Publications

2018

  • Yanchun Pan, Ying Zhu, Wei Yang, Eric Tycksen, Shaopeng Liu, John Palucki, Linjian Zhu, Yo Sasaki, Mukesh K Sharma, Albert H Kim, Bo Zhang, Hiroko Yano. The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity. Journal of Biological Chemistry, jbc. RA117. 001211
  • Nguyen PT Huynh, Bo Zhang, Farshid Guilak. High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesisThe FASEB Journal. 2018. fj. 201800534R
  • A Agrawal, YL Chou, CE Carey, DAA Baranger, B Zhang, R Sherva, L Wetherill, M Kapoor, JC Wang, S Bertelsen, AP Anokhin, V Hesselbrock, J Kramer, MT Lynskey, JL Meyers, JI Nurnberger, JP Rice, J Tischfield, LJ Bierut, L Degenhardt, LA Farrer, J Gelernter, AR Hariri, AC Heath, HR Kranzler, PAF Madden, NG Martin, GW Montgomery, B Porjesz, T Wang, JB Whitfield, HJ Edenberg, T Foroud, AM Goate, R Bogdan, EC Nelson. Genome-wide association study identifies a novel locus for cannabis dependenceMolecular Psychiatry, 2018. 23 (5), 1293
  • Ting Wang, Erica C Pehrsson, Deepak Purushotham, Daofeng Li, Xiaoyu Zhuo, Bo Zhang, Heather A Lawson, Michael A Province, Christopher Krapp, Yemin Lan, Cristian Coarfa, Tiffany A Katz, Wan Yee Tang, Zhibin Wang, Shyam Biswal, Sanjay Rajagopalan, Justin A Colacino, Zing Tsung-Yeh Tsai, Maureen A Sartor, Kari Neier, Dana C Dolinoy, Jayant Pinto, Robert B Hamanaka, Gokhan M Mutlu, Heather B Patisaul, David L Aylor, Gregory E Crawford, Tim Wiltshire, Lisa H Chadwick, Christopher G Duncan, Amanda E Garton, Kimberly A McAllister, Marisa S Bartolomei, Cheryl L Walker, Frederick L Tyson, TaRGET II Consortium. The NIEHS TaRGET II Consortium and environmental epigenomicsNature biotechnology36, 225–227 (2018)
  • RH Brophy, B Zhang, L Cai, RW Wright, LJ Sandell, MF Rai. Transcriptome comparison of the meniscus from patients with and without osteoarthritisOsteoarthritis and Cartilage 26 (3), 422-432
  • Matheus B Victor, Michelle Richner, Hannah E Olsen, Seong Won Lee, Alejandro M Monteys, Chunyu Ma, Christine J Huh, Bo Zhang, Beverly L Davidson, X William Yang, Andrew S Yoo. Striatal neurons directly converted from Huntington’s disease patient fibroblasts recapitulate age-associated disease phenotypes. Nature Neuroscience 21 (3), 341. 2018
  • Elizabeth L Ostrander, Won Kyun Koh, Cates Mallaney, Ashley C Kramer, W Casey Wilson, Bo Zhang, Grant A Challen. The GNASR201C mutation associated with clonal hematopoiesis supports transplantable hematopoietic stem cell activity. Experimental Hematology, 2018
  • Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang. Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. DNA Methylation Protocols (Pages 209-246), 2018

 

2017

  • Kesavan Meganathan, Emily MA Lewis, Paul Gontarz, Shaopeng Liu, Edouard G Stanley, Andrew G Elefanty, James E Huettner, Bo Zhang, Kristen L Kroll. Regulatory networks specifying cortical interneurons from human embryonic stem cells reveal roles for CHD2 in interneuron development. Proceedings of the National Academy of Sciences, 2017
  • Jia Zhou, Renee L Sears, Xiaoyun Xing, Bo Zhang, Daofeng Li, Nicole B Rockweiler, Hyo Sik Jang, Mayank NK Choudhary, Hyung Joo Lee, Rebecca F Lowdon, Jason Arand, Brianne Tabers, C Charles Gu, Theodore J Cicero, Ting Wang. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. BMC Genomics, 2017
  • David Brocks, Christopher R Schmidt, Michael Daskalakis, Hyo Sik Jang, Nakul M Shah, Daofeng Li, Jing Li, Bo Zhang, Yiran Hou, Sara Laudato, Daniel B Lipka, Johanna Schott, Holger Bierhoff, Yassen Assenov, Monika Helf, Alzbeta Ressnerova, Md Saiful Islam, Anders M Lindroth, Simon Haas, Marieke Essers, Charles D Imbusch, Benedikt Brors, Ina Oehme, Olaf Witt, Michael Lübbert, Jan-Philipp Mallm, Karsten Rippe, Rainer Will, Dieter Weichenhan, Georg Stoecklin, Clarissa Gerhäuser, Christopher C Oakes, Ting Wang & Christoph Plass . DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nature Genetics (2017) doi:10.1038/ng.3889
  • Bo Zhang, Pamela Madden, Junchen Gu, Xiaoyun Xing, Savita Sankar, Jennifer Flynn, Kristen Kroll and Ting Wang. Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissuesBMC Genomics2017 18:439
  • AC Kramer, A Kothari, WC Wilson, H Celik, J Nikitas, C Mallaney, EL Ostrander, E Eultgen, A Martens, MC Valentine, AL Young, TE Druley, ME Figueroa, B Zhang, GA Challen. Dnmt3a regulates T-cell development and suppresses T-ALL transformationLeukemia. 2017 Apr 11. doi: 10.1038/leu.2017.89
  • J Li, X Xing, D Li, B Zhang, DG Mutch, IS Hagemann, T Wang.Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. Neoplasia 19 (2), 100-111
  • Lo HG, Jin RU, Sibbel G, Liu D, Karki A, Joens MS, Madison BB, Zhang B, Blanc V, Fitzpatrick JA, Davidson NO, Konieczny SF, Mills JC. A single transcription factor is sufficient to induce and maintain secretory cell architecture. Genes Dev. 2017 Jan 15;31(2):154-171

 

2016

  • S Sankar, D Yellajoshyula, B Zhang, B Teets, N Rockweiler, KL Kroll. Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1. Scientific Reports 6. 2016
  • Huh, Christine J; Zhang, Bo; Victor, Matheus; Dahiya, Sonika; Batista, Luis FZ; Horvath, Steve; Yoo, Andrew S; Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts. eLife .5 e18648 2016
  • Cox, Jane A; Zhang, Bo; Pope, Holly M; Voigt, Mark M; Transcriptome Analysis of Chemically-Induced Sensory Neuron Ablation in Zebrafish. PloS One. 11 2 e0148726 2016
  • Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome. G3: Genes| Genomes| Genetics . 6 4 973-986 2016
  • Rai, Muhammad Farooq; Sandell, Linda J; Zhang, Bo; Wright, Rick W; Brophy, Robert H; RNA Microarray Analysis of Macroscopically Normal Articular Cartilage from Knees Undergoing Partial Medial Meniscectomy: Potential Prediction of the Risk for Developing Osteoarthritis. PloS one .11 5 e0155373 2016

2015

  • Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven JM Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, Roadmap Epigenomics Consortium; Integrative analysis of 111 reference human epigenomes. Nature .518 7539 317-330 2015
  • Zhou, Xin; Li, Daofeng; Zhang, Bo; Lowdon, Rebecca F; Rockweiler, Nicole B; Sears, Renee L; Madden, Pamela AF; Smirnov, Ivan; Costello, Joseph F; Wang, Ting; Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nature biotechnology .2015
  • Lee, Hyung Joo; Lowdon, Rebecca F; Maricque, Brett; Zhang, Bo; Stevens, Michael; Li, Daofeng; Johnson, Stephen L; Wang, Ting; Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nature communications .6 2015
  • Nelson, Elliot C; Agrawal, Arpana; Heath, Andrew C; Bogdan, Ryan; Sherva, Richard; Zhang, Bo; Al-Hasani, Ream; Bruchas, Michael R; Chou, Yi-Ling; Demers, Catherine H; Evidence of CNIH3 involvement in opioid dependence. Molecular Psychiatry. 2015
  • Carey, Caitlin E; Agrawal, Arpana; Zhang, Bo; Conley, Emily D; Degenhardt, Louisa; Heath, Andrew C; Li, Daofeng; Lynskey, Michael T; Martin, Nicholas G; Montgomery, Grant W; Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis. Journal of abnormal psychology .124 4 860 2015
  • Li, Daofeng; Zhang, Bo; Xing, Xiaoyun; Wang, Ting; Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods .72 29-40 2015

2014

  • Nagarajan, Raman P; Zhang, Bo; Bell, Robert JA; Johnson, Brett E; Olshen, Adam B; Sundaram, Vasavi; Li, Daofeng; Graham, Ashley E; Diaz, Aaron; Fouse, Shaun D; Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome research .24 5 761-774 2014
  • Zhang, Bo; Xing, XiaoYun; Li, Jing; Lowdon, Rebecca F; Zhou, Yan; Lin, Nan; Zhang, Baoxue; Sundaram, Vasavi; Chiappinelli, Katherine B; Hagemann, Ian S; Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. BMC Genomics .15 1 1 2014
  • Lowdon, Rebecca F; Zhang, Bo; Bilenky, Misha; Mauro, Thea; Li, Daofeng; Gascard, Philippe; Sigaroudinia, Mahvash; Farnham, Peggy J; Bastian, Boris C; Tlsty, Thea D; Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nature communications .5 2014

2013

  • Zhang B, Zhou Y, Lin N, Lowdon RF, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Reseach. 2013.
  • Xie M, Hong C, Zhang B, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genetics. 2013.

2012

  • B Chen, B Zhang, et al. Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells. Int.J of Cell Biology. 2012.

2011

  • B Zhang, B Chen, et al. Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC Bioinformatics 2011.
  • B Zhang, B Chen, T Wu, et al. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PloS one. 2011

2009

  • Y Tan, B Zhang, et al. Transcriptional inhibition of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC molecular biology.  2009