Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning
Wang, Daqi, Zhang, Chengdong, Wang, Bei, Li, Bin, Wang, Qiang, Liu, Dong, Wang, Hongyan, Zhou, Yan, Shi, Leming, Lan, Feng, Wang, Yongming
Published in Nature communications (19.09.2019)
Published in Nature communications (19.09.2019)
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Characterizing and annotating the genome using RNA-seq data
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Book Review
Multi-Omics Profiling Reveals Distinct Microenvironment Characterization and Suggests Immune Escape Mechanisms of Triple-Negative Breast Cancer
Xiao, Yi, Ma, Ding, Zhao, Shen, Suo, Chen, Shi, Jinxiu, Xue, Meng-Zhu, Ruan, Miao, Wang, Hai, Zhao, Jingjing, Li, Qin, Wang, Peng, Shi, Leming, Yang, Wen-Tao, Huang, Wei, Hu, Xin, Yu, Ke-Da, Huang, Shenglin, Bertucci, François, Jiang, Yi-Zhou, Shao, Zhi-Ming
Published in Clinical cancer research (15.08.2019)
Published in Clinical cancer research (15.08.2019)
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Journal Article
Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies
Jiang, Yi-Zhou, Ma, Ding, Suo, Chen, Shi, Jinxiu, Xue, Mengzhu, Hu, Xin, Xiao, Yi, Yu, Ke-Da, Liu, Yi-Rong, Yu, Ying, Zheng, Yuanting, Li, Xiangnan, Zhang, Chenhui, Hu, Pengchen, Zhang, Jing, Hua, Qi, Zhang, Jiyang, Hou, Wanwan, Ren, Luyao, Bao, Ding, Li, Bingying, Yang, Jingcheng, Yao, Ling, Zuo, Wen-Jia, Zhao, Shen, Gong, Yue, Ren, Yi-Xing, Zhao, Ya-Xin, Yang, Yun-Song, Niu, Zhenmin, Cao, Zhi-Gang, Stover, Daniel G., Verschraegen, Claire, Kaklamani, Virginia, Daemen, Anneleen, Benson, John R., Takabe, Kazuaki, Bai, Fan, Li, Da-Qiang, Wang, Peng, Shi, Leming, Huang, Wei, Shao, Zhi-Ming
Published in Cancer cell (18.03.2019)
Published in Cancer cell (18.03.2019)
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Journal Article
A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
Li, Bin, Qing, Tao, Zhu, Jinhang, Wen, Zhuo, Yu, Ying, Fukumura, Ryutaro, Zheng, Yuanting, Gondo, Yoichi, Shi, Leming
Published in Scientific reports (23.06.2017)
Published in Scientific reports (23.06.2017)
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Journal Article
High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers
Molina-Mora, José Arturo, Campos-Sánchez, Rebeca, Rodríguez, César, Shi, Leming, García, Fernando
Published in Scientific reports (29.01.2020)
Published in Scientific reports (29.01.2020)
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Journal Article
Genomic and immune profiling of pre-invasive lung adenocarcinoma
Chen, Haiquan, Carrot-Zhang, Jian, Zhao, Yue, Hu, Haichuan, Freeman, Samuel S., Yu, Su, Ha, Gavin, Taylor, Alison M., Berger, Ashton C., Westlake, Lindsay, Zheng, Yuanting, Zhang, Jiyang, Ramachandran, Aruna, Zheng, Qiang, Pan, Yunjian, Zheng, Difan, Zheng, Shanbo, Cheng, Chao, Kuang, Muyu, Zhou, Xiaoyan, Zhang, Yang, Li, Hang, Ye, Ting, Ma, Yuan, Gao, Zhendong, Tao, Xiaoting, Han, Han, Shang, Jun, Yu, Ying, Bao, Ding, Huang, Yechao, Li, Xiangnan, Zhang, Yawei, Xiang, Jiaqing, Sun, Yihua, Li, Yuan, Cherniack, Andrew D., Campbell, Joshua D., Shi, Leming, Meyerson, Matthew
Published in Nature communications (29.11.2019)
Published in Nature communications (29.11.2019)
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Journal Article
The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation
Pandey, Gaurav Kumar, Mitra, Sanhita, Subhash, Santhilal, Hertwig, Falk, Kanduri, Meena, Mishra, Kankadeb, Fransson, Susanne, Ganeshram, Abiarchana, Mondal, Tanmoy, Bandaru, Sashidhar, Östensson, Malin, Akyürek, Levent M., Abrahamsson, Jonas, Pfeifer, Susan, Larsson, Erik, Shi, Leming, Peng, Zhiyu, Fischer, Matthias, Martinsson, Tommy, Hedborg, Fredrik, Kogner, Per, Kanduri, Chandrasekhar
Published in Cancer cell (10.11.2014)
Published in Cancer cell (10.11.2014)
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Journal Article
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
Wang, Charles, Gong, Binsheng, Bushel, Pierre R, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Xu, Joshua, Fang, Hong, Hong, Huixiao, Shen, Jie, Su, Zhenqiang, Meehan, Joe, Li, Xiaojin, Yang, Lu, Li, Haiqing, Łabaj, Paweł P, Kreil, David P, Megherbi, Dalila, Gaj, Stan, Caiment, Florian, van Delft, Joost, Kleinjans, Jos, Scherer, Andreas, Devanarayan, Viswanath, Wang, Jian, Yang, Yong, Qian, Hui-Rong, Lancashire, Lee J, Bessarabova, Marina, Nikolsky, Yuri, Furlanello, Cesare, Chierici, Marco, Albanese, Davide, Jurman, Giuseppe, Riccadonna, Samantha, Filosi, Michele, Visintainer, Roberto, Zhang, Ke K, Li, Jianying, Hsieh, Jui-Hua, Svoboda, Daniel L, Fuscoe, James C, Deng, Youping, Shi, Leming, Paules, Richard S, Auerbach, Scott S, Tong, Weida
Published in Nature biotechnology (01.09.2014)
Published in Nature biotechnology (01.09.2014)
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Exploring functions of long noncoding RNAs across multiple cancers through co-expression network
Li, Suqing, Li, Bin, Zheng, Yuanting, Li, Menglong, Shi, Leming, Pu, Xuemei
Published in Scientific reports (07.04.2017)
Published in Scientific reports (07.04.2017)
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Journal Article
Similarities and Differences in the Expression of Drug-Metabolizing Enzymes between Human Hepatic Cell Lines and Primary Human Hepatocytes
LEI GUO, DIAL, Stacey, LEMING SHI, BRANHAM, William, JIE LIU, FANG, Jia-Long, GREEN, Bridgett, HELEN DENG, KAPUT, Jim, BAITANG NING
Published in Drug metabolism and disposition (01.03.2011)
Published in Drug metabolism and disposition (01.03.2011)
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Journal Article
Similarities and differences between variants called with human reference genome HG19 or HG38
Pan, Bohu, Kusko, Rebecca, Xiao, Wenming, Zheng, Yuanting, Liu, Zhichao, Xiao, Chunlin, Sakkiah, Sugunadevi, Guo, Wenjing, Gong, Ping, Zhang, Chaoyang, Ge, Weigong, Shi, Leming, Tong, Weida, Hong, Huixiao
Published in BMC bioinformatics (14.03.2019)
Published in BMC bioinformatics (14.03.2019)
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Journal Article
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire
Ostrov, David A, Grant, Barry J, Pompeu, Yuri A, Sidney, John, Harndahl, Mikkel, Southwood, Scott, Oseroff, Carla, Lu, Shun, Jakoncic, Jean, de Oliveira, Cesar Augusto F, Yang, Lun, Mei, Hu, Shi, Leming, Shabanowitz, Jeffrey, English, A. Michelle, Wriston, Amanda, Lucas, Andrew, Phillips, Elizabeth, Mallal, Simon, Grey, Howard M, Sette, Alessandro, Hunt, Donald F, Buus, Soren, Peters, Bjoern
Published in Proceedings of the National Academy of Sciences - PNAS (19.06.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (19.06.2012)
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Endoplasmic reticulum stress and MAPK signaling pathway activation underlie leflunomide-induced toxicity in HepG2 Cells
Ren, Zhen, Chen, Si, Qing, Tao, Xuan, Jiekun, Couch, Letha, Yu, Dianke, Ning, Baitang, Shi, Leming, Guo, Lei
Published in Toxicology (Amsterdam) (01.12.2017)
Published in Toxicology (Amsterdam) (01.12.2017)
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Journal Article
High-throughput autoantibody profiling of different stages of Schistosomiasis japonica
Zhou, Xiaorong, Wang, Xi, Xu, Jing, Tang, Qi, Bergquist, Robert, Shi, Leming, Qin, Zhiqiang
Published in Autoimmunity (Chur, Switzerland) (31.12.2023)
Published in Autoimmunity (Chur, Switzerland) (31.12.2023)
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Journal Article
Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach
Molina-Mora, José Arturo, Chinchilla-Montero, Diana, Chavarría-Azofeifa, Maribel, Ulloa-Morales, Alejandro J., Campos-Sánchez, Rebeca, Mora-Rodríguez, Rodrigo, Shi, Leming, García, Fernando
Published in Scientific reports (13.08.2020)
Published in Scientific reports (13.08.2020)
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Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
Yu, Ying, Zhang, Naixin, Mai, Yuanbang, Ren, Luyao, Chen, Qiaochu, Cao, Zehui, Chen, Qingwang, Liu, Yaqing, Hou, Wanwan, Yang, Jingcheng, Hong, Huixiao, Xu, Joshua, Tong, Weida, Dong, Lianhua, Shi, Leming, Fang, Xiang, Zheng, Yuanting
Published in Genome Biology (07.09.2023)
Published in Genome Biology (07.09.2023)
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Journal Article
Hidden biases in germline structural variant detection
Khayat, Michael M, Sahraeian, Sayed Mohammad Ebrahim, Zarate, Samantha, Carroll, Andrew, Hong, Huixiao, Pan, Bohu, Shi, Leming, Gibbs, Richard A, Mohiyuddin, Marghoob, Zheng, Yuanting, Sedlazeck, Fritz J
Published in Genome Biology (20.12.2021)
Published in Genome Biology (20.12.2021)
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