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Publications

Publication in 2016

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, X Shirley Liu
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.
Nucleic Acids Res.: 2017, 45(D1);D658-D662
[PubMed:27789702] [WorldCat.org] [DOI] (I p)

Qian Qin, Shenglin Mei, Qiu Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Han Xu, Yiwen Chen, Clifford A Meyer, Yong Zhang, Myles Brown, Henry W Long, X Shirley Liu
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
BMC Bioinformatics: 2016, 17(1);404
[PubMed:27716038] [WorldCat.org] [DOI] (I e)


Publication in 2015

Shivali Kapoor, Lisha Zhu, Cara Froyd, Tao Liu, Laura N Rusche
Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin.
Proc. Natl. Acad. Sci. U.S.A.: 2015, 112(39);12139-44
[PubMed:26371315] [WorldCat.org] [DOI] (I p)

H-T Hsu, H-M Chen, Z Yang, J Wang, N K Lee, A Burger, K Zaret, T Liu, E Levine, S E Mango
TRANSCRIPTION. Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4.
Science: 2015, 348(6241);1372-6
[PubMed:26089518] [WorldCat.org] [DOI] (I p)

Kaiyu Jiang, Lisha Zhu, Michael J Buck, Yanmin Chen, Bradley Carrier, Tao Liu, James N Jarvis
Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells.
Arthritis Rheumatol: 2015, 67(7);1966-77
[PubMed:25833190] [WorldCat.org] [DOI] (I p)


Publication in 2014

Joshua W K Ho, Youngsook L Jung, Tao Liu, Burak H 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 N 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.
Nature: 2014, 512(7515);449-52
[PubMed:25164756] [WorldCat.org] [DOI] (I p)

Dimphna H Meijer, Yu Sun, Tao Liu, Michael F Kane, John A Alberta, Guillaume Adelmant, Robert Kupp, Jarrod A Marto, David H Rowitch, Yoshihiro Nakatani, Charles D Stiles, Shwetal Mehta
An amino terminal phosphorylation motif regulates intranuclear compartmentalization of Olig2 in neural progenitor cells.
J. Neurosci.: 2014, 34(25);8507-18
[PubMed:24948806] [WorldCat.org] [DOI] (I p)

Tao Liu
Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells.
Methods Mol. Biol.: 2014, 1150;81-95
[PubMed:24743991] [WorldCat.org] [DOI] (I p)


Publications in 2013

André Catic, Carol Y Suh, Cedric T Hill, Laurence Daheron, Theresa Henkel, Keith W Orford, David M Dombkowski, Tao Liu, X Shirley Liu, David T Scadden
Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.
Cell: 2013, 155(6);1380-95
[PubMed:24315104] [WorldCat.org] [DOI] (I p)

Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang
Practical guidelines for the comprehensive analysis of ChIP-seq data.
PLoS Comput. Biol.: 2013, 9(11);e1003326
[PubMed:24244136] [WorldCat.org] [DOI] (I p)

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 W Long, X Shirley Liu
CistromeFinder for ChIP-seq and DNase-seq data reuse.
Bioinformatics: 2013, 29(10);1352-4
[PubMed:23508969] [WorldCat.org] [DOI] (I p)


Publications before joining UB (2013-1-2)

Kexin Xu, Zhenhua Jeremy Wu, Anna C Groner, Housheng Hansen He, Changmeng Cai, Rosina T Lis, Xiaoqiu Wu, Edward C Stack, Massimo Loda, Tao Liu, Han Xu, Laura Cato, James E Thornton, Richard I Gregory, Colm Morrissey, Robert L Vessella, Rodolfo Montironi, Cristina Magi-Galluzzi, Philip W Kantoff, Steven P Balk, X Shirley Liu, Myles Brown
EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.
Science: 2012, 338(6113);1465-9
[PubMed:23239736] [WorldCat.org] [DOI] (I p)

Stephen G Landt, Georgi K Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E Bernstein, Peter Bickel, James B Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles Epstein, Katherine I Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J Hartemink, Michael M Hoffman, Vishwanath R Iyer, Youngsook L Jung, Subhradip Karmakar, Manolis Kellis, Peter V Kharchenko, Qunhua Li, Tao Liu, X Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, Richard M Myers, Peter J Park, Michael J Pazin, Marc D Perry, Debasish Raha, Timothy E Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, John A Stamatoyannopoulos, Michael Y Tolstorukov, Kevin P White, Simon Xi, Peggy J Farnham, Jason D Lieb, Barbara J Wold, Michael Snyder
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Genome Res.: 2012, 22(9);1813-31
[PubMed:22955991] [WorldCat.org] [DOI] (I p)

Jianxing Feng, Tao Liu, Bo Qin, Yong Zhang, Xiaole Shirley Liu
Identifying ChIP-seq enrichment using MACS.
Nat Protoc: 2012, 7(9);1728-40
[PubMed:22936215] [WorldCat.org] [DOI] (I p)

Yiwen Chen, Nicolas Negre, Qunhua Li, Joanna O Mieczkowska, Matthew Slattery, Tao Liu, Yong Zhang, Tae-Kyung Kim, Housheng Hansen He, Jennifer Zieba, Yijun Ruan, Peter J Bickel, Richard M Myers, Barbara J Wold, Kevin P White, Jason D Lieb, X Shirley Liu
Systematic evaluation of factors influencing ChIP-seq fidelity.
Nat. Methods: 2012, 9(6);609-14
[PubMed:22522655] [WorldCat.org] [DOI] (I p)

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, X Shirley Liu
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.
Bioinformatics: 2012, 28(10);1411-2
[PubMed:22495751] [WorldCat.org] [DOI] (I p)

Qianzi Tang, Yiwen Chen, Clifford Meyer, Tim Geistlinger, Mathieu Lupien, Qian Wang, Tao Liu, Yong Zhang, Myles Brown, Xiaole Shirley Liu
A comprehensive view of nuclear receptor cancer cistromes.
Cancer Res.: 2011, 71(22);6940-7
[PubMed:21940749] [WorldCat.org] [DOI] (I p)

Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Cistrome: an integrative platform for transcriptional regulation studies.
Genome Biol.: 2011, 12(8);R83
[PubMed:21859476] [WorldCat.org] [DOI] (I e)

Jianxing Feng, Tao Liu, Yong Zhang
Using MACS to identify peaks from ChIP-Seq data.
Curr Protoc Bioinformatics: 2011, Chapter 2;Unit 2.14
[PubMed:21633945] [WorldCat.org] [DOI] (I p)

Dan Feng, Tao Liu, Zheng Sun, Anne Bugge, Shannon E Mullican, Theresa Alenghat, X Shirley Liu, Mitchell A Lazar
A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.
Science: 2011, 331(6022);1315-9
[PubMed:21393543] [WorldCat.org] [DOI] (I p)

Xiangfeng Wang, John D Laurie, Tao Liu, Jacqueline Wentz, X Shirley Liu
Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.
Genomics: 2011, 97(4);235-43
[PubMed:21295131] [WorldCat.org] [DOI] (I p)

Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.
Genome Biol.: 2011, 12(2);R11
[PubMed:21284836] [WorldCat.org] [DOI] (I p)

Mark B Gerstein, Zhi John Lu, Eric L Van Nostrand, Chao Cheng, Bradley I Arshinoff, Tao Liu, Kevin Y Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami, Pedro Alves, Aurelien Chateigner, Marc Perry, Mitzi Morris, Raymond K Auerbach, Xin Feng, Jing Leng, Anne Vielle, Wei Niu, Kahn Rhrissorrakrai, Ashish Agarwal, Roger P Alexander, Galt Barber, Cathleen M Brdlik, Jennifer Brennan, Jeremy Jean Brouillet, Adrian Carr, Ming-Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O Dannenberg, Abby F Dernburg, Arshad Desai, Lindsay Dick, Andréa C Dosé, Jiang Du, Thea Egelhofer, Sevinc Ercan, Ghia Euskirchen, Brent Ewing, Elise A Feingold, Reto Gassmann, Peter J Good, Phil Green, Francois Gullier, Michelle Gutwein, Mark S Guyer, Lukas Habegger, Ting Han, Jorja G Henikoff, Stefan R Henz, Angie Hinrichs, Heather Holster, Tony Hyman, A Leo Iniguez, Judith Janette, Morten Jensen, Masaomi Kato, W James Kent, Ellen Kephart, Vishal Khivansara, Ekta Khurana, John K Kim, Paulina Kolasinska-Zwierz, Eric C Lai, Isabel Latorre, Amber Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F Lowdon, Yaniv Lubling, Rachel Lyne, Michael MacCoss, Sebastian D Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer Merrihew, David M Miller, Andrew Muroyama, John I Murray, Siew-Loon Ooi, Hoang Pham, Taryn Phippen, Elicia A Preston, Nikolaus Rajewsky, Gunnar Rätsch, Heidi Rosenbaum, Joel Rozowsky, Kim Rutherford, Peter Ruzanov, Mihail Sarov, Rajkumar Sasidharan, Andrea Sboner, Paul Scheid, Eran Segal, Hyunjin Shin, Chong Shou, Frank J Slack, Cindie Slightam, Richard Smith, William C Spencer, E O Stinson, Scott Taing, Teruaki Takasaki, Dionne Vafeados, Ksenia Voronina, Guilin Wang, Nicole L Washington, Christina M Whittle, Beijing Wu, Koon-Kiu Yan, Georg Zeller, Zheng Zha, Mei Zhong, Xingliang Zhou, modENCODE Consortium, Julie Ahringer, Susan Strome, Kristin C Gunsalus, Gos Micklem, X Shirley Liu, Valerie Reinke, Stuart K Kim, LaDeana W Hillier, Steven Henikoff, Fabio Piano, Michael Snyder, Lincoln Stein, Jason D Lieb, Robert H Waterston
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Science: 2010, 330(6012);1775-87
[PubMed:21177976] [WorldCat.org] [DOI] (I p)

Tao Liu, Andreas Rechtsteiner, Thea A Egelhofer, Anne Vielle, Isabel Latorre, Ming-Sin Cheung, Sevinc Ercan, Kohta Ikegami, Morten Jensen, Paulina Kolasinska-Zwierz, Heidi Rosenbaum, Hyunjin Shin, Scott Taing, Teruaki Takasaki, A Leonardo Iniguez, Arshad Desai, Abby F Dernburg, Hiroshi Kimura, Jason D Lieb, Julie Ahringer, Susan Strome, X Shirley Liu
Broad chromosomal domains of histone modification patterns in C. elegans.
Genome Res.: 2011, 21(2);227-36
[PubMed:21177964] [WorldCat.org] [DOI] (I p)

Hyunjin Shin, Tao Liu, Arjun K Manrai, X Shirley Liu
CEAS: cis-regulatory element annotation system.
Bioinformatics: 2009, 25(19);2605-6
[PubMed:19689956] [WorldCat.org] [DOI] (I p)

Paulina Kolasinska-Zwierz, Thomas Down, Isabel Latorre, Tao Liu, X Shirley Liu, Julie Ahringer
Differential chromatin marking of introns and expressed exons by H3K36me3.
Nat. Genet.: 2009, 41(3);376-81
[PubMed:19182803] [WorldCat.org] [DOI] (I p)

Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu
Model-based analysis of ChIP-Seq (MACS).
Genome Biol.: 2008, 9(9);R137
[PubMed:18798982] [WorldCat.org] [DOI] (I p)

Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao, Runsheng Chen
MicroRNA-encoding long non-coding RNAs.
BMC Genomics: 2008, 9;236
[PubMed:18492288] [WorldCat.org] [DOI] (I e)

Libin Deng, Yuezheng Zhang, Jian Kang, Tao Liu, Hongbin Zhao, Yang Gao, Chaohua Li, Hao Pan, Xiaoli Tang, Dunmei Wang, Tianhua Niu, Huanming Yang, Changqing Zeng
An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism.
Hum. Mutat.: 2008, 29(10);1209-16
[PubMed:18473345] [WorldCat.org] [DOI] (I p)

Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen
NONCODE v2.0: decoding the non-coding.
Nucleic Acids Res.: 2008, 36(Database issue);D170-2
[PubMed:18000000] [WorldCat.org] [DOI] (I p)

Housheng He, Jie Wang, Tao Liu, X Shirley Liu, Tiantian Li, Yunfei Wang, Zuwei Qian, Haixia Zheng, Xiaopeng Zhu, Tao Wu, Baochen Shi, Wei Deng, Wei Zhou, Geir Skogerbø, Runsheng Chen
Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.
Genome Res.: 2007, 17(10);1471-7
[PubMed:17785534] [WorldCat.org] [DOI] (P p)

Housheng He, Lun Cai, Geir Skogerbø, Wei Deng, Tao Liu, Xiaopeng Zhu, Yudong Wang, Dong Jia, Zhihua Zhang, Yong Tao, Haipan Zeng, Muhammad Nauman Aftab, Yan Cui, Guozhen Liu, Runsheng Chen
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
Nucleic Acids Res.: 2006, 34(10);2976-83
[PubMed:16738136] [WorldCat.org] [DOI] (I e)

Donna M Muzny, Steven E Scherer, Rajinder Kaul, Jing Wang, Jun Yu, Ralf Sudbrak, Christian J Buhay, Rui Chen, Andrew Cree, Yan Ding, Shannon Dugan-Rocha, Rachel Gill, Preethi Gunaratne, R Alan Harris, Alicia C Hawes, Judith Hernandez, Anne V Hodgson, Jennifer Hume, Andrew Jackson, Ziad Mohid Khan, Christie Kovar-Smith, Lora R Lewis, Ryan J Lozado, Michael L Metzker, Aleksandar Milosavljevic, George R Miner, Margaret B Morgan, Lynne V Nazareth, Graham Scott, Erica Sodergren, Xing-Zhi Song, David Steffen, Sharon Wei, David A Wheeler, Mathew W Wright, Kim C Worley, Ye Yuan, Zhengdong Zhang, Charles Q Adams, M Ali Ansari-Lari, Mulu Ayele, Mary J Brown, Guan Chen, Zhijian Chen, James Clendenning, Kerstin P Clerc-Blankenburg, Runsheng Chen, Zhu Chen, Clay Davis, Oliver Delgado, Huyen H Dinh, Wei Dong, Heather Draper, Stephen Ernst, Gang Fu, Manuel L Gonzalez-Garay, Dawn K Garcia, Will Gillett, Jun Gu, Bailin Hao, Eric Haugen, Paul Havlak, Xin He, Steffen Hennig, Songnian Hu, Wei Huang, Laronda R Jackson, Leni S Jacob, Susan H Kelly, Michael Kube, Ruth Levy, Zhangwan Li, Bin Liu, Jing Liu, Wen Liu, Jing Lu, Manjula Maheshwari, Bao-Viet Nguyen, Geoffrey O Okwuonu, Anthony Palmeiri, Shiran Pasternak, Lesette M Perez, Karen A Phelps, Farah J H Plopper, Boqin Qiang, Christopher Raymond, Ruben Rodriguez, Channakhone Saenphimmachak, Jireh Santibanez, Hua Shen, Yan Shen, Sandhya Subramanian, Paul E Tabor, Daniel Verduzco, Lenee Waldron, Jian Wang, Jun Wang, Qiaoyan Wang, Gabrielle A Williams, Gane K-S Wong, Zhijian Yao, JingKun Zhang, Xiuqing Zhang, Guoping Zhao, Jianling Zhou, Yang Zhou, David Nelson, Hans Lehrach, Richard Reinhardt, Susan L Naylor, Huanming Yang, Maynard Olson, George Weinstock, Richard A Gibbs
The DNA sequence, annotation and analysis of human chromosome 3.
Nature: 2006, 440(7088);1194-8
[PubMed:16641997] [WorldCat.org] [DOI] (I p)