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Multi-modal molecular programs regulate melanoma cell state.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31510-1
By:
- Andrews, Miles C.;
- Oba, Junna;
- Wu, Chang-Jiun;
- Zhu, Haifeng;
- Karpinets, Tatiana;
- Creasy, Caitlin A.;
- Forget, Marie-Andrée;
- Yu, Xiaoxing;
- Song, Xingzhi;
- Mao, Xizeng;
- Robertson, A. Gordon;
- Romano, Gabriele;
- Li, Peng;
- Burton, Elizabeth M.;
- Lu, Yiling;
- Sloane, Robert Szczepaniak;
- Wani, Khalida M.;
- Rai, Kunal;
- Lazar, Alexander J.;
- Haydu, Lauren E.
Publication type:
Article
Somatic Mutations in Circulating Cell-Free DNA and Risk for Hepatocellular Carcinoma in Hispanics.
Published in:
International Journal of Molecular Sciences, 2021, v. 22, n. 14, p. 7411, doi. 10.3390/ijms22147411
By:
- Jiao, Jingjing;
- Sanchez, Jessica I.;
- Thompson, Erika J.;
- Mao, Xizeng;
- McCormick, Joseph B.;
- Fisher-Hoch, Susan P.;
- Futreal, P. Andrew;
- Zhang, Jianhua;
- Beretta, Laura
Publication type:
Article
DMINDA: an integrated web server for DNA motif identification and analyses.
Published in:
Nucleic Acids Research, 2014, v. 42, n. W1, p. W12, doi. 10.1093/nar/gku315
By:
- Ma, Qin;
- Zhang, Hanyuan;
- Mao, Xizeng;
- Zhou, Chuan;
- Liu, Bingqiang;
- Chen, Xin;
- Xu, Ying
Publication type:
Article
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Published in:
Nucleic Acids Research, 2014, v. 42, n. D1, p. D654, doi. 10.1093/nar/gkt1048
By:
- Mao, Xizeng;
- Ma, Qin;
- Zhou, Chuan;
- Chen, Xin;
- Zhang, Hanyuan;
- Yang, Jincai;
- Mao, Fenglou;
- Lai, Wei;
- Xu, Ying
Publication type:
Article
The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces.
Published in:
Nucleic Acids Research, 2012, v. 40, n. 17, p. 8210, doi. 10.1093/nar/gks605
By:
- Mao, Xizeng;
- Zhang, Han;
- Yin, Yanbin;
- Xu, Ying
Publication type:
Article
dbCAN: a web resource for automated carbohydrate-active enzyme annotation.
Published in:
Nucleic Acids Research, 2012, v. 40, p. W445, doi. 10.1093/nar/gks479
By:
- Yanbin Yin;
- Xizeng Mao;
- Jincai Yang;
- Xin Chen;
- Fenglou Mao;
- Ying Xu
Publication type:
Article
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
Published in:
Nucleic Acids Research, 2011, v. 39, n. 22, p. e150, doi. 10.1093/nar/gkr766
By:
- Li, Guojun;
- Ma, Qin;
- Mao, Xizeng;
- Yin, Yanbin;
- Zhu, Xiaoran;
- Xu, Ying
Publication type:
Article
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Published in:
Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W316, doi. 10.1093/nar/gkr483
By:
- Xie, Chen;
- Mao, Xizeng;
- Huang, Jiaju;
- Ding, Yang;
- Wu, Jianmin;
- Dong, Shan;
- Kong, Lei;
- Gao, Ge;
- Li, Chuan-Yun;
- Wei, Liping
Publication type:
Article
The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27341-1
By:
- Tang, Ming;
- Abbas, Hussein A.;
- Negrao, Marcelo V.;
- Ramineni, Maheshwari;
- Hu, Xin;
- Hubert, Shawna Marie;
- Fujimoto, Junya;
- Reuben, Alexandre;
- Varghese, Susan;
- Zhang, Jianhua;
- Li, Jun;
- Chow, Chi-Wan;
- Mao, Xizeng;
- Song, Xingzhi;
- Lee, Won-Chul;
- Wu, Jia;
- Little, Latasha;
- Gumbs, Curtis;
- Behrens, Carmen;
- Moran, Cesar
Publication type:
Article
Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data.
Published in:
BioEnergy Research, 2016, v. 9, n. 1, p. 172, doi. 10.1007/s12155-015-9674-2
By:
- Chen, Xin;
- Ma, Qin;
- Rao, Xiaolan;
- Tang, Yuhong;
- Wang, Yan;
- Li, Gaoyang;
- Zhang, Chi;
- Mao, Xizeng;
- Dixon, Richard;
- Xu, Ying
Publication type:
Article
New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes.
Published in:
BioEnergy Research, 2014, v. 7, n. 4, p. 1481, doi. 10.1007/s12155-014-9486-9
By:
- Zhou, Chuan;
- Ma, Qin;
- Mao, Xizeng;
- Liu, Bingqiang;
- Yin, Yanbin;
- Xu, Ying
Publication type:
Article
Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective.
Published in:
SCIENCE CHINA Life Sciences, 2014, v. 57, n. 11, p. 1121, doi. 10.1007/s11427-014-4734-y
By:
- Ma, Qin;
- Chen, Xin;
- Liu, Chao;
- Mao, XiZeng;
- Zhang, HanYuan;
- Ji, Fei;
- Wu, ChunGuo;
- Xu, Ying
Publication type:
Article
Hypoxia and miscoupling between reduced energy efficiency and signaling to cell proliferation drive cancer to grow increasingly faster.
Published in:
Journal of Molecular Cell Biology, 2012, v. 4, n. 3, p. 174, doi. 10.1093/jmcb/mjs017
By:
- Cui, Juan;
- Mao, Xizeng;
- Olman, Victor;
- Hastings, P. J.;
- Xu, Ying
Publication type:
Article
Elucidation of How Cancer Cells Avoid Acidosis through Comparative Transcriptomic Data Analysis.
Published in:
PLoS ONE, 2013, v. 8, n. 8, p. 1, doi. 10.1371/journal.pone.0071177
By:
- Xu, Kun;
- Mao, Xizeng;
- Mehta, Minesh;
- Cui, Juan;
- Zhang, Chi;
- Mao, Fenglou;
- Xu, Ying
Publication type:
Article
CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes.
Published in:
PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0051252
By:
- Xizeng Mao;
- Xin Chen;
- Yu Zhang;
- Pangle, Spencer;
- Ying Xu
Publication type:
Article
A Comparative Study of Gene-Expression Data of Basal Cell Carcinoma and Melanoma Reveals New Insights about the Two Cancers.
Published in:
PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0030750
By:
- Kun Xu;
- Xizeng Mao;
- Minesh Mehta;
- Juan Cui;
- Chi Zhang;
- Ying Xu
Publication type:
Article
SEAS: A System for SEED-Based Pathway Enrichment Analysis.
Published in:
PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022556
By:
- Xizeng Mao;
- Yu Zhang;
- Ying Xu
Publication type:
Article
Genomic and immune heterogeneity are associated with differential responses to therapy in melanoma.
Published in:
NPJ Genomic Medicine, 2017, v. 2, n. 1, p. N.PAG, doi. 10.1038/s41525-017-0013-8
By:
- Reuben, Alexandre;
- Spencer, Christine N.;
- Prieto, Peter A.;
- Gopalakrishnan, Vancheswaran;
- Reddy, Sangeetha M.;
- Miller, John P.;
- Mao, Xizeng;
- De Macedo, Mariana Petaccia;
- Chen, Jiong;
- Song, Xingzhi;
- Jiang, Hong;
- Chen, Pei-Ling;
- Beird, Hannah C.;
- Garber, Haven R.;
- Roh, Whijae;
- Wani, Khalida;
- Chen, Eveline;
- Haymaker, Cara;
- Forget, Marie-Andrée;
- Little, Latasha D.
Publication type:
Article
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
Published in:
BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/s12859-015-0805-8
By:
- Xizeng Mao;
- Qin Ma;
- Bingqiang Liu;
- Xin Chen;
- Hanyuan Zhang;
- Ying Xu
Publication type:
Article
Genome comparison using Gene Ontology (GO) with statistical testing.
Published in:
BMC Bioinformatics, 2006, v. 7, p. 374, doi. 10.1186/1471-2105-7-374
By:
- Zhaotao Cai;
- Xizeng Mao;
- Songgang Li;
- Liping Wei
Publication type:
Article
KOBAS server: a web-based platform for automated annotation and pathway identification.
Published in:
Nucleic Acids Research, 2006, v. 34, n. 11, p. w720
By:
- Wu, Jianmin;
- Mao, Xizeng;
- Cai, Tao;
- Luo, Jingchu;
- Wei, Liping
Publication type:
Article
Genes and (Common) Pathways Underlying Drug Addiction.
Published in:
PLoS Computational Biology, 2008, v. 4, n. 1, p. e2, doi. 10.1371/journal.pcbi.0040002
By:
- Chuan-Yun Li;
- Xizeng Mao;
- Liping Wei
Publication type:
Article
Genomic heterogeneity of multiple synchronous lung cancer.
Published in:
Nature Communications, 2016, v. 7, n. 10, p. 13200, doi. 10.1038/ncomms13200
By:
- Liu, Yu;
- Zhang, Jianjun;
- Li, Lin;
- Yin, Guangliang;
- Zhang, Jianhua;
- Zheng, Shan;
- Cheung, Hannah;
- Wu, Ning;
- Lu, Ning;
- Mao, Xizeng;
- Yang, Longhai;
- Zhang, Jiexin;
- Zhang, Li;
- Seth, Sahil;
- Chen, Huang;
- Song, Xingzhi;
- Liu, Kan;
- Xie, Yongqiang;
- Zhou, Lina;
- Zhao, Chuanduo
Publication type:
Article
Blocking immunosuppressive neutrophils deters pY696-EZH2–driven brain metastases.
Published in:
Science Translational Medicine, 2020, v. 12, n. 545, p. 1, doi. 10.1126/scitranslmed.aaz5387
By:
- Zhang, Lin;
- Yao, Jun;
- Wei, Yongkun;
- Zhou, Zhifen;
- Li, Ping;
- Qu, Jingkun;
- Badu-Nkansah, Akosua;
- Yuan, Xiangliang;
- Huang, Yu-Wen;
- Fukumura, Kazutaka;
- Mao, Xizeng;
- Chang, Wei-Chao;
- Saunus, Jodi;
- Lakhani, Sunil;
- Huse, Jason T.;
- Hung, Mien-Chie;
- Yu, Dihua
Publication type:
Article
Metabolic reprogramming toward oxidative phosphorylation identifies a therapeutic target for mantle cell lymphoma.
Published in:
Science Translational Medicine, 2019, v. 11, n. 491, p. N.PAG, doi. 10.1126/scitranslmed.aau1167
By:
- Zhang, Liang;
- Yao, Yixin;
- Zhang, Shaojun;
- Liu, Yang;
- Guo, Hui;
- Ahmed, Makhdum;
- Bell, Taylor;
- Zhang, Hui;
- Han, Guangchun;
- Lorence, Elizabeth;
- Badillo, Maria;
- Zhou, Shouhao;
- Sun, Yuting;
- Di Francesco, M. Emilia;
- Feng, Ningping;
- Haun, Randy;
- Lan, Renny;
- Mackintosh, Samuel G.;
- Mao, Xizeng;
- Song, Xingzhi
Publication type:
Article
Comprehensive characterization of the genomic alterations in human gastric cancer.
Published in:
International Journal of Cancer, 2015, v. 137, n. 1, p. 86, doi. 10.1002/ijc.29352
By:
- Cui, Juan;
- Yin, Yanbin;
- Ma, Qin;
- Wang, Guoqing;
- Olman, Victor;
- Zhang, Yu;
- Chou, Wen‐Chi;
- Hong, Celine S.;
- Zhang, Chi;
- Cao, Sha;
- Mao, Xizeng;
- Li, Ying;
- Qin, Steve;
- Zhao, Shaying;
- Jiang, Jing;
- Hastings, Phil;
- Li, Fan;
- Xu, Ying
Publication type:
Article
Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state.
Published in:
Acta Neuropathologica, 2021, v. 142, n. 3, p. 565, doi. 10.1007/s00401-021-02341-z
By:
- Kochat, Veena;
- Raman, Ayush T.;
- Landers, Sharon M.;
- Tang, Ming;
- Schulz, Jonathan;
- Terranova, Christopher;
- Landry, Jace P.;
- Bhalla, Angela D.;
- Beird, Hannah C.;
- Wu, Chia-Chin;
- Jiang, Yingda;
- Mao, Xizeng;
- Lazcano, Rossana;
- Gite, Swati;
- Ingram, Davis R.;
- Yi, Min;
- Zhang, Jianhua;
- Keung, Emily Z.;
- Scally, Christopher P.;
- Roland, Christina L.
Publication type:
Article
Multi-omic molecular profiling reveals potentially targetable abnormalities shared across multiple histologies of brain metastasis.
Published in:
Acta Neuropathologica, 2021, v. 141, n. 2, p. 303, doi. 10.1007/s00401-020-02256-1
By:
- Fukumura, Kazutaka;
- Malgulwar, Prit Benny;
- Fischer, Grant M.;
- Hu, Xiaoding;
- Mao, Xizeng;
- Song, Xingzhi;
- Hernandez, Sharia D.;
- Zhang, Xiang H.-F.;
- Zhang, Jianhua;
- Parra, Edwin Roger;
- Yu, Dihua;
- Debeb, Bisrat G.;
- Davies, Michael A.;
- Huse, Jason T.
Publication type:
Article
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.
Published in:
Bioinformatics, 2005, v. 21, n. 19, p. 3787, doi. 10.1093/bioinformatics/bti430
By:
- Xizeng Mao;
- Tao Cai
Publication type:
Article
Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing.
Published in:
2018
By:
- Wang, Jacqueline F.;
- Pu, Xingxiang;
- Zhang, Xiaoshan;
- Chen, Ken;
- Xi, Yuanxin;
- Wang, Jing;
- Mao, Xizeng;
- Zhang, Jianhua;
- Heymach, John V.;
- Antonoff, Mara B.;
- Hofstetter, Wayne L.;
- Mehran, Reza J.;
- Rice, David C.;
- Roth, Jack A.;
- Sepesi, Boris;
- Swisher, Stephen G.;
- Vaporciyan, Ara A.;
- Walsh, Garrett L.;
- Meng, Qing H.;
- Shaw, Kenna R.
Publication type:
journal article
Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.
Published in:
BMC Genomics, 2010, v. 11, p. 291, doi. 10.1186/1471-2164-11-291
By:
- Xizeng Mao;
- Olman, Victor;
- Stuart, Rhona;
- Paulsen, Ian T.;
- Palenik, Brian;
- Ying Xu
Publication type:
Article
Telomere dysfunction activates YAP1 to drive tissue inflammation.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-18420-w
By:
- Chakravarti, Deepavali;
- Hu, Baoli;
- Mao, Xizeng;
- Rashid, Asif;
- Li, Jiexi;
- Li, Jun;
- Liao, Wen-ting;
- Whitley, Elizabeth M.;
- Dey, Prasenjit;
- Hou, Pingping;
- LaBella, Kyle A.;
- Chang, Andrew;
- Wang, Guocan;
- Spring, Denise J.;
- Deng, Pingna;
- Zhao, Di;
- Liang, Xin;
- Lan, Zhengdao;
- Lin, Yiyun;
- Sarkar, Sharmistha
Publication type:
Article
Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15538-9
By:
- Mitra, Akash;
- Andrews, Miles C.;
- Roh, Whijae;
- De Macedo, Marianna Petaccia;
- Hudgens, Courtney W.;
- Carapeto, Fernando;
- Singh, Shailbala;
- Reuben, Alexandre;
- Wang, Feng;
- Mao, Xizeng;
- Song, Xingzhi;
- Wani, Khalida;
- Tippen, Samantha;
- Ng, Kwok-Shing;
- Schalck, Aislyn;
- Sakellariou-Thompson, Donald A.;
- Chen, Eveline;
- Reddy, Sangeetha M.;
- Spencer, Christine N.;
- Wiesnoski, Diana
Publication type:
Article

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