Xiaole Shirley Liu

29 papers Journal 27Unranked 2
YearRankTypeTitle / Venue / Authors
2020 J jnl
CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma.
Genom. Proteom. Bioinform.
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
2020 J jnl
TIMER2.0 for analysis of tumor-infiltrating immune cells.
Nucleic Acids Res.
Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, Xiaole Shirley Liu
2019 J jnl
A Bayesian model for single cell transcript expression analysis on MERFISH data.
Bioinform.
Johannes Köster, Myles Brown, Xiaole Shirley Liu
2019 J jnl
A Bayesian model for single cell transcript expression analysis on MERFISH data.
Bioinform.
Johannes Köster, Myles Brown, Xiaole Shirley Liu
2019 J jnl
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.
Nucleic Acids Res.
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
2019 J jnl
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.
Nucleic Acids Res.
Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A. Meyer, Xiaole Shirley Liu
2018 J jnl
Improved design and analysis of CRISPR knockout screens.
Bioinform.
Chen-Hao Chen, Tengfei Xiao, Han Xu, Peng Jiang, Clifford A. Meyer, Wei Li, Myles Brown, Xiaole Shirley Liu
2018 J jnl
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.
BMC Bioinform.
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
2017 J jnl
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.
Nucleic Acids Res.
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
2016 J jnl
CRISPR-DO for genome-wide CRISPR design and optimization.
Bioinform.
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
2015 J jnl
Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model.
PLoS Comput. Biol.
Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, Xiaole Shirley Liu
2014 J jnl
CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.
Nucleic Acids Res.
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
2014 J jnl
Comparative analysis of metazoan chromatin organization Open.
Nat.
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
2014 J jnl
Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop).
Quant. Biol.
Mengyi Sun, Bingyu Yan, Chengkun Wu, Xiaole Shirley Liu
2013 J jnl
CistromeFinder for ChIP-seq and DNase-seq data reuse.
Bioinform.
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
2013 J jnl
Computational methodology for ChIP-seq analysis.
Quant. Biol.
Hyunjin Shin, Tao Liu, Xikun Duan, Yong Zhang, Xiaole Shirley Liu
2012 J jnl
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.
Bioinform.
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
2012 J jnl
DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
Bioinform.
Kai Fu, Qianzi Tang, Jianxing Feng, Xiaole Shirley Liu, Yong Zhang
2012 J jnl
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.
Bioinform.
Jianxing Feng, Clifford A. Meyer, Qian Wang, Jun S. Liu, Xiaole Shirley Liu, Yong Zhang
2011 J jnl
BINOCh: binding inference from nucleosome occupancy changes.
Bioinform.
Clifford A. Meyer, Housheng H. He, Myles Brown, Xiaole Shirley Liu
2011 J jnl
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.
Nucleic Acids Res.
Qingyi Cao, Meng Zhou, Xujun Wang, Clifford A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, Xiaole Shirley Liu
2009 J jnl
CEAS:
Bioinform.
Hyunjin Shin, Tao Liu, Arjun K. Manrai, Xiaole Shirley Liu
2007 J jnl
Getting Started in Tiling Microarray Analysis.
PLoS Comput. Biol.
Xiaole Shirley Liu
2007 J jnl
Microarray blob-defect removal improves array analysis.
Bioinform.
Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu
2007 — conf
xMAN: extreme MApping of oligoNucleotides.
BIOCOMP
Wei Li, Jason S. Carroll, Myles Brown, Xiaole Shirley Liu
2006 J jnl
CEAS:
Nucleic Acids Res.
Xuwo Ji, Wei Li, Jun Song, Liping Wei, Xiaole Shirley Liu
2005 J jnl
A boosting approach for motif modeling using ChIP-chip data.
Bioinform.
Pengyu Hong, Xiaole Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong
2005 — conf
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.
ISMB (Supplement of Bioinformatics)
Wei Li, Clifford A. Meyer, Xiaole Shirley Liu
2004 J jnl
A suite of web-based programs to search for transcriptional regulatory motifs.
Nucleic Acids Res.
Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu