2024
- Hu H, Vomund AN, Peterson OJ, Srivastava N, Li T, Kain L, Beatty WL, Zhang B, Hsieh CS, Teyton L, Lichti CF, Unanue ER, Wan X. Crinophagic granules in pancreatic β cells contribute to mouse autoimmune diabetes by diversifying pathogenic epitope repertoire. Nat Commun. 2024
- Kohler JN, Legro NR, Baldridge D, Shin J, Bowman A, Ugur B, Jackstadt MM, Shriver LP, Patti GJ, Zhang B, Feng W, McAdow AR, Goddard P, Ungar RA, Jensen T, Smith KS, Fresard L, Alvarez R, Bonner D, Reuter CM, McCormack C, Kravets E, Marwaha S, Holt JM, Worthey EA, Ashley EA, Montgomery SB, Fisher PG, Postlethwait J, De Camilli P, Solnica-Krezel L, Bernstein JA, Wheeler MT. Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genet Med. 2024
- Srivastava N, Hu H, Peterson OJ, Vomund AN, Stremska M, Zaman M, Giri S, Li T, Lichti CF, Zakharov PN, Zhang B, Abumrad NA, Chen YG, Ravichandran KS, Unanue ER, Wan X. CXCL16-dependent scavenging of oxidized lipids by islet macrophages promotes differentiation of pathogenic CD8(+) T cells in diabetic autoimmunity. Immunity. 2024 .
- Robert Nims, Daniel R Palmer, Jordan Kassab, Bo Zhang, Farshid Guilak. The chondrocyte “mechanome”: Activation of the mechanosensitive ion channels TRPV4 and PIEZO1 drives unique transcriptional signatures. The FASEB Journal. 2024
- Liang Fang, Zhongting Liu, Cuicui Wang, Meng Shi, Yonghua He, Aiwu Lu, Xiaofei Li, Tiandao Li, Donghui Zhu, Bo Zhang, Jianjun Guan, Jie Shen. Vascular restoration through local delivery of angiogenic factors stimulates bone regeneration in critical size defects. Bioactive Materials. 2024
- Siyuan Cheng, Benpeng Miao, Tiandao Li, Guoyan Zhao, Bo Zhang. Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data. Genomics, Proteomics & Bioinformatics. 2024.
- Heather E Raphael, Ghandi F Hassan, Omar A Osorio, Lucy S Cohen, Morgan D Payne, Ella Katz-Kiriakos, Ishana Tata, Jamie Hicks, Derek E Byers, Bo Zhang, Jen Alexander-Brett. Activator protein transcription factors coordinate human IL-33 expression from noncanonical promoters in chronic airway disease. The Journal of Clinical Investigation, 2024
- Nimrod S Barashi, Tiandao Li, Duminduni H Angappulige, Bo Zhang, Harry O’Gorman, Charles U Nottingham, Anup S Shetty, Joseph E Ippolito, Gerald L Andriole, Nupam P Mahajan, Eric H Kim, Kiran Mahajan. Symptomatic benign prostatic hyperplasia with suppressed epigenetic regulator HOXB13 shows a lower incidence of prostate cancer development. Cancer. 2024
- Xiao, D., Fang, L., Liu, Z., He, Y., Ying, J., Qin, H., Lu, A., Shi, M., Li, T., Zhang, B. and Guan, J., 2024. DNA methylation–mediated Rbpjk suppression protects against fracture nonunion caused by systemic inflammation. The Journal of Clinical Investigation, 134(3).
2023
- Benpeng Miao, Xiaoyun Xing, Viktoriia Bazylianska, Pamela Madden, Anna Moszczynska, Bo Zhang. Methamphetamine induced regional-specific transcriptomic and epigenetic changes in the rat brain. Communications Biology 6 (1), 991
- YHaocheng Qin, Cuicui Wang, Yonghua He, Aiwu Lu, Tiandao Li, Bo Zhang, Jie Shen. Silencing miR-146a-5p Protects against Injury-Induced Osteoarthritis in Mice. Biomolecules. 2023/1
- Ren, Z., Zhao, S., Li, T., Wedner, H.J. and Atkinson, J.P., 2023. Insights into the pathogenesis of hereditary angioedema using genetic sequencing and recombinant protein expression analyses. Journal of Allergy and Clinical Immunology, 151(4), pp.1040-1049.
- Matsiukevich, D., Kovacs, A., Li, T., Kokkonen-Simon, K., Matkovich, S.J., Oladipupo, S.S. and Ornitz, D.M., 2023. Characterization of a robust mouse model of heart failure with preserved ejection fraction. American Journal of Physiology-Heart and Circulatory Physiology, 325(2), pp.H203-H231.
- Nguyen, T., Sridaran, D., Chouhan, S., Weimholt, C., Wilson, A., Luo, J., Li, T., Koomen, J., Fang, B., Putluri, N. and Sreekumar, A., 2023. Histone H2A Lys130 acetylation epigenetically regulates androgen production in prostate cancer. Nature Communications, 14(1), p.3357.
- Sawant, M., Wilson, A., Sridaran, D., Mahajan, K., O’Conor, C.J., Hagemann, I.S., Luo, J., Weimholt, C., Li, T., Roa, J.C. and Pandey, A., 2023. Epigenetic reprogramming of cell cycle genes by ACK1 promotes breast cancer resistance to CDK4/6 inhibitor. Oncogene, pp.1-15.
- Kotnik, E.N., Mullen, M.M., Spies, N.C., Li, T., Inkman, M., Zhang, J., Martins-Rodrigues, F., Hagemann, I.S., McCourt, C.K., Thaker, P.H. and Hagemann, A.R., 2023. Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival. Communications biology, 6(1), p.688.
- Boyer, Kevin, Louis Li, Tiandao Li, Bo Zhang, and Guoyan Zhao. MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks. Plos one 18, no. 11 (2023): e0294724.
2022
- Young Mi Oh, Seong Won Lee, Woo Kyung Kim, Shawei Chen, Victoria A Church, Kitra Cates, Tiandao Li, Bo Zhang, Roland E Dolle, Sonika Dahiya, Stephen C Pak, Gary A Silverman, David H Perlmutter, Andrew S Yoo. Age-related Huntington’s disease progression modeled in directly reprogrammed patient-derived striatal neurons highlights impaired autophagy. Nature neuroscience. 2022/11
- Mithila Sawant, Kiran Mahajan, Arun Renganathan, Cody Weimholt, Jingqin Luo, Vandna Kukshal, Joseph M Jez, Myung Sik Jeon, Bo Zhang, Tiandao Li, Bin Fang, Yunting Luo, Nicholas J Lawrence, Harshani R Lawrence, Felix Y Feng, Nupam P Mahajan. Chronologically modified androgen receptor in recurrent castration-resistant prostate cancer and its therapeutic targeting. Science translational medicine. 2022/6/15
- Chen Dong, Shuhua Fu, Rowan M Karvas, Brian Chew, Laura A Fischer, Xiaoyun Xing, Jessica K Harrison, Pooja Popli, Ramakrishna Kommagani, Ting Wang, Bo Zhang, Thorold W Theunissen. A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. Nature communications. 2022/5/10
- Avraham, O., Le, J., Leahy, K., Li, T., Zhao, G. and Cavalli, V., 2022. Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration. Frontiers in Molecular Neuroscience, 15, p.967472.
- Zhang, C.R., Ostrander, E.L., Kukhar, O., Mallaney, C., Sun, J., Haussler, E., Celik, H., Koh, W.K., King, K.Y., Gontarz, P. and Challen, G.A., 2022. Txnip enhances fitness of Dnmt3a-mutant hematopoietic stem cells via p21. Blood cancer discovery, 3(3), pp.220-239.
2021
- Kesavan Meganathan, Ramachandran Prakasam, Dustin Baldridge, Paul Gontarz, Bo Zhang, Fumihiko Urano, Azad Bonni, Susan E Maloney, Tychele N Turner, James E Huettner, John N Constantino, Kristen L Kroll. Altered neuronal physiology, development, and function associated with a common chromosome 15 duplication involving CHRNA7. BMC biology. 2021/12
- Celik H, Krug E, Zhang CR, Han W, Issa N, Koh WK, Bjeije H, Kukhar O, Allen M, Li T, Fisher DA. A humanized animal model predicts clonal evolution and therapeutic vulnerabilities in myeloproliferative neoplasms. Cancer discovery. 2021 Dec 1;11(12):3126-41.
- Xin Huang, Kyoung-mi Park, Paul Gontarz, Bo Zhang, Joshua Pan, Zachary McKenzie, Laura A Fischer, Chen Dong, Sabine Dietmann, Xiaoyun Xing, Pavel V Shliaha, Jihong Yang, Dan Li, Junjun Ding, Tenzin Lungjangwa, Maya Mitalipova, Shafqat A Khan, Sumeth Imsoonthornruksa, Nick Jensen, Ting Wang, Cigall Kadoch, Rudolf Jaenisch, Jianlong Wang, Thorold W Theunissen.OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nature Communications. 2021/8/26
- Shaopeng Liu, Daofeng Li, Cheng Lyu, Paul M Gontarz, Benpeng Miao, Pamela AF Madden, Ting Wang, Bo Zhang. AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. Genomics, Proteomics & Bioinformatics. 2021/7/15
- Jennifer A Karlow, Benpeng Miao, Xiaoyun Xing, Ting Wang, Bo Zhang. Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. Communications biology. 2021/5/21
- Bo Zhang, M Yvonne Kim, GiNell Elliot, Yan Zhou, Guangfeng Zhao, Daofeng Li, Rebecca F Lowdon, Matthew Gormley, Mirhan Kapidzic, Joshua F Robinson, Michael T McMaster, Chibo Hong, Tali Mazor, Emily Hamilton, Renee L Sears, Erica C Pehrsson, Marco A Marra, Steven JM Jones, Misha Bilenky, Martin Hirst, Ting Wang, Joseph F Costello, Susan J Fisher. Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. Developmental cell. 2021/5/3
- Robert J Nims, Lara Pferdehirt, Noelani B Ho, Alireza Savadipour, Jeremiah Lorentz, Sima Sohi, Jordan Kassab, Alison K Ross, Christopher J O’Conor, Wolfgang B Liedtke, Bo Zhang, Amy L McNulty, Farshid Guilak. A synthetic mechanogenetic gene circuit for autonomous drug delivery in engineered tissues. Science Advances. 2021/1/1
- Ou, T., Huang, G., Wilson, B., Gontarz, P., Skeath, J.B. and Johnson, A.N., 2021. A genetic screen for regulators of muscle morphogenesis in Drosophila. G3, 11(8), p.jkab172.
2020
- Benpeng Miao, Shuhua Fu, Cheng Lyu, Paul Gontarz, Ting Wang, Bo Zhang. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biology. 21, 255 (2020).
- Kitra Cates, Matthew J McCoy, Ji-Sun Kwon, Yangjian Liu, Daniel G Abernathy, Bo Zhang, Shaopeng Liu, Paul Gontarz, Woo Kyung Kim, Shawei Chen, Wenjun Kong, Joshua N Ho, Kyle F Burbach, Harrison W Gabel, Samantha A Morris, Andrew S Yoo. Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. Cell Stem Cell, 2020
- Catherine E Lipovsky, Jesus Jimenez, Qiusha Guo, Gang Li, Tiankai Yin, Stephanie C Hicks, Somya Bhatnagar, Kentaro Takahashi, David M Zhang, Brittany D Brumback, Uri Goldsztejn, Rangarajan D Nadadur, Carlos Perez-Cervantez, Ivan P Moskowitz, Shaopeng Liu, Bo Zhang, Stacey L Rentschler. Chamber-specific transcriptional responses in atrial fibrillation. JCI insight. 2020;5(18):e135319.
- Christopher J Chermside‐Scabbo, Taylor L Harris, Michael D Brodt, Ingrid Braenne, Bo Zhang, Charles R Farber, Matthew J Silva. Old Mice Have Less Transcriptional Activation But Similar Periosteal Cell Proliferation Compared to Young‐Adult Mice in Response to in vivo Mechanical Loading. Journal of Bone and Mineral Research. 2020/9
- F Qu, IC Palte, PM Gontarz, B Zhang, F Guilak. Transcriptomic analysis of bone and fibrous tissue morphogenesis during digit tip regeneration in the adult mouse. The FASEB Journal .34 (7), 9740-9754
- 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.
- Troutwine, B.R., Gontarz, P., Konjikusic, M.J., Minowa, R., Monstad-Rios, A., Sepich, D.S., Kwon, R.Y., Solnica-Krezel, L. and Gray, R.S., 2020. The Reissner fiber is highly dynamic in vivo and controls morphogenesis of the spine. Current Biology, 30(12), pp.2353-2362.
- Bohnert, K.L., Hastings, M.K., Sinacore, D.R., Johnson, J.E., Klein, S.E., McCormick, J.J., Gontarz, P. and Meyer, G.A., 2020. Skeletal muscle regeneration in advanced diabetic peripheral neuropathy. Foot & ankle international, 41(5), pp.536-548.
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 neurons. Molecular 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
- Christopher J Chermside‐Scabbo, Taylor L Harris, Michael D Brodt, Ingrid Braenne, Bo Zhang, Charles R Farber, Matthew J Silva. 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 leukemogenesis. Leukemia. 2019
- C Ma, P Madden, P Gontarz, T Wang, B Zhang. FeatSNP: an interactive database for brain-specific epigenetic annotation of human SNPs. Front. 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 chondrogenesis. The 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 dependence. Molecular 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 epigenomics. Nature biotechnology. 36, 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 osteoarthritis. Osteoarthritis 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 tissues. BMC Genomics. 2017 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 transformation. Leukemia. 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