2020

  • Xiaoying Chen, Bo Zhang, Ting Wang, Azad Bonni, Guoyan Zhao. Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. BMC Bioinformatics .volume 21, Article number: 269 (2020)
  • Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela Madden, Kitra Cates, Andrew Yoo, Anna Moszczynska, Ting Wang, Bo Zhang. Comparison of differential accessibility analysis strategies for ATAC-seq data. Scientific Reports .volume 10, Article number: 10150 (2020)
  • Emily MA Lewis, Savita Sankar, Caili Tong, Ethan Patterson, Laura E Waller, Paul Gontarz, Bo Zhang, David M Ornitz, Kristen L Kroll. Geminin is required for Hox gene regulation to pattern the developing limb. Developmental Biology. Volume 464, Issue 1, 1 August 2020, Pages 11-23
  • Nguyen PT Huynh, Catherine C Gloss, Jeremiah Lorentz, Ruhang Tang, Jonathan M Brunger, Audrey McAlinden, Bo Zhang, Farshid Guilak. Long non-coding RNA GRASLND enhances chondrogenesis via suppression of the interferon type II signaling pathway.  eLife, 9, e49558
  • Andrew S Hagan, Bo Zhang, David M Ornitz. Identification of a FGF18-expressing alveolar myofibroblast that is developmentally cleared during alveologenesis.
  • Dong, C., Beltcheva, M., Gontarz. P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K., Yoon, E., Xing, X., Kommagani, R., Wang, T., Solnica-Krezel, L. and T.W. Theunissen (2020). Derivation of trophoblast stem cells from naive human pluripotent stem cells. eLife, 9, e52504.

2019

  • Emily MA Lewis, Kesavan Meganathan, Dustin Baldridge, Paul Gontarz, Bo Zhang, Azad Bonni, John N Constantino, Kristen L Kroll. Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neuronsMolecular Autism. volume 10, Article number: 51 (2019)
  • Brandon A Coates, Jennifer A McKenzie, Evan G Buettmann, Xiaochen Liu, Paul M Gontarz, Bo Zhang, Matthew J Silva.Transcriptional profiling of intramembranous and endochondral ossification after fracture in mice. Bone.Volume 127, October 2019, Pages 577-591 
  • Davis JL, Cox L, Shao C, Lyu C et al. Conditional Activation of NF-κB Inducing Kinase (NIK) in the Osteolineage Enhances Both Basal and Loading-Induced Bone Formation. J Bone Miner Res 2019 Nov;34(11):2087-2100.
  • Cates Mallaney, Elizabeth L Ostrander, Hamza Celik, Ashley C Kramer, Andrew Martens, Alok Kothari, Won Kyun Koh, Emily Haussler, Naoki Iwamori, Paul Gontarz, Bo Zhang, Grant A Challen. Kdm6b regulates context-dependent hematopoietic stem cell self-renewal and leukemogenesisLeukemia. 2019
  • C Ma, P Madden, P Gontarz, T Wang, B Zhang. FeatSNP: an interactive database for brain-specific epigenetic annotation of human SNPsFront. Genet. 2019.  10:262. doi: 10.3389/fgene.2019.00262

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, 2018. 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 Zic1Scientific 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