From 7bc13fc9f6ed1ec851331917e019dd2fe4fc6402 Mon Sep 17 00:00:00 2001 From: Guangchuang Yu Date: Thu, 12 Dec 2024 18:12:40 +0800 Subject: [PATCH] update --- index.xml | 2 +- publications/index.html | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/index.xml b/index.xml index 37d0615..2a5f1ea 100644 --- a/index.xml +++ b/index.xml @@ -132,7 +132,7 @@ http://yulab-smu.top/publications/ Mon, 01 Jan 0001 00:00:00 +0000 http://yulab-smu.top/publications/ - <style> @media only screen and (max-width: 768px) { td { display: block; } } </style> <table style="border:none; font-size: 90%; width:100%;"> <tr style="border:none;"> <td style="border:none;"> <ul> <li><sup>#</sup> Co-first authors</li> <li><sup>*</sup> Co-corresponding authors</li> <li><i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i>：ESI Highly Cited Paper (9X)</li> <li>分区：文章发表当年的中科院小类分区</li> <li>IF：文章发表当年的影响因子</li> <li><a href="http://yulab-smu.top/awards" >课题组学术榜</a></li> </ul> </td> <td style="border:none;"> <a href="https://scholar.google.com/citations?user=DO5oG40AAAAJ"><img src="http://yulab-smu.top/images/citation.png" height='200px'/></a> </td> </tr> </table> <h2 id="year-2025"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2025 <a class="heading-link" href="#year-2025"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>M Chen<sup>#</sup>, X Luo<sup>#</sup>, S Xu<sup>#</sup>, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen__<sup>*</sup>, TTY Lam__<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. <strong><em>iMeta</em></strong>. accepted.</li> <li>D Zeng<sup>#</sup>, Y Fang<sup>#</sup>, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, W Liao<sup>*</sup>. <a href="https://doi.org/10.1016/j.crmeth.2024.100910" class="external-link" target="_blank" rel="noopener">Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0</a>. <strong><em>Cell Reports Methods</em></strong>. accepted.</li> </ul> <h2 id="year-2024"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2024 <a class="heading-link" href="#year-2024"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>M Luo<sup>*#</sup>, W Yang<sup>#</sup>, L Bai<sup>#</sup>, L Zhang<sup>#</sup>, JW Huang<sup>#</sup>, Y Cao<sup>#</sup>, Y Xie<sup>#</sup>, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, <strong>G Yu</strong>, C Tian, LN Jin, J Dai<sup>*</sup>, B Xia<sup>*</sup>, B Sun<sup>*</sup>, F Chen<sup>*</sup>, YZ Gao<sup>*</sup>, H Wang<sup>*</sup>, B Wang<sup>*</sup>, D Zhang<sup>*</sup>, X Cao<sup>*</sup>, H Wang<sup>*</sup>, T Huang<sup>*</sup>. <a href="https://doi.org/10.59717/j.xinn-life.2024.100105" class="external-link" target="_blank" rel="noopener">Artificial intelligence for life sciences: A comprehensive guide and future trends</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100105.</li> <li>Z Miao<sup>#</sup>, T Tian<sup>#</sup>, W Chen<sup>#</sup>, Q Wang<sup>#</sup>, L Ma<sup>#</sup>, D Zhang<sup>#</sup>, M Xie<sup>#</sup>, Z Yu<sup>#</sup>, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo<sup>*</sup>, M Luo<sup>*</sup>, L Yuan<sup>*</sup>, C Tian<sup>*</sup>, L Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, D Zhang<sup>*</sup>, S Sun<sup>*</sup>. <a href="https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100097" class="external-link" target="_blank" rel="noopener">Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100097.</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100722" class="external-link" target="_blank" rel="noopener">Thirteen years of clusterProfiler</a>. <strong><em>The Innovation</em></strong>. 2024, 5(6):100722.</li> <li>S Xu<sup>#</sup>, E Hu<sup>#</sup>, Y Cai<sup>#</sup>, Z Xie<sup>#</sup>, X Luo<sup>#</sup>, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.nature.com/articles/s41596-024-01020-z" class="external-link" target="_blank" rel="noopener">Using clusterProfiler to characterise Multi-Omics Data</a>. <strong><em>Nature Protocols</em></strong>. 2024, 19(11):3292-3320.</li> <li>Y Chen<sup>#</sup>, LN He<sup>#</sup>, Y Zhang, J Gong, S Xu, Y Shu, D Zhang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Z Zuo<sup>*</sup>. <a href="http://doi.org/10.1002/imt2.229" class="external-link" target="_blank" rel="noopener">tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package</a>. <strong><em>iMeta</em></strong>. 2024, 3(5):e229.</li> <li>D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://journals.lww.com/cmj/fulltext/2024/08200/reducing_language_barriers,_promoting_information.7.aspx" class="external-link" target="_blank" rel="noopener">Reducing language barriers, promoting information absorption, and communication using <em>fanyi</em></a>. <strong><em>Chinese Medical Journal</em></strong>. 2024, 137(16):1950-1956.</li> <li>XK Ma<sup>#</sup>, Y Yu<sup>#</sup>, T Huang<sup>#</sup><sup>*</sup>, D Zhang, C Tian, W Tang, M Luo, P Du<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, L Yang<sup>*</sup>. <a href="https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100083" class="external-link" target="_blank" rel="noopener">Bioinformatics Software Development: principles and future directions</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100083.</li> <li>Y Yang<sup>#</sup>, S Xu<sup>#</sup>, Y Hong, Y Cai, W Tang, J Wang, B Shen<sup>*</sup>, H Zong<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.59717/j.xinn-life.2024.100079" class="external-link" target="_blank" rel="noopener">Computational modeling for medical data: from data collection to knowledge discovery</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100079.</li> <li>L Zhan<sup>#</sup>, X Luo<sup>#</sup>, W Xie<sup>#</sup>, XA Zhu<sup>#</sup>, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.sciencedirect.com/science/article/pii/S167385272400033X" class="external-link" target="_blank" rel="noopener">shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals</a>. <strong><em>Journal of Genetics and Genomics</em></strong>. 2024, 51(7):762-768.</li> <li>L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.sciencedirect.com/science/article/pii/S2667005424000206" class="external-link" target="_blank" rel="noopener">Resolving Tumor Evolution: A Phylogenetic Approach</a>. <strong><em>Journal of the National Cancer Center</em></strong>. 2024, 4(2):97-106.</li> <li>Q Wang, W Tang, L Chen, L Deng, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100637" class="external-link" target="_blank" rel="noopener">Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data</a>. <strong><em>The Innovation</em></strong>. 2024, 5(4):100637.</li> <li>Y Cai<sup>#</sup>, W Hu<sup>#</sup>, Y Pei, Hao Zhao<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100627" class="external-link" target="_blank" rel="noopener">Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic</a>. <strong><em>The Innovation</em></strong>. 2024, 5(3):100627.</li> <li>Y Lai<sup>#</sup>, W Tang<sup>#</sup>, X Luo, H Zheng, Y Zhang<sup>*</sup>, M Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Min Yang<sup>*</sup>. <a href="https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1369116" class="external-link" target="_blank" rel="noopener">Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis</a>. <strong><em>Frontiers in Immunology</em></strong>. 2024, 15:1369116.</li> <li>CH Gao, C Chen, T Akyol, A Dusa, <strong>G Yu</strong>, B Cao, P Cai<sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/10.1002/imt2.177" class="external-link" target="_blank" rel="noopener">ggVennDiagram: intuitive Venn diagram software extended</a>. <strong><em>iMeta</em></strong>. 2024, 3(1):e177.</li> <li>Y Ye<sup>#</sup>, MH Shum<sup>#</sup>, JL Tsui<sup>#</sup>, <strong>G Yu</strong><sup>#</sup>, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam<sup>*</sup>. <a href="https://doi.org/10.1371/journal.pcbi.1011871" class="external-link" target="_blank" rel="noopener">Robust expansion of phylogeny for fast-growing genome sequence data</a>. <strong><em>PLoS Computational Biology</em></strong>. 2024, 20(2):e1011871.</li> <li>S Wen, S Mo, J Zhou, Y Lv, K Khazaie<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fcell.2024.1365242/full" class="external-link" target="_blank" rel="noopener">Single-cell and spatial-omics in delineating immune-related diseases</a>. <strong><em>Frontiers in Cell and Developmental Biology</em></strong>. 2024, 12:1365242.</li> </ul> <h2 id="year-2023"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2023 <a class="heading-link" href="#year-2023"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>X Zhang, B Liang, Y Huang, H Meng, Z Li, J Du, L Zhou, Y Zhong, B Wang, X Lin, <strong>G Yu</strong>, X Chen, W Lu, ZS Chen, X Yang, Z Huang<sup>*</sup>. <a href="https://doi.org/10.1002/advs.202303753" class="external-link" target="_blank" rel="noopener">Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics</a>. <strong><em>Advanced Science</em></strong>. 2023, 10(36):2303753. (IF = 14.3，一区)</li> <li>M Kang, F Lin, Z Jiang, X Tan, X Lin, Z Liang, C Xiao, Y Xia, W Guan, Z Yang, <strong>G Yu</strong>, M Zanin, S Tang<sup>*</sup>, SS Wong<sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/irv.13172" class="external-link" target="_blank" rel="noopener">The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults</a>. <strong><em>Influenza and Other Respiratory Viruses</em></strong>. 2023, 17(7):e13172. (IF = 4.3，四区)</li> <li>W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, <strong>G Yu</strong><sup>*</sup>. <a href="https://dx.doi.org/10.1080/19490976.2023.2223349" class="external-link" target="_blank" rel="noopener">MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm</a>. <strong><em>Gut Microbes</em></strong>. 2023, 15(1):2223349. (IF = 12.2，一区)</li> <li>S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2023.100388" class="external-link" target="_blank" rel="noopener">MicrobiotaProcess: A comprehensive R package for deep mining microbiome</a>. <strong><em>The Innovation</em></strong>. 2023, 4(2):100388. (IF = 33.2，一区)</li> <li>S Guo<sup>*</sup>, D Zhang, H Wang, Q An, <strong>G Yu</strong>, J Han, C Jiang, J Huang. <a href="https://www.frontiersin.org/articles/10.3389/fmed.2023.1146896/full" class="external-link" target="_blank" rel="noopener">Computational and Systematic Analysis of Multi-omics Data for Drug Discovery and Development</a>. <strong><em>Frontiers in Medicine</em></strong>. 2023, 10:1146896. (IF = 3.1，三区)</li> </ul> <h2 id="year-2022"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2022 <a class="heading-link" href="#year-2022"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, <strong>G Yu</strong><sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56" class="external-link" target="_blank" rel="noopener">Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data</a>. <strong><em>iMeta</em></strong>, 2022, 1(4):e56.</li> <li>Q Wang<sup>#</sup>, M Li<sup>#</sup>, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1002/cpz1.585" class="external-link" target="_blank" rel="noopener">Exploring epigenomic datasets by ChIPseeker</a>. <strong><em>Current Protocols</em></strong>, 2022, 2(10): e585. <a href="https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585" class="external-link" target="_blank" rel="noopener"><i class="fa fa-file-pdf-o fa-2x" aria-hidden="true" style="color:black;font-size: 150%;"></i></a></li> <li>Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2022.951774" class="external-link" target="_blank" rel="noopener">Characterization of toxin-antitoxin systems from public sequencing data: a case study in <em>Pseudomonas aeruginosa</em></a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:951774. (IF = 5.2，二区，Top期刊)</li> <li>T Feng<sup>#</sup>, T Wu<sup>#</sup>, Y Zhang<sup>#</sup>, L Zhou<sup>#</sup>, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang<sup>*</sup>, X Shang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fonc.2022.912694/" class="external-link" target="_blank" rel="noopener">Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells</a>. <strong><em>Frontiers in Oncology</em></strong>. 2022, 12:912694. (IF = 4.7，三区)</li> <li>L Zhou<sup>#</sup>, T Feng<sup>#</sup>, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/bib/bbac222" class="external-link" target="_blank" rel="noopener">ggmsa: a visual exploration tool for multiple sequence alignment and associated data</a>. <strong><em>Briefings in Bioinformatics</em></strong>. 2022, 23(4):bbac222. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF = 9.5，一区，Top期刊)</li> <li>N Sato, Y Tamada, <strong>G Yu</strong>, Y Okuno<sup>*</sup>. <a href="https://doi.org/10.1093/bioinformatics/btac175" class="external-link" target="_blank" rel="noopener">CBNplot: Bayesian network plots for enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2022, 38(10):2959-2960. (IF=5.8，一区，Top期刊)</li> <li>T Wu, CL Xiao, TT Lam, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2022.890775/full" class="external-link" target="_blank" rel="noopener">Biomedical Data Visualization: Methods and Applications</a>. <strong><em>Frontiers in Genetics</em></strong>. 2022, 13:890775. (IF=3.7，三区)</li> <li>X Zhao<sup>#</sup>, W Tang<sup>#</sup>, H Wan<sup>#</sup>, Z Lan H Qin, Q Lin, Y Hu, <strong>G Yu</strong><sup>*</sup>, N Jiang<sup>*</sup>, B Yu<sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2022.723791/full" class="external-link" target="_blank" rel="noopener">Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection</a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:723791. (IF = 5.2，二区，Top期刊)</li> </ul> <h2 id="year-2021"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2021 <a class="heading-link" href="#year-2021"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>S Xu<sup>#</sup>, M Chen<sup>#</sup>, T Feng, L Zhan, L Zhou, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2021.774846" class="external-link" target="_blank" rel="noopener">Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:774846. (IF=4.772，三区)</li> <li>CH Gao, <strong>G Yu</strong>, P Cai<sup>*</sup>. <a href="https://doi.org/10.3389/fgene.2021.706907" class="external-link" target="_blank" rel="noopener">ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:706907. (IF=4.772，三区)</li> <li>S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang<sup>*</sup>, X Bo<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/molbev/msab166" class="external-link" target="_blank" rel="noopener">ggtreeExtra: Compact visualization of richly annotated phylogenetic data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2021, 38(9):4039-4042. (IF=8.800，一区，Top期刊)</li> <li>T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2021.100141" class="external-link" target="_blank" rel="noopener">clusterProfiler 4.0: A universal enrichment tool for interpreting omics data</a>. <strong><em>The Innovation</em></strong>. 2021, 2(3):100141.</li> <li>D Zeng<sup>#</sup>, Z Ye<sup>#</sup>, R Shen, <strong>G Yu</strong>, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao<sup>*</sup>. <a href="https://doi.org/10.3389/fimmu.2021.687975" class="external-link" target="_blank" rel="noopener">IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures</a>. <strong><em>Frontiers in Immunology</em></strong>. 2021, 12:687975. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=8.786，二区，Top期刊)</li> <li>T Wu, E Hu, X Ge<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.7717/peerj.11421" class="external-link" target="_blank" rel="noopener">nCov2019: an R package for studying the COVID-19 coronavirus pandemic</a>. <strong><em>PeerJ</em></strong>. 2021, 9:e11421. (IF=3.061，三区)</li> <li>R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, <strong>G Yu</strong>, SC Hicks, MD Robinson<sup>*</sup>. <a href="https://doi.org/10.12688/f1000research.26669.2" class="external-link" target="_blank" rel="noopener">TreeSummarizedExperiment: a S4 class for data with hierarchical structure</a>. <strong><em>F1000Research</em></strong>. 2021, 9:1246.</li> <li>S Liu, <strong>G Yu</strong><sup>*</sup>, L Liu<sup>*</sup>, X Zou, L Zhou, E Hu, Y Song. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2021.625236" class="external-link" target="_blank" rel="noopener">Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:625236. (IF=4.772，三区)</li> </ul> <h2 id="year-2020"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2020 <a class="heading-link" href="#year-2020"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>J He<sup>#</sup>, S Xu<sup>#</sup>, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href="https://doi.org/10.18632/aging.103168" class="external-link" target="_blank" rel="noopener">Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis</a>. <strong><em>Aging (Albany NY)</em></strong>. 2020, 12(9):8583-8604. (IF=5.682，二区)</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1002/cpbi.96" class="external-link" target="_blank" rel="noopener">Using ggtree to Visualize Data on Tree-Like Structure</a>. <strong><em>Current Protocols in Bioinformatics</em></strong>. 2020, 69(1):e96. (<em><strong>Invited paper</strong></em>) <a href="https://onlinelibrary.wiley.com/share/author/WQ5Z45WFKYDM43DXQGAI?target=10.1002/cpbi.96" class="external-link" target="_blank" rel="noopener"><i class="fa fa-file-pdf-o fa-2x" aria-hidden="true" style="color:black;font-size: 150%;"></i></a></li> <li>LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/molbev/msz240" class="external-link" target="_blank" rel="noopener">treeio: an R package for phylogenetic tree input and output with richly annotated and associated data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2020, 37(2):599-603. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (<strong>IF=16.240</strong>，一区，Top期刊)</li> <li>Z Hao, D Lv, Y Ge, J Shi, D Weijers, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href="https://peerj.com/articles/cs-251/" class="external-link" target="_blank" rel="noopener">RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms</a>. <strong><em>PeerJ Computer Science</em></strong>. 2020, 6:e251. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=1.392，三区)</li> </ul> <h2 id="year-2018"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2018 <a class="heading-link" href="#year-2018"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li><strong>G Yu</strong><sup>*</sup>, TTY Lam, H Zhu, Y Guan<sup>*</sup>. <a href="https://academic.oup.com/mbe/article-abstract/35/12/3041/5142656" class="external-link" target="_blank" rel="noopener">Two methods for mapping and visualizing associated data on phylogeny using ggtree</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2018, 35(12):3041-3043. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (<strong>IF=14.797</strong>，一区， Top期刊)</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/bioinformatics/bty410" class="external-link" target="_blank" rel="noopener">Using meshes for MeSH term enrichment and semantic analyses</a>. <strong><em>Bioinformatics</em></strong>. 2018, 34(21):3766-3767. (IF=4.531, 一区， Top期刊)</li> </ul> <h2 id="year-2010-2017"> <i class="fa fa-bar-chart fa-1x" aria-hidden="true"></i> Selected publications (2010-2017) <a class="heading-link" href="#year-2010-2017"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract" class="external-link" target="_blank" rel="noopener">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=6.363, 一区，Top期刊)</li> <li><strong>G Yu</strong>, QY He<sup>*</sup>. <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E" class="external-link" target="_blank" rel="noopener">ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization</a>. <strong><em>Molecular BioSystems</em></strong>. 2016, 12(2):477-479. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=2.781，三区)</li> <li><strong>G Yu</strong><sup>*</sup>, LG Wang, QY He<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145" class="external-link" target="_blank" rel="noopener">ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(14):2382-2383. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=5.766, 一区， Top期刊)</li> <li><strong>G Yu</strong><sup>*</sup>, LG Wang, GR Yan, QY He<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu684" class="external-link" target="_blank" rel="noopener">DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(4):608-609. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=5.766, 一区， Top期刊)</li> <li><strong>G Yu</strong>, LG Wang, Y Han, QY He<sup>*</sup>. <a href="http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118" class="external-link" target="_blank" rel="noopener">clusterProfiler: an R package for comparing biological themes among gene clusters</a>. <strong><em>OMICS: A Journal of Integrative Biology</em></strong>. 2012, 16(5):284-287. (IF=2.730， 四区)</li> <li><strong>G Yu</strong><sup>#</sup>, F Li<sup>#</sup>, Y Qin, X Bo<sup>*</sup>, Y Wu, S Wang<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976" class="external-link" target="_blank" rel="noopener">GOSemSim: an R package for measuring semantic similarity among GO terms and gene products</a>. <strong><em>Bioinformatics</em></strong>. 2010, 26(7):976-978. (IF=4.877, 二区， Top期刊)</li> </ul> <h2 id="books"> <i class="fa fa-book fa-1x" aria-hidden="true"></i> Books <a class="heading-link" href="#books"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>沈百荣，杨恩策. 基于理工信的医学数据采集与分析（基础医学“101计划”核心教材）. <strong><em>北京大学医学出版社</em></strong>, 2024. ISBN: <a href="https://www.pumpedu.com/en-shop/7263.html" class="external-link" target="_blank" rel="noopener">9787565931987</a></li> <li><strong>余光创（著）</strong>, 李林, 罗晓（译）. R实战：系统发育树的数据集成操作及可视化. <strong><em>电子工业出版社</em></strong>, 2023. ISBN: <a href="https://u.jd.com/uu7G4qC" class="external-link" target="_blank" rel="noopener">9787121451829</a></li> <li><strong>G Yu</strong>. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). <strong><em>Chapman and Hall/CRC</em></strong>, 2023. doi: <a href="https://doi.org/10.1201/9781003279242" class="external-link" target="_blank" rel="noopener">10.1201/9781003279242</a>, ISBN: <a href="https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational/dp/1032233575" class="external-link" target="_blank" rel="noopener">9781032233574</a></li> <li><strong>Yu G</strong>. <a href="http://dx.doi.org/10.1007/978-1-0716-0301-7_11" class="external-link" target="_blank" rel="noopener">Gene Ontology Semantic Similarity Analysis Using GOSemSim</a>. In: Kidder B. (eds) Stem Cell Transcriptional Networks. <em><strong>Methods in Molecular Biology</strong></em>, 2020, 2117:207-215. Humana, New York, NY. ISBN: <a href="https://link.springer.com/book/10.1007/978-1-0716-0301-7" class="external-link" target="_blank" rel="noopener">9781071603000</a></li> </ul> + <style> @media only screen and (max-width: 768px) { td { display: block; } } </style> <table style="border:none; font-size: 90%; width:100%;"> <tr style="border:none;"> <td style="border:none;"> <ul> <li><sup>#</sup> Co-first authors</li> <li><sup>*</sup> Co-corresponding authors</li> <li><i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i>：ESI Highly Cited Paper (9X)</li> <li>分区：文章发表当年的中科院小类分区</li> <li>IF：文章发表当年的影响因子</li> <li><a href="http://yulab-smu.top/awards" >课题组学术榜</a></li> </ul> </td> <td style="border:none;"> <a href="https://scholar.google.com/citations?user=DO5oG40AAAAJ"><img src="http://yulab-smu.top/images/citation.png" height='200px'/></a> </td> </tr> </table> <h2 id="year-2025"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2025 <a class="heading-link" href="#year-2025"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>M Chen<sup>#</sup>, X Luo<sup>#</sup>, S Xu<sup>#</sup>, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen<sup>*</sup>, TTY Lam<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. <strong><em>iMeta</em></strong>. accepted.</li> <li>D Zeng<sup>#</sup>, Y Fang<sup>#</sup>, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, W Liao<sup>*</sup>. <a href="https://doi.org/10.1016/j.crmeth.2024.100910" class="external-link" target="_blank" rel="noopener">Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0</a>. <strong><em>Cell Reports Methods</em></strong>. accepted.</li> </ul> <h2 id="year-2024"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2024 <a class="heading-link" href="#year-2024"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>M Luo<sup>*#</sup>, W Yang<sup>#</sup>, L Bai<sup>#</sup>, L Zhang<sup>#</sup>, JW Huang<sup>#</sup>, Y Cao<sup>#</sup>, Y Xie<sup>#</sup>, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, <strong>G Yu</strong>, C Tian, LN Jin, J Dai<sup>*</sup>, B Xia<sup>*</sup>, B Sun<sup>*</sup>, F Chen<sup>*</sup>, YZ Gao<sup>*</sup>, H Wang<sup>*</sup>, B Wang<sup>*</sup>, D Zhang<sup>*</sup>, X Cao<sup>*</sup>, H Wang<sup>*</sup>, T Huang<sup>*</sup>. <a href="https://doi.org/10.59717/j.xinn-life.2024.100105" class="external-link" target="_blank" rel="noopener">Artificial intelligence for life sciences: A comprehensive guide and future trends</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100105.</li> <li>Z Miao<sup>#</sup>, T Tian<sup>#</sup>, W Chen<sup>#</sup>, Q Wang<sup>#</sup>, L Ma<sup>#</sup>, D Zhang<sup>#</sup>, M Xie<sup>#</sup>, Z Yu<sup>#</sup>, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo<sup>*</sup>, M Luo<sup>*</sup>, L Yuan<sup>*</sup>, C Tian<sup>*</sup>, L Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, D Zhang<sup>*</sup>, S Sun<sup>*</sup>. <a href="https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100097" class="external-link" target="_blank" rel="noopener">Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100097.</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100722" class="external-link" target="_blank" rel="noopener">Thirteen years of clusterProfiler</a>. <strong><em>The Innovation</em></strong>. 2024, 5(6):100722.</li> <li>S Xu<sup>#</sup>, E Hu<sup>#</sup>, Y Cai<sup>#</sup>, Z Xie<sup>#</sup>, X Luo<sup>#</sup>, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.nature.com/articles/s41596-024-01020-z" class="external-link" target="_blank" rel="noopener">Using clusterProfiler to characterise Multi-Omics Data</a>. <strong><em>Nature Protocols</em></strong>. 2024, 19(11):3292-3320.</li> <li>Y Chen<sup>#</sup>, LN He<sup>#</sup>, Y Zhang, J Gong, S Xu, Y Shu, D Zhang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Z Zuo<sup>*</sup>. <a href="http://doi.org/10.1002/imt2.229" class="external-link" target="_blank" rel="noopener">tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package</a>. <strong><em>iMeta</em></strong>. 2024, 3(5):e229.</li> <li>D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://journals.lww.com/cmj/fulltext/2024/08200/reducing_language_barriers,_promoting_information.7.aspx" class="external-link" target="_blank" rel="noopener">Reducing language barriers, promoting information absorption, and communication using <em>fanyi</em></a>. <strong><em>Chinese Medical Journal</em></strong>. 2024, 137(16):1950-1956.</li> <li>XK Ma<sup>#</sup>, Y Yu<sup>#</sup>, T Huang<sup>#</sup><sup>*</sup>, D Zhang, C Tian, W Tang, M Luo, P Du<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, L Yang<sup>*</sup>. <a href="https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100083" class="external-link" target="_blank" rel="noopener">Bioinformatics Software Development: principles and future directions</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100083.</li> <li>Y Yang<sup>#</sup>, S Xu<sup>#</sup>, Y Hong, Y Cai, W Tang, J Wang, B Shen<sup>*</sup>, H Zong<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.59717/j.xinn-life.2024.100079" class="external-link" target="_blank" rel="noopener">Computational modeling for medical data: from data collection to knowledge discovery</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100079.</li> <li>L Zhan<sup>#</sup>, X Luo<sup>#</sup>, W Xie<sup>#</sup>, XA Zhu<sup>#</sup>, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.sciencedirect.com/science/article/pii/S167385272400033X" class="external-link" target="_blank" rel="noopener">shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals</a>. <strong><em>Journal of Genetics and Genomics</em></strong>. 2024, 51(7):762-768.</li> <li>L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.sciencedirect.com/science/article/pii/S2667005424000206" class="external-link" target="_blank" rel="noopener">Resolving Tumor Evolution: A Phylogenetic Approach</a>. <strong><em>Journal of the National Cancer Center</em></strong>. 2024, 4(2):97-106.</li> <li>Q Wang, W Tang, L Chen, L Deng, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100637" class="external-link" target="_blank" rel="noopener">Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data</a>. <strong><em>The Innovation</em></strong>. 2024, 5(4):100637.</li> <li>Y Cai<sup>#</sup>, W Hu<sup>#</sup>, Y Pei, Hao Zhao<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2024.100627" class="external-link" target="_blank" rel="noopener">Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic</a>. <strong><em>The Innovation</em></strong>. 2024, 5(3):100627.</li> <li>Y Lai<sup>#</sup>, W Tang<sup>#</sup>, X Luo, H Zheng, Y Zhang<sup>*</sup>, M Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Min Yang<sup>*</sup>. <a href="https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1369116" class="external-link" target="_blank" rel="noopener">Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis</a>. <strong><em>Frontiers in Immunology</em></strong>. 2024, 15:1369116.</li> <li>CH Gao, C Chen, T Akyol, A Dusa, <strong>G Yu</strong>, B Cao, P Cai<sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/10.1002/imt2.177" class="external-link" target="_blank" rel="noopener">ggVennDiagram: intuitive Venn diagram software extended</a>. <strong><em>iMeta</em></strong>. 2024, 3(1):e177.</li> <li>Y Ye<sup>#</sup>, MH Shum<sup>#</sup>, JL Tsui<sup>#</sup>, <strong>G Yu</strong><sup>#</sup>, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam<sup>*</sup>. <a href="https://doi.org/10.1371/journal.pcbi.1011871" class="external-link" target="_blank" rel="noopener">Robust expansion of phylogeny for fast-growing genome sequence data</a>. <strong><em>PLoS Computational Biology</em></strong>. 2024, 20(2):e1011871.</li> <li>S Wen, S Mo, J Zhou, Y Lv, K Khazaie<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fcell.2024.1365242/full" class="external-link" target="_blank" rel="noopener">Single-cell and spatial-omics in delineating immune-related diseases</a>. <strong><em>Frontiers in Cell and Developmental Biology</em></strong>. 2024, 12:1365242.</li> </ul> <h2 id="year-2023"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2023 <a class="heading-link" href="#year-2023"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>X Zhang, B Liang, Y Huang, H Meng, Z Li, J Du, L Zhou, Y Zhong, B Wang, X Lin, <strong>G Yu</strong>, X Chen, W Lu, ZS Chen, X Yang, Z Huang<sup>*</sup>. <a href="https://doi.org/10.1002/advs.202303753" class="external-link" target="_blank" rel="noopener">Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics</a>. <strong><em>Advanced Science</em></strong>. 2023, 10(36):2303753. (IF = 14.3，一区)</li> <li>M Kang, F Lin, Z Jiang, X Tan, X Lin, Z Liang, C Xiao, Y Xia, W Guan, Z Yang, <strong>G Yu</strong>, M Zanin, S Tang<sup>*</sup>, SS Wong<sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/irv.13172" class="external-link" target="_blank" rel="noopener">The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults</a>. <strong><em>Influenza and Other Respiratory Viruses</em></strong>. 2023, 17(7):e13172. (IF = 4.3，四区)</li> <li>W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, <strong>G Yu</strong><sup>*</sup>. <a href="https://dx.doi.org/10.1080/19490976.2023.2223349" class="external-link" target="_blank" rel="noopener">MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm</a>. <strong><em>Gut Microbes</em></strong>. 2023, 15(1):2223349. (IF = 12.2，一区)</li> <li>S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2023.100388" class="external-link" target="_blank" rel="noopener">MicrobiotaProcess: A comprehensive R package for deep mining microbiome</a>. <strong><em>The Innovation</em></strong>. 2023, 4(2):100388. (IF = 33.2，一区)</li> <li>S Guo<sup>*</sup>, D Zhang, H Wang, Q An, <strong>G Yu</strong>, J Han, C Jiang, J Huang. <a href="https://www.frontiersin.org/articles/10.3389/fmed.2023.1146896/full" class="external-link" target="_blank" rel="noopener">Computational and Systematic Analysis of Multi-omics Data for Drug Discovery and Development</a>. <strong><em>Frontiers in Medicine</em></strong>. 2023, 10:1146896. (IF = 3.1，三区)</li> </ul> <h2 id="year-2022"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2022 <a class="heading-link" href="#year-2022"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, <strong>G Yu</strong><sup>*</sup>. <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56" class="external-link" target="_blank" rel="noopener">Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data</a>. <strong><em>iMeta</em></strong>, 2022, 1(4):e56.</li> <li>Q Wang<sup>#</sup>, M Li<sup>#</sup>, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1002/cpz1.585" class="external-link" target="_blank" rel="noopener">Exploring epigenomic datasets by ChIPseeker</a>. <strong><em>Current Protocols</em></strong>, 2022, 2(10): e585. <a href="https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585" class="external-link" target="_blank" rel="noopener"><i class="fa fa-file-pdf-o fa-2x" aria-hidden="true" style="color:black;font-size: 150%;"></i></a></li> <li>Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2022.951774" class="external-link" target="_blank" rel="noopener">Characterization of toxin-antitoxin systems from public sequencing data: a case study in <em>Pseudomonas aeruginosa</em></a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:951774. (IF = 5.2，二区，Top期刊)</li> <li>T Feng<sup>#</sup>, T Wu<sup>#</sup>, Y Zhang<sup>#</sup>, L Zhou<sup>#</sup>, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang<sup>*</sup>, X Shang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fonc.2022.912694/" class="external-link" target="_blank" rel="noopener">Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells</a>. <strong><em>Frontiers in Oncology</em></strong>. 2022, 12:912694. (IF = 4.7，三区)</li> <li>L Zhou<sup>#</sup>, T Feng<sup>#</sup>, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/bib/bbac222" class="external-link" target="_blank" rel="noopener">ggmsa: a visual exploration tool for multiple sequence alignment and associated data</a>. <strong><em>Briefings in Bioinformatics</em></strong>. 2022, 23(4):bbac222. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF = 9.5，一区，Top期刊)</li> <li>N Sato, Y Tamada, <strong>G Yu</strong>, Y Okuno<sup>*</sup>. <a href="https://doi.org/10.1093/bioinformatics/btac175" class="external-link" target="_blank" rel="noopener">CBNplot: Bayesian network plots for enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2022, 38(10):2959-2960. (IF=5.8，一区，Top期刊)</li> <li>T Wu, CL Xiao, TT Lam, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2022.890775/full" class="external-link" target="_blank" rel="noopener">Biomedical Data Visualization: Methods and Applications</a>. <strong><em>Frontiers in Genetics</em></strong>. 2022, 13:890775. (IF=3.7，三区)</li> <li>X Zhao<sup>#</sup>, W Tang<sup>#</sup>, H Wan<sup>#</sup>, Z Lan H Qin, Q Lin, Y Hu, <strong>G Yu</strong><sup>*</sup>, N Jiang<sup>*</sup>, B Yu<sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2022.723791/full" class="external-link" target="_blank" rel="noopener">Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection</a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:723791. (IF = 5.2，二区，Top期刊)</li> </ul> <h2 id="year-2021"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2021 <a class="heading-link" href="#year-2021"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>S Xu<sup>#</sup>, M Chen<sup>#</sup>, T Feng, L Zhan, L Zhou, <strong>G Yu</strong><sup>*</sup>. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2021.774846" class="external-link" target="_blank" rel="noopener">Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:774846. (IF=4.772，三区)</li> <li>CH Gao, <strong>G Yu</strong>, P Cai<sup>*</sup>. <a href="https://doi.org/10.3389/fgene.2021.706907" class="external-link" target="_blank" rel="noopener">ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:706907. (IF=4.772，三区)</li> <li>S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang<sup>*</sup>, X Bo<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/molbev/msab166" class="external-link" target="_blank" rel="noopener">ggtreeExtra: Compact visualization of richly annotated phylogenetic data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2021, 38(9):4039-4042. (IF=8.800，一区，Top期刊)</li> <li>T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1016/j.xinn.2021.100141" class="external-link" target="_blank" rel="noopener">clusterProfiler 4.0: A universal enrichment tool for interpreting omics data</a>. <strong><em>The Innovation</em></strong>. 2021, 2(3):100141.</li> <li>D Zeng<sup>#</sup>, Z Ye<sup>#</sup>, R Shen, <strong>G Yu</strong>, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao<sup>*</sup>. <a href="https://doi.org/10.3389/fimmu.2021.687975" class="external-link" target="_blank" rel="noopener">IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures</a>. <strong><em>Frontiers in Immunology</em></strong>. 2021, 12:687975. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=8.786，二区，Top期刊)</li> <li>T Wu, E Hu, X Ge<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.7717/peerj.11421" class="external-link" target="_blank" rel="noopener">nCov2019: an R package for studying the COVID-19 coronavirus pandemic</a>. <strong><em>PeerJ</em></strong>. 2021, 9:e11421. (IF=3.061，三区)</li> <li>R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, <strong>G Yu</strong>, SC Hicks, MD Robinson<sup>*</sup>. <a href="https://doi.org/10.12688/f1000research.26669.2" class="external-link" target="_blank" rel="noopener">TreeSummarizedExperiment: a S4 class for data with hierarchical structure</a>. <strong><em>F1000Research</em></strong>. 2021, 9:1246.</li> <li>S Liu, <strong>G Yu</strong><sup>*</sup>, L Liu<sup>*</sup>, X Zou, L Zhou, E Hu, Y Song. <a href="https://www.frontiersin.org/articles/10.3389/fgene.2021.625236" class="external-link" target="_blank" rel="noopener">Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:625236. (IF=4.772，三区)</li> </ul> <h2 id="year-2020"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2020 <a class="heading-link" href="#year-2020"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>J He<sup>#</sup>, S Xu<sup>#</sup>, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href="https://doi.org/10.18632/aging.103168" class="external-link" target="_blank" rel="noopener">Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis</a>. <strong><em>Aging (Albany NY)</em></strong>. 2020, 12(9):8583-8604. (IF=5.682，二区)</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1002/cpbi.96" class="external-link" target="_blank" rel="noopener">Using ggtree to Visualize Data on Tree-Like Structure</a>. <strong><em>Current Protocols in Bioinformatics</em></strong>. 2020, 69(1):e96. (<em><strong>Invited paper</strong></em>) <a href="https://onlinelibrary.wiley.com/share/author/WQ5Z45WFKYDM43DXQGAI?target=10.1002/cpbi.96" class="external-link" target="_blank" rel="noopener"><i class="fa fa-file-pdf-o fa-2x" aria-hidden="true" style="color:black;font-size: 150%;"></i></a></li> <li>LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, <strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/molbev/msz240" class="external-link" target="_blank" rel="noopener">treeio: an R package for phylogenetic tree input and output with richly annotated and associated data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2020, 37(2):599-603. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (<strong>IF=16.240</strong>，一区，Top期刊)</li> <li>Z Hao, D Lv, Y Ge, J Shi, D Weijers, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href="https://peerj.com/articles/cs-251/" class="external-link" target="_blank" rel="noopener">RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms</a>. <strong><em>PeerJ Computer Science</em></strong>. 2020, 6:e251. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=1.392，三区)</li> </ul> <h2 id="year-2018"> <i class="fa fa-calendar fa-1x" aria-hidden="true"></i> 2018 <a class="heading-link" href="#year-2018"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li><strong>G Yu</strong><sup>*</sup>, TTY Lam, H Zhu, Y Guan<sup>*</sup>. <a href="https://academic.oup.com/mbe/article-abstract/35/12/3041/5142656" class="external-link" target="_blank" rel="noopener">Two methods for mapping and visualizing associated data on phylogeny using ggtree</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2018, 35(12):3041-3043. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (<strong>IF=14.797</strong>，一区， Top期刊)</li> <li><strong>G Yu</strong><sup>*</sup>. <a href="https://doi.org/10.1093/bioinformatics/bty410" class="external-link" target="_blank" rel="noopener">Using meshes for MeSH term enrichment and semantic analyses</a>. <strong><em>Bioinformatics</em></strong>. 2018, 34(21):3766-3767. (IF=4.531, 一区， Top期刊)</li> </ul> <h2 id="year-2010-2017"> <i class="fa fa-bar-chart fa-1x" aria-hidden="true"></i> Selected publications (2010-2017) <a class="heading-link" href="#year-2010-2017"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract" class="external-link" target="_blank" rel="noopener">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=6.363, 一区，Top期刊)</li> <li><strong>G Yu</strong>, QY He<sup>*</sup>. <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E" class="external-link" target="_blank" rel="noopener">ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization</a>. <strong><em>Molecular BioSystems</em></strong>. 2016, 12(2):477-479. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=2.781，三区)</li> <li><strong>G Yu</strong><sup>*</sup>, LG Wang, QY He<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145" class="external-link" target="_blank" rel="noopener">ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(14):2382-2383. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=5.766, 一区， Top期刊)</li> <li><strong>G Yu</strong><sup>*</sup>, LG Wang, GR Yan, QY He<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu684" class="external-link" target="_blank" rel="noopener">DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(4):608-609. <i class="fa fa-trophy fa-2x" aria-hidden="true" style="color:#CC5500;font-size: 150%;"></i> (IF=5.766, 一区， Top期刊)</li> <li><strong>G Yu</strong>, LG Wang, Y Han, QY He<sup>*</sup>. <a href="http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118" class="external-link" target="_blank" rel="noopener">clusterProfiler: an R package for comparing biological themes among gene clusters</a>. <strong><em>OMICS: A Journal of Integrative Biology</em></strong>. 2012, 16(5):284-287. (IF=2.730， 四区)</li> <li><strong>G Yu</strong><sup>#</sup>, F Li<sup>#</sup>, Y Qin, X Bo<sup>*</sup>, Y Wu, S Wang<sup>*</sup>. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976" class="external-link" target="_blank" rel="noopener">GOSemSim: an R package for measuring semantic similarity among GO terms and gene products</a>. <strong><em>Bioinformatics</em></strong>. 2010, 26(7):976-978. (IF=4.877, 二区， Top期刊)</li> </ul> <h2 id="books"> <i class="fa fa-book fa-1x" aria-hidden="true"></i> Books <a class="heading-link" href="#books"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <ul> <li>沈百荣，杨恩策. 基于理工信的医学数据采集与分析（基础医学“101计划”核心教材）. <strong><em>北京大学医学出版社</em></strong>, 2024. ISBN: <a href="https://www.pumpedu.com/en-shop/7263.html" class="external-link" target="_blank" rel="noopener">9787565931987</a></li> <li><strong>余光创（著）</strong>, 李林, 罗晓（译）. R实战：系统发育树的数据集成操作及可视化. <strong><em>电子工业出版社</em></strong>, 2023. ISBN: <a href="https://u.jd.com/uu7G4qC" class="external-link" target="_blank" rel="noopener">9787121451829</a></li> <li><strong>G Yu</strong>. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). <strong><em>Chapman and Hall/CRC</em></strong>, 2023. doi: <a href="https://doi.org/10.1201/9781003279242" class="external-link" target="_blank" rel="noopener">10.1201/9781003279242</a>, ISBN: <a href="https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational/dp/1032233575" class="external-link" target="_blank" rel="noopener">9781032233574</a></li> <li><strong>Yu G</strong>. <a href="http://dx.doi.org/10.1007/978-1-0716-0301-7_11" class="external-link" target="_blank" rel="noopener">Gene Ontology Semantic Similarity Analysis Using GOSemSim</a>. In: Kidder B. (eds) Stem Cell Transcriptional Networks. <em><strong>Methods in Molecular Biology</strong></em>, 2020, 2117:207-215. Humana, New York, NY. ISBN: <a href="https://link.springer.com/book/10.1007/978-1-0716-0301-7" class="external-link" target="_blank" rel="noopener">9781071603000</a></li> </ul> Second snippet diff --git a/publications/index.html b/publications/index.html index 4f23f9e..b82fd07 100644 --- a/publications/index.html +++ b/publications/index.html @@ -39,7 +39,7 @@ -M Chen#, X Luo#, S Xu#, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen__*, TTY Lam__*, G Yu*. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. iMeta. accepted. +M Chen#, X Luo#, S Xu#, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen*, TTY Lam*, G Yu*. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. iMeta. accepted. D Zeng#, Y Fang#, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu*, G Yu*, W Liao*. Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0. Cell Reports Methods. accepted. @@ -172,12 +172,12 @@ - + - + @@ -332,7 +332,7 @@