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<!DOCTYPE html>
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<title>Publications in Wang Lab</title>
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<header class="jumbotron subhead" id="overview">
<h1><font color='#FFC300'>Wang Lab</font></h1>
<p class="lead"><font size=4, color='#FFC300'>Tissue Regeneration and Bioinformatics, GIBH</font></p>
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<li><a href="#Publications"> Journal Publications</a></li>
<li><a class="subhead" href="#Selected"> Selected Publications</a></li>
<li><a class="subhead" href="#Others"> All Others </a></li>
<li><a href="#Preparation"> In Review and Preparation</a></li>
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<div class="span8 offset1">
<section id="Publications">
<div class="page-header">
<h3>Journal Publications <font size=4>(# co-first author, * corresponding author)</font> </h3>
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<section id="Selected">
<h3>Selected Publications</h3>
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<a href="https://www.science.org/toc/science/370/6519" class="thumbnail">
<img class="publications-thumb" src="thumbs/Science_cover.jpg" alt="Gene regulatory networks controlling vertebrate retinal regeneration"/>
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<h4>Gene regulatory networks controlling vertebrate retinal regeneration</h4>
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<p>Hoang T#, <b>Wang J#</b>, Boyd P, Wang F, Santiago C, Jiang L, Yoo S, Lahne M, Todd LJ, Jia M, Saez C, Keuthan C, Palazzo I, Squires N, Campbell WA, Rajaii F, Payail T, Trinh V, Kim DW, Wang G, Campbell LJ, Ash J, Fischer AJ, Hyde DR*, Qian J*, Blackshaw S*.</p>
<a href="https://www.science.org/doi/abs/10.1126/science.abb8598"><b><i>Science</i></b> 2020, 370 (6519): eabb8598.</a>
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<a href="https://www.nature.com/articles/s41467-018-03856-y" class="thumbnail">
<img class="publications-thumb" src="thumbs/nature-communications.jpg" alt="ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration"/>
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<h4>ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration</h4>
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<p><b>Wang J#</b>, Zibetti C#, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs S, Zack D, Handa JT, Sinha D, Blackshaw S*, Qian J*.</p>
<a href="https://www.nature.com/articles/s41467-018-03856-y"><b><i>Nature Communications</i></b> 2018, 9(1): 1-13.</a>
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<a href="https://aacrjournals.org/clincancerres/issue/23/1" class="thumbnail">
<img class="publications-thumb" src="thumbs/clincanres_cover.png" alt="The prediction of clinical outcome in hepatocellular carcinoma based on a six-gene metastasis signature"/>
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<h4>The prediction of clinical outcome in hepatocellular carcinoma based on a six-gene metastasis signature</h4>
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<p>Yuan S#, <b>Wang J#*</b>, Yang Y, Zhang J, Liu H, Xiao J, Xu Q, Huang X, Xiang B, Zhu S, Li L*, Liu J*, Liu L*, Zhou W*.</p>
<a href="https://aacrjournals.org/clincancerres/article/23/1/289/122938/"><b><i>Clinical Cancer Research</i></b> 2017, 23(1): 289-297.</a>
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<a href="https://aasldpubs.onlinelibrary.wiley.com/toc/15273350/2016/63/2" class="thumbnail">
<img class="publications-thumb" src="thumbs/hep.v63.2.cover.gif" alt="Long noncoding RNA DANCR increases stemness features of hepatocellular carcinoma by derepression of CTNNB1"/>
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<div class="span9">
<h4>Long noncoding RNA DANCR increases stemness features of hepatocellular carcinoma by derepression of CTNNB1</h4>
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<p>Yuan S#, <b>Wang J#</b>, Yang F#, Tao Q#, Zhang J, Wang L, Yang Y, Liu H, Wang Z, Xu Q, Fan J, Liu L*, Sun S* and Zhou W*.</p>
<a href="https://aasldpubs.onlinelibrary.wiley.com/doi/full/10.1002/hep.27893"><b><i>Hepatology</i></b> 2016, 63(2): 499-511.</a>
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<div class="span3">
<a href="https://academic.oup.com/bib/issue/25/4" class="thumbnail">
<img class="publications-thumb" src="thumbs/BiB2024_cover.jpeg" alt="CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data"/>
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<h4>CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data</h4>
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<p>Jiang J#, Li J#, Huang S, Jiang F, Liang Y, Xu X*, <b>Wang J*</b>.</p>
<a href="https://academic.oup.com/bib/article/25/4/bbae283/7690342"><b><i>Briefings in Bioinformatics</i></b> 2024, 25: bbae283.</a>
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</section>
<hr>
<section id="Others">
<h3>All Others</h3>
<br/>
<ol>
<li class="publication">Fu Y#, Jiang F#, Zhang X, Pan Y, Xu R, Liang X, Wu X, Li X, Lin K, Shi R, Zhang X, Ferrandon D, Liu J, Pei D, <b>Wang J*</b>, Wang T*. Perturbation of METTL1-mediated tRNA N7- methylguanosine modification induces senescence and aging. <a href="https://www.nature.com/articles/s41467-024-49796-8"><b><i>Nature Communications</i></b> 2024, 15(1): 1-21.</a></li>
<li class="publication">Jiang J#, Lyu P#, Li J#, Huang S, Tao J, Blackshaw S, Qian J, <b>Wang J*</b>. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. <a href="https://www.cell.com/iscience/fulltext/S2589-0042(22)01631-5"><b><i>iScience</i></b> 2022, 25(11): 105359.</a></li>
<li class="publication">Sun D#, Gan X#, Liu L#, Yang Y#, Ding D, Li W, Jiang J, Ding W, Zhao L, Hou G, Yu J, <b>Wang J*</b>, Yang F*, Yuan S*, Zhou W*. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. <a href="https://www.nature.com/articles/s41419-022-04895-6"><b><i>Cell Death & Disease</i></b> 2022, 13:446.</a></li>
<li class="publication">Xin Y#, Lyu P#, Jiang J, Zhou F, <b>Wang J</b>, Blackshaw S, Qian J*. LRLoop: a method to predict feedback loops in cell–cell communication. <a href="https://academic.oup.com/bioinformatics/article-abstract/38/17/4117/6631225"><b><i>Bioinformatics</i></b> 2022, 38(17): 4117-4126.</a></li>
<li class="publication">8. Datta S, Cano M, Satyanarayana G, Liu T, Wang L, <b>Wang J</b>, Cheng J, Itoh K, Sharma A, Bhutto I, Kannan R, Qian J, Sinha D, Handa JT*. Mitophagy initiates retrograde mitochondrial-nuclear signaling to guide retinal pigment cell heterogeneity. <a href="https://www.tandfonline.com/doi/abs/10.1080/15548627.2022.2109286"><b><i>Autophagy</i></b> 2022, 13:1-18.</a></li>
<li class="publication">Ma D, Zhan D, Fu Y, Wei S, Lal B, <b>Wang J</b>, Li Y, Lopez-Bertoni H, Yalcin F, Dzaye O, Eberhart CG, Laterra J, Wilson MA, Ying M, Xia S*. Mutant IDH1 promotes phagocytic function of microglia/macrophages in gliomas by downregulating ICAM1. <a href="https://www.sciencedirect.com/science/article/abs/pii/S030438352100269X"><b><i>Cancer Letters</i></b> 2021, 517: 35-45.</a></li>
<li class="publication">Wang L, Kaya KD, Kim S, Brooks MJ, <b>Wang J</b>, Xin Y, Qian J, Swaroop A, Handa JT*. Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. <a href="https://www.sciencedirect.com/science/article/pii/S0891584920310923"><b><i>Free Radical Biology and Medicine</i></b> 2020, 156: 176-189.</a></li>
<li class="publication">Kallman A, Capowski EE, <b>Wang J</b>, Kaushik AM, Jansen AD, Edwards KL, Chen L, Berlinicke CA, Phillips MJ, Pierce EA, Qian J, Wang TH, Gamm DM*, Zack DJ*. Investigating cone photoreceptor development using patient-derived NRL null retinal organoids. <a href="https://www.nature.com/articles/s42003-020-0808-5"><b><i>Communications biology</i></b> 2020, 3(1): 1-13.</a></li>
<li class="publication">Wei S, <b>Wang J</b>, Oyinlade O, Ma D, Wang S, Kratz L, Lal B, Xu Q, Liu S, Shah S, Zhang H, Li Y, Quinones-Hinojosa A, Zhu H, Chen L, Qian J, Xia S*. Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP. <a href="https://www.nature.com/articles/s41388-018-0334-9"><b><i>Oncogene</i></b> 2018, 37(38): 5160–5174.</a></li>
<li class="publication">Newman EA, Kim DW, Wan J, <b>Wang J</b>, Qian J, Blackshaw S*. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. <a href="https://www.sciencedirect.com/science/article/pii/S0012160617309065"><b><i>Developmental Biology</i></b> 2018, 439(2): 102-111.</a></li>
<li class="publication">Han X, Wang J, <b>Wang J</b>, Liu S, Hu J, Zhu H, Qian J*. ScaPD: a database for human scaffold proteins. <a href="https://link.springer.com/article/10.1186/s12859-017-1806-6"><b><i>BMC Bioinformatics</i></b> 2017, 18(11): 87-91.</a></li>
<li class="publication"><b>Wang J</b>, Xia S, Arand B, Zhu H, Machiraju R, Huang K, Ji H, Qian J*. Single-cell co-expression analysis reveals distinct functional modules, co-regulation mechanisms and clinical outcomes. <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004892"><b><i>PLOS Computational Biology</i></b> 2016, 12(4): e1004892.</a></li>
<li class="publication">Yuan X#, <b>Wang J#</b>, Tang X, Li Y, Xia P*, Gao X*. Berberine ameliorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and lncRNA expression profiles. <a href="https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-015-0383-6"><b><i>Journal of Translational Medicine</i></b> 2015, 13(1): 1-11.</a></li>
<li class="publication">Zhang M, <b>Wang J</b>, Jiang J, Zhan X, Ling Y, Lu Z, Guo J, Gao X*. Von Hippel-Lindau disease type 2 in a Chinese family with a VHL p. W88X truncation. <a href="https://link.springer.com/article/10.1007/s12020-014-0368-x"><b><i>Endocrine</i></b> 2015, 48(1): 83-88.</a></li>
<li class="publication">Yuan S#, Tao Q#, <b>Wang J#</b>, Yang F#, Liu L, Wang L, Zhang J, Yang Y, Liu H, Wang F, Sun S*, Zhou W*. Antisense long noncoding RNA PCNA-AS1 promotes tumor growth by regulating proliferating cell nuclear antigen in hepatocellular carcinoma. <a href="https://www.sciencedirect.com/science/article/pii/S0304383514001980"><b><i>Cancer Letters</i></b> 2014, 349(1): 87-94.</a></li>
<li class="publication"><b>Wang J</b>, Wang Y, Wang Z*, Liu L*, Zhu XG*, Ma X*. Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to telo-box motif enrichment. <a href="https://link.springer.com/article/10.1186/1471-2148-11-161"><b><i>BMC Evolutionary Biology</i></b> 2011, 11(1): 1-15.</a></li>
</ol>
</section>
</section>
<hr>
<section id="Preparation">
<div class="page-header">
<h3>In Review and Preparation</h3>
</div>
<p><li class="publication">Hepatic Stellate Cells Express Lhx2 to Balance Liver Regeneration and Fibrosis</li></p>
<p><li class="publication">ScReNI: Single-cell regulatory network inference through integrating scRNA-seq and scATAC-seq profiles</li></p>
</section>
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