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USD 60 /hr
Hire Dr. Xinyu Z.
United States
USD 60 /hr
20+ Yrs in Computational Biology: AI & High-Throughput Omics Analysis for Disease Prediction
Profile Summary
Subject Matter Expertise
Services
Writing
Technical Writing
Research
Meta-Research,
Scientific and Technical Research
Consulting
Healthcare Consulting,
Scientific and Technical Consulting
Data & AI
Predictive Modeling,
Statistical Analysis,
Image Processing,
Image Analysis,
Algorithm Design-Non ML,
Algorithm Design-ML,
Data Visualization,
Big Data Analytics,
Text Mining & Analytics,
Data Mining
Product Development
Product Evaluation,
Quality Assurance & Control (QA/QC),
Prototyping
Work Experience
Yale University
- Present 
Research Scientist
Yale University Medical School
June 2014 - July 2024
Associate Professor
Chinese Academy of Sciences, Institute of Microbiology
March 2009 - June 2014
Bioinformatics Scientist
Cancer Institute, Chinese Academy of Sciences
October 2000 - September 2004
Education
Tsinghua University
- Present
Doctor of Philosophy (PhD), Bioinformatics
Tsinghua University
September 2004 - July 2007
Master of Science (MS), Biochemistry
Institute of Oceanology, Chinese Academy of Sciences
September 1996 - July 1999
Bachelor of Science (BS), Biochemistry
Shandong University
September 1991 - June 1995
Certifications
- Certification details not provided.
Publications
JOURNAL ARTICLE
Epigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans <head>
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</head> . Translational Psychiatry.
Xinyu Zhang, Weimiao Wu, Zhong Wang, Ke Xu, Amei Amei, Joel Gelernter, Hongyu Zhao, Amy C. Justice, Zuoheng Wang(2019). Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use . Genetics. 213. (4). p. 1225--1236. Genetics Society of America
Xinyu Zhang(2018). DNA Methylation Signatures Predict HIV Prognosis and Mortality . protocols.io.
Xinyu Zhang, Ying Hu, Amy C Justice, Boyang Li, Zuoheng Wang, Hongyu Zhao, John H Krystal, Ke Xu (2017). DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty . Nature Communications.
Xinyu Zhang, Guohua Xiao, Qiang Gao(2017). Bioinformatic Approaches for Fungal Omics . BioMed Research International. 2017. p. 1--1. Hindawi Publishing Corporation
Ge, Y. Y., Wang, Y. C., Liu, Y. X., Tan, Y. M., Ren, X. X., Zhang, X. Y., Hyde, K. D., Liu, Y. F., Liu, Z. Y.(2016). Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus . Bmc Genomics. 17.
Zhang, Xinyu, Xu, Ke, Wang, Zuoheng, Hu, Ying, Sinha, Rajita(2016). Epigenome-wide association analysis revealed that SOCS3 methylation influences the effect of cumulative stress on obesity . Biological psychology.
Zhang, Xinyu, Justice, Amy C., Hu, Ying, Wang, Zuoheng, Zhao, Hongyu, Wang, Guilin, Johnson, Eric O., Emu, Brinda, Sutton, Richard E., Krystal, John H.(2016). Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals . Epigenetics. 11. (10). p. 750-760.
Wei, X., Xiaoling, Z., Kai, M., Rui, W., Jing, X., Min, G., Zhonghong, W., Jianhui, T., Xinyu, Z., Lei, A.(2016). Characterization and comparative analyses of transcriptomes for in vivo and in vitro produced peri-implantation conceptuses and endometria from sheep . Journal of Reproduction and Development. 62. (3). p. 279-287.
Xu, C., Ju, X., Song, D., Huang, F., Tang, D., Zou, Z., Zhang, C., Joshi, T., Jia, L., Xu, W.(2015). An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus . Molecular psychiatry. 20. (4). p. 536-544.
Zhang, XinYu, Wang, YanYan, Zhou, QiMing, Zhang, XiaoLing, Wei, JiangChun(2015). Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms . Science China Life Sciences. 58. (1). p. 89-100.
Zhang, Xinyu, Yue, Qun, Chen, Li, Li, Yan, Bills, Gerald F., Xiang, Meichun, Li, Shaojie, Che, Yongsheng, Wang, Chengshu, Niu, Xuemei, et al.(2015). Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes) . Mbio. 6. (3).
Zhang, Xinyu, Wang, Xiuna, Zhang, Xiaoling, Liu, Ling, Xiang, Meichun, Wang, Wenzhao, Sun, Xiang, Che, Yongsheng, Guo, Liangdong, Liu, Gang, et al.(2015). Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products . Bmc Genomics. 16.
Zhang, Xinyu, Lai, Yiling, Liu, Keke, Zhang, Xiaoling, Li, Kuan, Wang, Niuniu, Shu, Chi, Wu, Yunpeng, Wang, Chengshu, Bushley, Kathryn E.(2014). Comparative genomics and transcriptomics analyses reveal divergent lifestyle features of nematode endoparasitic fungus Hirsutella minnesotensis . Genome biology and evolution. 6. (11). p. 3077-3093.
Zhang, Xinyu, Liu, Keke, Zhang, Weiwei, Lai, Yiling, Xiang, Meichun, Wang, Xiuna, Liu, Xingzhong(2014). Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi . Bmc Genomics. 15.
Wang, Yan-Yan, Liu, Bin, Zhang, Xin-Yu, Zhou, Qi-Ming, Zhang, Tao, Li, Hui, Yu, Yu-Fei, Zhang, Xiao-Ling, Hao, Xi-Yan, Wang, Meng, et al.(2014). Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota) . Bmc Genomics. 15.
Zhang, Xinyu, Hu, Xiao, Xiao, Guohua, Zheng, Peng, Shang, Yanfang, Su, Yao, Liu, Xingzhong, Zhan, Shuai, Leger, Raymond J. St, Wang, Chengshu(2014). Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation . Proceedings of the National Academy of Sciences. 111. (47). p. 16796-16801.
Zhang, Xinyu, Sun, Xianyun, Kang, Shu, Zhang, Yongjie, Tan, Xinqiu, Yu, Yufei, He, Haiyong, Liu, Yongfeng, Wang, Shu, Sun, Wenxian, et al.(2013). Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea virens in China . Plos One. 8. (9).
Hu, Xiao, Zhang, YongJie, Xiao, GuoHua, Zheng, Peng, Xia, YongLiang, Zhang, XingYu, St Leger, Raymond J, Liu, XingZhong, Wang, ChengShu(2013). Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus . Chinese Science Bulletin. 58. (23). p. 2846-2854.
Zhang, Xinyu, Chen, Li, Yue, Qun, Xiang, Meichun, Wang, Chengshu, Li, Shaojie, Che, Yongsheng, Ortiz-Lopez, Francisco Javier, Bills, Gerald F., Liu, Xingzhong, et al.(2013). Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis . Bmc Genomics. 14.
Zhang, Xinyu, Sun, Xianyun, Yu, Luning, Lan, Nan, Wei, Shiping, Yu, Yufei, Zhang, Hanxing, Li, Shaojie(2012). Analysis of the role of transcription factor VAD-5 in conidiation of Neurospora crassa . Fungal Genetics and Biology. 49. (5). p. 379-387.
Zhang, Xinyu, Zhang, Yu, Zhang, Zhenying, Zhang, Hanxing, Sun, Xianyun, Hu, Chengcheng, Li, Shaojie(2012). CDR4 is the major contributor to azole resistance among four Pdr5p-like ABC transporters in Neurospora crassa . Fungal biology. 116. (7). p. 848-854.
Zhang, Xinyu, Yang, Ence, Xu, Lingling, Yang, Ying, Xiang, Meichun, Wang, Chengshu, An, Zhiqiang, Liu, Xingzhong(2012). Origin and evolution of carnivorism in the Ascomycota (fungi) . Proceedings of the National Academy of Sciences. 109. (27). p. 10960-10965.
Zhang, Xinyu, Liu, Li, Wu, Chen, Wang, Ying, Zhong, Rong, Duan, Shengyu, Wei, Sheng, Lin, Songyi, Tan, Wen, Yu, Dianke(2011). Combined effect of genetic polymorphisms in P53, P73, and MDM2 on non-small cell lung cancer survival . Journal of Thoracic Oncology. 6. (11). p. 1793-1800.
A functional polymorphism (− 1607 1G→ 2G) in the matrix metalloproteinase‐1 promoter is associated with development and progression of lung cancer @article{RID:0215171657869-86,
title = {A functional polymorphism (− 1607 1G→ 2G) in the matrix metalloproteinase‐1 promoter is associated with development and progression of lung cancer},
journal = {Cancer},
year = {2011},
author = {Liu, Li and Wu, Jing and Wu, Chen and Wang, Ying and Zhong, Rong and Zhang, Xinyu and Tan, Wen and Nie, Shaofa and Miao, Xiaoping and Lin, Dongxin},
volume = {117},
number = {22},
pages = {5172-5181}
}. Cancer.
Zhang, Xin-yu, Shi, Lin, Liu, Yan, Tian, Feng, Zhao, Hai-tao, Miao, Xiao-ping, Huang, Ming-lie, Zhu, Xiao-yan(2010). ICPS: an integrative cancer profiler system . Bioinformatics. 26. (20). p. 2649-2650.
Zhang, Xin-Yu, Zhang, Kai-Tai, Tian, Feng, Xia, Yongjing, Wu, Yi-Qing, Liu, Xiang-Jun(2007). Integrative analysis and validation of robust gene signature in lung cancer . Biochemical and Biophysical Research Communications. 358. (3). p. 710-715.
Wang, Hong-Bao, Li, Hui, Wang, Qi-Gui, Zhang, Xin-Yu, Wang, Shou-Zhi, Wang, Yu-Xiang, Wang, Xiu-Ping(2007). Profiling of chicken adipose tissue gene expression by genome array . Bmc Genomics. 8.
Zhang, Xinyu, Tian, Feng, Zhang, Huayue, Song, Chi, Xia, Yongjing, Wu, Yiqing, Liu, Xiangjun(2007). miRAS: a data processing system for miRNA expression profiling study . Bmc Bioinformatics. 8.
Zhang, Xin-yu, Li, Tian-tian, Liu, Xiang-jun(2007). Detecting robust gene signature through integrated analysis of multiple types of high-throughput data in liver cancer . Acta Pharmacologica Sinica. 28. (12). p. 2005-2010.
Zhang, Xinyu, Liu, Yan, Sun, Wenyue, Zhang, Kaitai, Zheng, Hongwei, Ma, Ying, Lin, Dongmei, Feng, Lin, Lei, Wendong, Zhang, Ziqiang(2007). Identification of genes differentially expressed in human primary lung squamous cell carcinoma . Lung Cancer. 56. (3). p. 307-317.
Zhang, Xinyu, Wang, Xiaosong, Zhao, Haitao, Xu, Qingwen, Jin, Weibo, Liu, Changning, Zhang, Huagang, Huang, Zhibin, Zhang, Yu, Xin, Dianqi, et al.(2006). HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma . Nucleic Acids Research. 34. p. D607-D612.
Zhang, XY, Hu, Y, Cui, YP, Miao, XP, Tian, F, Xia, YJ, Wu, YQ, Liu, XJ(2006). Integrated genome-wide gene expression map and high-resolution analysis of aberrant chromosomal regions in squamous cell lung cancer . Febs Letters. 580. (11). p. 2774-2778.
Zhang, XM, Miao, XP, Tan, W, Ning, BT, Liu, ZH, Hong, Y, Song, WG, Guo, YL, Zhang, XY, Shen, Y, et al.(2005). Identification of functional genetic variants in cyclooxygenase-2 and their association with risk of esophageal cancer . Gastroenterology. 129. (2). p. 565-576.
Sun, WY, Zhang, KT, Zhang, XY, Lei, WD, Xiao, T, Ma, JF, Guo, SP, Shao, SJ, Zhang, HS, Liu, Y, et al.(2004). Identification of differentially expressed genes in human lung squamous cell carcinoma using suppression subtractive hybridization . Cancer Letters. 212. (1). p. 83-93.
张新宇,, 高燕宁(2004). PCR 引物设计及软件使用技巧. 生物信息学. 2. (4). p. 15-18.
张新宇,, 孙文越,, 程书钧,, 高燕宁(2004). SAGEmap 分析及 DNA 序列染色体定位的电子自动化实现. 生物信息学. 1. p. 005.
Yue, CM, Bi, MX, Tan, W, Deng, DJ, Zhang, XY, Guo, LP, Lin, DX, Lu, SH(2004). Short tandem repeat polymorphism in a novel esophageal cancer-related gene (ECRG2) implicates susceptibility to esophageal cancer in Chinese population . International Journal of Cancer. 108. (2). p. 232-236.
Cui, YP, Wang, JB, Zhang, XY, Lang, RG, Bi, MX, Guo, LP, Lu, SH(2003). ECRG2, a novel candidate of tumor suppressor gene in the esophageal carcinoma, interacts directly with metallothionein 2A and links to apoptosis . Biochemical and Biophysical Research Communications. 302. (4). p. 904-915.
Cui, YP, Wang, JB, Zhang, XY, Bi, MX, Guo, LP, Lu, SH(2003). Using yeast two-hybrid system to identify ECRG2 associated proteins and their possible interactions with ECRG2 gene . World Journal of Gastroenterology. 9. (9). p. 1892-1896.
张新宇, 孙文越, 程书钧, 高燕宁(2003). cDNA (EST) 文库的高通量生物信息学分析体系的构建与应用. 生物信息学. 1. p. 002.
徐洪涛,, 朴春爱,, 杨朵,, 王雷,, 张新宇,, 侯云德(2000). PCR 方法制备地高辛标记 DNA 探针检测中国对虾非包涵体型杆状病毒. 病毒学报. 16. (1). p. 73-75.
张新宇, 王雷, 李光友, 朱延雄(2000). 绿色巴夫藻硒多糖的提取, 分离与纯化. 海洋与湖沼. 31. (6). p. 643-646.
PREPRINT
Xinyu Zhang, Ying Hu, Ke Xu(2018). DNA Methylation Signatures Predict HIV Prognosis and Mortality v2 . {ZappyLab}, Inc.
Xinyu Zhang, Ying Hu, Ke Xu(2018). DNA Methylation Signatures Predict HIV Prognosis and Mortality v1 . {ZappyLab}, Inc.
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