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ORCIDXiaole Shirley Liu
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- affiliation: Dana Farber Harvard Cancer Center, Boston, USA
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Journal Articles
- 2022
[j31]Wubing Zhang
, Shourya S. Roy Burman, Jiaye Chen, Katherine A. Donovan, Yang Cao, Chelsea Shu, Boning Zhang, Zexian Zeng, Shengqing Gu, Yi Zhang, Dian Li, Eric S. Fischer, Collin Tokheim, X. Shirley Liu:
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation. Genom. Proteom. Bioinform. 20(5): 882-898 (2022)- [j30]Zexian Zeng, Cheryl J. Wong, Lin Yang, Nofal Ouardaoui, Dian Li, Wubing Zhang, Shengqing Gu, Yi Zhang, Yang Liu, Xiaoqing Wang, Jingxin Fu, Liye Zhou, Boning Zhang, Sarah Kim, Kathleen B. Yates, Myles Brown, Gordon J. Freeman, Ravindra Uppaluri, Robert Manguso, X. Shirley Liu:
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. Nucleic Acids Res. 50(D1): 1391-1397 (2022) - 2021
- [j29]Xintao Qiu, Avery S. Feit, Ariel Feiglin, Yingtian Xie, Nikolas Kesten, Len Taing, Joseph Perkins, Shengqing Gu, Yihao Li, Paloma Cejas, Ningxuan Zhou, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long:
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis. Genom. Proteom. Bioinform. 19(4): 652-661 (2021) - [j28]Yi Zhang, Yang Liu, X. Shirley Liu:
Neural network architecture search with AMBER. Nat. Mach. Intell. 3(5): 372-373 (2021) - 2020
- [j27]Ziyi Li, Binbin Wang, Shengqing Gu, Peng Jiang, Avinash Das Sahu, Chen-Hao Chen, Tong Han, Sailing Shi, Xiaoqing Wang, Nicole Traugh, Hailing Liu, Yin Liu, Qiu Wu, Myles Brown, Tengfei Xiao, Genevieve M. Boland, Xiaole Shirley Liu:
CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma. Genom. Proteom. Bioinform. 18(1): 26-40 (2020) - [j26]Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, Xiaole Shirley Liu:
TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 48(Webserver-Issue): W509-W514 (2020) - 2019
- [j25]Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinform. 35(6): 995-1001 (2019) - [j24]Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinform. 35(13): 2347 (2019) - [j23]Rongbin Zheng, Changxin Wan, Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Chen-Hao Chen, Myles Brown, Xiaoyan Zhang, Clifford A. Meyer, Xiaole Shirley Liu:
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 47(Database-Issue): D729-D735 (2019) - [j22]Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A. Meyer, Xiaole Shirley Liu:
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. Nucleic Acids Res. 47(Webserver-Issue): W206-W211 (2019) - 2018
- [j21]Chen-Hao Chen, Tengfei Xiao, Han Xu, Peng Jiang, Clifford A. Meyer, Wei Li, Myles Brown, Xiaole Shirley Liu:
Improved design and analysis of CRISPR knockout screens. Bioinform. 34(23): 4095-4101 (2018) - [j20]MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, Xiaole Shirley Liu, Henry W. Long:
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinform. 19(1): 135:1-135:14 (2018) - 2017
- [j19]Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A. Meyer, Xiaole Shirley Liu:
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 45(Database-Issue): D658-D662 (2017) - 2016
- [j18]Jian Ma, Johannes Köster, Qian Qin, Shengen Hu, Wei Li, Chenhao Chen, Qingyi Cao, Jinzeng Wang, Shenglin Mei, Qi Liu, Han Xu, Xiaole Shirley Liu:
CRISPR-DO for genome-wide CRISPR design and optimization. Bioinform. 32(21): 3336-3338 (2016) - 2015
- [j17]Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, Xiaole Shirley Liu:
Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model. PLoS Comput. Biol. 11(9) (2015) - 2014
- [j16]Qixuan Wang, Jinyan Huang, Hanfei Sun, Jing Liu, Juan Wang, Qian Wang, Qian Qin, Shenglin Mei, Chengchen Zhao, Xiaoqin Yang, Xiaole Shirley Liu, Yong Zhang:
CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res. 42(Database-Issue): 450-458 (2014) - [j15]Joshua Wing Kei Ho, Youngsook L. Jung, Tao Liu, Burak Han Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowman, Q. Brent Chen, Ron A.-J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingston, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, Peter J. Park:
Comparative analysis of metazoan chromatin organization Open. Nat. 512(7515): 449-452 (2014) - [j14]Mengyi Sun, Bingyu Yan, Chengkun Wu, Xiaole Shirley Liu:
Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop). Quant. Biol. 2(2): 80-84 (2014) - 2013
- [j13]Hanfei Sun, Bo Qin, Tao Liu, Qixuan Wang, Jing Liu, Juan Wang, Xueqiu Lin, Yulin Yang, Len Taing, Prakash K. Rao, Myles Brown, Yong Zhang, Henry Long, Xiaole Shirley Liu:
CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinform. 29(10): 1352-1354 (2013) - [j12]Hyunjin Shin, Tao Liu, Xikun Duan, Yong Zhang, Xiaole Shirley Liu:
Computational methodology for ChIP-seq analysis. Quant. Biol. 1(1): 54-70 (2013) - 2012
- [j11]Bo Qin, Meng Zhou, Ying Ge, Len Taing, Tao Liu, Qian Wang, Su Wang, Junsheng Chen, Lingling Shen, Xikun Duan, Sheng'en Hu, Wei Li, Henry Long, Yong Zhang, Xiaole Shirley Liu:
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinform. 28(10): 1411-1412 (2012) - [j10]Kai Fu, Qianzi Tang, Jianxing Feng, Xiaole Shirley Liu, Yong Zhang:
DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinform. 28(15): 1965-1971 (2012) - [j9]Jianxing Feng, Clifford A. Meyer, Qian Wang, Jun S. Liu, Xiaole Shirley Liu, Yong Zhang:
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinform. 28(21): 2782-2788 (2012) - 2011
- [j8]Clifford A. Meyer, Housheng H. He, Myles Brown, Xiaole Shirley Liu:
BINOCh: binding inference from nucleosome occupancy changes. Bioinform. 27(13): 1867-1868 (2011) - [j7]Qingyi Cao, Meng Zhou, Xujun Wang, Clifford A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, Xiaole Shirley Liu:
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 39(Database-Issue): 968-974 (2011) - 2009
- [j6]Hyunjin Shin, Tao Liu, Arjun K. Manrai, Xiaole Shirley Liu:
CEAS: cis-regulatory element annotation system. Bioinform. 25(19): 2605-2606 (2009) - 2007
- [j5]Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu:
Microarray blob-defect removal improves array analysis. Bioinform. 23(8): 966-971 (2007) - [j4]Xiaole Shirley Liu:
Getting Started in Tiling Microarray Analysis. PLoS Comput. Biol. 3(10) (2007) - 2006
- [j3]Xuwo Ji, Wei Li, Jun Song, Liping Wei, Xiaole Shirley Liu:
CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 34(Web-Server-Issue): 551-554 (2006) - 2005
- [j2]Pengyu Hong, Xiaole Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong:
A boosting approach for motif modeling using ChIP-chip data. Bioinform. 21(11): 2636-2643 (2005) - 2004
- [j1]Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu:
A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res. 32(Web-Server-Issue): 204-207 (2004)
Conference and Workshop Papers
- 2007
- [c2]Wei Li, Jason S. Carroll, Myles Brown, Xiaole Shirley Liu:
xMAN: extreme MApping of oligoNucleotides. BIOCOMP 2007: 631-637 - 2005
- [c1]Wei Li, Clifford A. Meyer, Xiaole Shirley Liu:
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. ISMB (Supplement of Bioinformatics) 2005: 274-282
Coauthor Index
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