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Tao Liu

TaoLiu.jpg

Assistant Professor, Department of Biochemistry, University at Buffalo

  • (O) 716-829-2749
  • e-mail: tliu4@buffalo.edu

Mailing address:

University at Buffalo-COEBLS
701 Ellicott St, B2-163
Buffalo, NY 14203-1221

Professional Summary

My research is focused on developing bioinformatics algorithms especially through sequencing analysis and data integration, to understand better transcriptional and epigenetic regulation.

Transcription factor often binds to DNA and interferes with transcription machinery to enhance or repress gene expression. Epigenetic features such as histone modification, chromatin remodeling factor binding, DNA methylation, and chromatin 3D organization add yet another layer of information, making it more complex to understand the regulation dynamics within the nucleus.

With advancing sequencing technology, however, such information now can be measured and quantified on genome scale, though the growing number of big genomic datasets creates challenges as well as opportunities for bioinformatics methodologies. The focus of our lab is to build algorithms, analysis platforms and databases to integrate big datasets from the public domain into various biological questions and disease models.

The MACS (Genome Biology 2008) algorithm, on which I worked to develop, is one of the most widely-used algorithms for predicting cis-regulatory elements from Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). The algorithm has been evolving over years to accommodate various factor types from punctuate transcription factor binding to long-range histone modifications. It has been used to process hundreds of publicly-available datasets in the mod/ENCODE project, and it continues as a focus of my lab.

I also worked to build an integrative platform for ChIP analysis based on Galaxy framework, named Cistrome (Genome Biology 2011). This platform provides both a user-friendly interface and rich functionality for biologists to manage and process their high-throughput genomic data and to publish the results conveniently over the Internet. The Cistrome platform will continue as a collaborative project between my UB lab and research partners at Harvard University.

I have also been involved in many collaborative research projects, such as circadian binding of histone deacetylase and nuclear receptor Rev-Erba in mouse liver (Science 2011), and the modENCODE consortium project to elucidate chromatin factor functions of C. elegans (Genome Research 2011 and Science 2010).

Education and Training

  • Postdoctoral Fellow, Dana-Farber Cancer Institute, Harvard School of Public Health (2012)
  • PhD, Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences (2008)

Employment

  • Post Doctoral Fellow, Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health (2007–2012)

Publications

Important Publications

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)

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)

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)

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)

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)

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)

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)


Other Publications

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)

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)

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)

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)

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)

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)

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)

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, 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)