranded biopolymer and is made of ribonucleotides. The self-complementary sequencing within/between RNAs leads to form intramolecular base-pairing structures and intermolecular RNA interactions, respectively. RNA structures and interactions play important roles in many cellular processes, ranging from carrying genetic information, to catalysis, regulation of gene expression, and beyond. Directly determining base pairs or tertiary contacts of RNA structures and interactions are critical steps toward decoding the structural basis of RNA-mediated regulation in cells. To achieve the above purpose, we and others developed a set of novel approaches to determine RNA structures and interactions, based on the principle of crosslinking, proximity ligation, and high-throughput sequencing, such as PARIS2-seq and SHARC-seq. Currently, our lab is interested in combining computational, chemical, and biological approaches to elucidate the fundamental mechanisms of “RNA machines”, including: </p><ol><li><p>Optimize our developed chemical tools to efficiently decode in vivo RNA secondary (2D) and RNA tertiary (3D) structures; </p></li><li><p>Identify genetic variations that will affect RNA structures; </p></li><li><p>Investigate the roles of RNA structures and RNA-RNA interactions in human diseases.</p></li></ol><img src="/2023/09/25/ZHANG-Lab-TMU/RNA.png" class="" title="error"><p>High throughput RNA structure determination methods and their applications.</p><span id="more"></span>]]></content>
<summary type="html"><h3 id="Laboratory-of-RNA-structural-functions"><a href="#Laboratory-of-RNA-structural-functions" class="headerlink" title="Laboratory of RNA structural functions"></a>Laboratory of RNA structural functions</h3><p>RNA typically is a single-stranded biopolymer and is made of ribonucleotides. The self-complementary sequencing within&#x2F;between RNAs leads to form intramolecular base-pairing structures and intermolecular RNA interactions, respectively. RNA structures and interactions play important roles in many cellular processes, ranging from carrying genetic information, to catalysis, regulation of gene expression, and beyond. Directly determining base pairs or tertiary contacts of RNA structures and interactions are critical steps toward decoding the structural basis of RNA-mediated regulation in cells. To achieve the above purpose, we and others developed a set of novel approaches to determine RNA structures and interactions, based on the principle of crosslinking, proximity ligation, and high-throughput sequencing, such as PARIS2-seq and SHARC-seq. Currently, our lab is interested in combining computational, chemical, and biological approaches to elucidate the fundamental mechanisms of “RNA machines”, including: </p>
<ol>
<li><p>Optimize our developed chemical tools to efficiently decode in vivo RNA secondary (2D) and RNA tertiary (3D) structures; </p>
</li>
<li><p>Identify genetic variations that will affect RNA structures; </p>
</li>
<li><p>Investigate the roles of RNA structures and RNA-RNA interactions in human diseases.</p>
</li>
</ol>
<img src="/2023/09/25/ZHANG-Lab-TMU/RNA.png" class="" title="error">
<p>High throughput RNA structure determination methods and their applications.</p></summary>
</entry>
<entry>
<title>Publication</title>
<link href="https://phoenixr-zhanglab.github.io/2023/09/22/Publication/"/>
<id>https://phoenixr-zhanglab.github.io/2023/09/22/Publication/</id>
<published>2023-09-22T02:02:00.000Z</published>
<updated>2023-09-25T13:13:52.831Z</updated>
<content type="html"><![CDATA[<p># Co-first author. * Corresponding author.</p><p>1. <u><strong>Zhang M</strong>#</u>, Li K#, Bai J#, Van Damme R, Zhang W, Alba M, Stiles BL, Chen JF and Lu Z*. snoRNA-guided tRNA 2’-O-methylation controls codon-biased gene expression and cellular states.<em><strong>Proceedings of the National Academy of Sciences</strong></em>. 2023. in press.</p><p>2. Lee WH, <u><strong>Zhang M</strong></u> and Lu Z*. Integrated analysis of crosslink-ligation data for the detection of RNA 2D/3D conformations in vivo. <em><strong>Methods in Molecular Biology</strong></em>. 2023. in press.</p><p>3. <u><strong>Zhang M</strong>#</u> Hwang I#, Li K, Bai J, Chen J, Weismann T, Zou J, Lu Z*. Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers. <em><strong>Genome Research</strong></em>. 2022 May;32(5):968-985.</p><span id="more"></span><p>4. Damme R#, Li K#, <u><strong>Zhang M</strong>#</u>, Bai J, Lee W, Yesselman J, Lu Z*, Velema W*. Chemical Reversible Crosslinking Enables Measurement of RNA 3D Distances and Alternative Conformations in Cells. <em><strong>Nature Communications.</strong></em> 2022 Feb 17;13(1):911. (Recommended article in Faculty Opinions by Dr. Janusz Bujnicki)</p><p>5. <u><strong>Zhang M</strong>#</u>, Li K#, Bai J#, Velema W, Yu C, Damme R, Lee W, Corpuz M, Chen J, Lu Z*. Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases. <em><strong>Nature Communications</strong></em>. 2021 Apr 20;12(1):2344. </p><p>6. Li T, Liu J, Feng J, Liu Z, Liu S, <u><strong>Zhang M</strong></u>, Zhang Y, Hou Y, Wu D, Li C, Chen Y, Chen H, Lu X*. Variation in the life history strategy underlies functional diversity of tumors. <em><strong>National Science Review</strong></em>. 2020 Jun 5;8(2):nwaa124.</p><p>7. Chen X, <u><strong>Zhang M</strong></u>, Gan H, Wang H, Lee J, Fang D, Kitange G, He L, Hu Z, Parney I, Meyer F, Giannini C, Sarkaria J, Zhang Z*. A novel enhancer regulates MGMT expression and promotes temozolomide resistance in glioblastoma. <em><strong>Nature Communications</strong></em>. 2018 Jul 27;9(1):2949.</p><p>8. <u><strong>Zhang M</strong>#</u>, Wang L#, An K#, Cai J, Li G, Yang C, Liu H, Du F, Han X, Zhang Z, Zhao Z, Pei D, Long Y, Xie X, Zhou Q, Sun Y*. Increased Lower genomic stability of induced pluripotent stem cells reflects increased non‐homologous end joining. <em><strong>Cancer Communicati</strong></em>ons. 2018 Jul 25;38(1):49.</p><p>9. Li G#, <u><strong>Zhang M</strong>#</u>, Chen H, An K, Liu Z, Du F, Yang C, Han X, Jin L, Li H, Zhang Y, Qiao J*, Sun Y*. Deep pedigree analysis reveals family specific ′′fingerprint″ pattern of DNA methylation for men. <em><strong>Science Bulletin</strong></em>. 2018. 63(2018):7-10. </p><p>10. Han X#, Zhao Z#, <u><strong>Zhang M</strong>#</u>, Li G, Yang C, Du F, Wang J, Zhang Y, Wang Y, Jia Y, Li B, Sun Y*. Maternal trans-general analysis of the human mitochondrial DNA pattern. <em><strong>Biochemical and Biophysical Research Communications</strong></em>. 2017. 493(1):643-649.</p><p>11. An K#, Du F#, Meng H#, Li G, <u><strong>Zhang M</strong></u>, Liu Z, Zhao Z, Zhang Z, Yu D, Wang D, Yang C, Ma W, Yuan Li, Zhou M, Duan L, Jin L, Li H, Zhang Y, Qiao J*, Sun Y*. Transgenerational analysis of H3K4me3 and H3K27me3 by ChIP-Seq links epigenetic inheritance to metabolism. <em><strong>Journal of Genetics and Genomics</strong></em>. 2017. S1673-8527(17)30197 -2.</p><p>12. <u><strong>Zhang M</strong>#</u>, Wang C#, Yang C#, Meng H, Agbagwa I, Wang L, Wang Y, Yan S, Ren S, Sun Y, Pei G, Liu X, Liu J, Jin L, Li H*, Sun Y*. Epigenetic Pattern on the Human Y Chromosome is Evolutionarily Conserved. <em><strong>PLoS ONE</strong></em>. 2016. 11(1):e0146402. </p><p>13. Shu J#, Zhang K#, <u><strong>Zhang M</strong>#</u>, Yao A, Shao S, Du F, Yang C, Chen W, Wu C, Yang W, Sun Y*, Deng H*. GATA Family Members as Inducers for Cellular Reprogramming to Pluripotency. <em><strong>Cell Research</strong></em>. 2015, 25(2):169-180. </p><p>14. Yao L#, Ren S#, <u><strong>Zhang M</strong>#</u>, Du F, Zhu Y, Yu H, Zhang C, Li X, Yang C, Liu H, Wang D, Meng H, Chang S, Han X, Sun Y*. Identification of specific DNA methylation sites on the Y-chromosome as biomarker in prostate cancer. <em><strong>Oncotarget</strong></em>. 2015, 6(38):40611-40621.</p><p>15. Du F, <u><strong>Zhang M</strong></u>, Li X, Yang C, Meng H, Wang D, Chang S, Xu Y, Brendan P, Sun Y*. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair. <em><strong>Biochemical and Biophysical Research Communications</strong></em>. 2014, 452(4):1034-1039.</p><p>16. <u><strong>Zhang M</strong></u>, Yang C, Liu H, Sun Y*. Induced Pluripotent Stem Cells Are Sensitive to DNA Damage. <em><strong>Genomics, Proteomics & Bioinformatics</strong></em>. 2013, 11(5): 320-326.</p>]]></content>
<summary type="html">这是首页显示的内容</summary>
</entry>
<entry>
<title>Lab members</title>
<link href="https://phoenixr-zhanglab.github.io/2023/09/20/Lab%20members/"/>
<id>https://phoenixr-zhanglab.github.io/2023/09/20/Lab%20members/</id>
<published>2023-09-20T02:47:00.000Z</published>
<updated>2023-10-07T03:06:34.086Z</updated>
<content type="html"><![CDATA[<img src="ZMJ.jpg" width="15%" height="15%"> <p><u>Minjie Zhang</u> (张敏杰), PhD<br>PI<br>Department of Bioinformatics<br>School of Basic Medical Sciences<br>Tianjin Medical University</p><p><strong>Education and Training</strong><br>2018-2023, Research associate in University of Southern California (USC)<br>2016-2018, Postdoc in Columbia University<br>2011-2016, PhD in Chinese Academy of Sciences, Beijing Institute of Genomics<br>2007-2011, BS in Hainan University </p><img src="LML.jpeg" width="15%" height="15%"> <p><u>Mengling Li</u> (李梦玲)<br>PhD student in TMU<br>Contact: <a href="mailto:limengling199801@163.com">limengling199801@163.com</a><br><strong>Education and Training</strong><br>2020-2023, MS in China Medical University<br>2016-2020, BS in Beijing University of Chinese Medicine </p><img src="LZY.png" width="15%" height="15%"> <p><u>Ziyang Li</u> (李子扬)<br>MS student in TMU<br>Contact: <a href="mailto:liziyangchina@163.com">liziyangchina@163.com</a><br><strong>Education and Training</strong><br>2018-2022, MS in Tianjin Medical University </p><img src="RZH.jpg" width="15%" height="15%"> <p><u>Zihan Rong</u> (容梓涵)<br>MS student in TMU<br>Contact: <a href="mailto:rzh1142940577@163.com">rzh1142940577@163.com</a><br><strong>Education and Training</strong><br>2019-2023, MS in Hebei University</p>]]></content>
<summary type="html">Minjie Zhang(张敏杰) PhD
Mengling Li(李梦玲) PhD student
Ziyang Li(李子扬) MS student
Zihan Rong(容梓涵)MS student</summary>
</entry>
<entry>
<title>Contact</title>
<link href="https://phoenixr-zhanglab.github.io/2023/09/19/Contacts/"/>
<id>https://phoenixr-zhanglab.github.io/2023/09/19/Contacts/</id>
<published>2023-09-19T03:03:00.000Z</published>
<updated>2023-10-07T01:36:48.877Z</updated>
<content type="html"><![CDATA[<p>Minjie Zhang (张敏杰)</p><p>Department of Bioinformatics<br>School of Basic Medical Sciences<br>Tianjin Medical University<br>No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China, 300070<br>Phone: +86-18822329402<br>Email:<a href="mailto:zhangmj@tmu.edu.cn">zhangmj@tmu.edu.cn</a></p><span id="more"></span>]]></content>
<summary type="html"><p>Minjie Zhang (张敏杰)</p>
<p>Department of Bioinformatics<br>School of Basic Medical Sciences<br>Tianjin Medical University<br>No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China, 300070<br>Phone: +86-18822329402<br>Email:<a href="mailto:&#x7a;&#x68;&#97;&#x6e;&#x67;&#109;&#x6a;&#64;&#x74;&#109;&#117;&#46;&#101;&#x64;&#x75;&#x2e;&#x63;&#110;">&#x7a;&#x68;&#97;&#x6e;&#x67;&#109;&#x6a;&#64;&#x74;&#109;&#117;&#46;&#101;&#x64;&#x75;&#x2e;&#x63;&#110;</a></p></summary>
</entry>
</feed>