Xiaole Shirley Liu

According to our database, Xiaole Shirley Liu authored at least 32 papers between 2004 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2022

Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.

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

Genom. Proteom. Bioinform., October, 2022

TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

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

Nucleic Acids Res., 2022

2021

Neural network architecture search with AMBER.

Yi Zhang, Yang Liu, X. Shirley Liu

Nat. Mach. Intell., 2021

CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis.

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

Genom. Proteom. Bioinform., 2021

2020

TIMER2.0 for analysis of tumor-infiltrating immune cells.

Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, Xiaole Shirley Liu

Nucleic Acids Res., 2020

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma.

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

Genom. Proteom. Bioinform., 2020

2019

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.

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

Nucleic Acids Res., 2019

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.

Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A. Meyer, Xiaole Shirley Liu

Nucleic Acids Res., 2019

A Bayesian model for single cell transcript expression analysis on MERFISH data.

Johannes Köster, Myles Brown, Xiaole Shirley Liu

Bioinform., 2019

2018

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

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

BMC Bioinform., 2018

Improved design and analysis of CRISPR knockout screens.

Chen-Hao Chen, Tengfei Xiao, Han Xu, Peng Jiang, Clifford A. Meyer, Wei Li, Myles Brown, Xiaole Shirley Liu

Bioinform., 2018

2017

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

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

Nucleic Acids Res., 2017

2016

CRISPR-DO for genome-wide CRISPR design and optimization.

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

Bioinform., 2016

2015

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model.

Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, Xiaole Shirley Liu

PLoS Comput. Biol., 2015

2014

Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop).

Mengyi Sun, Bingyu Yan, Chengkun Wu, Xiaole Shirley Liu

Quant. Biol., 2014

Comparative analysis of metazoan chromatin organization Open.

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

Nat., 2014

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.

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

Nucleic Acids Res., 2014

2013

Computational methodology for ChIP-seq analysis.

Hyunjin Shin, Tao Liu, Xikun Duan, Yong Zhang, Xiaole Shirley Liu

Quant. Biol., 2013

CistromeFinder for ChIP-seq and DNase-seq data reuse.

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

Bioinform., 2013

2012

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.

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

Bioinform., 2012

DiNuP: a systematic approach to identify regions of differential nucleosome positioning.

Kai Fu, Qianzi Tang, Jianxing Feng, Xiaole Shirley Liu, Yong Zhang

Bioinform., 2012

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

Jianxing Feng, Clifford A. Meyer, Qian Wang, Jun S. Liu, Xiaole Shirley Liu, Yong Zhang

Bioinform., 2012

2011

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.

Qingyi Cao, Meng Zhou, Xujun Wang, Clifford A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, Xiaole Shirley Liu

Nucleic Acids Res., 2011

BINOCh: binding inference from nucleosome occupancy changes.

Clifford A. Meyer, Housheng H. He, Myles Brown, Xiaole Shirley Liu

Bioinform., 2011

2009

CEAS: <i>cis</i>-regulatory element annotation system.

Hyunjin Shin, Tao Liu, Arjun K. Manrai, Xiaole Shirley Liu

Bioinform., 2009

2007

Getting Started in Tiling Microarray Analysis.

Xiaole Shirley Liu

PLoS Comput. Biol., 2007

Microarray blob-defect removal improves array analysis.

Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu

Bioinform., 2007

xMAN: extreme MApping of oligoNucleotides.

Wei Li, Jason S. Carroll, Myles Brown, Xiaole Shirley Liu

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

2006

CEAS: <i>cis</i>-regulatory element annotation system.

Xuwo Ji, Wei Li, Jun Song, Liping Wei, Xiaole Shirley Liu

Nucleic Acids Res., 2006

2005

A boosting approach for motif modeling using ChIP-chip data.

Pengyu Hong, Xiaole Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong

Bioinform., 2005

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.

Wei Li, Clifford A. Meyer, Xiaole Shirley Liu

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

A suite of web-based programs to search for transcriptional regulatory motifs.

Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu

Nucleic Acids Res., 2004