Publications

2023

• Kotnik EN, Mullen MM, Spies NC, Li T, Inkman M, Zhang J, Martins-Rodrigues F, Hagemann IS, McCourt CK, Thaker PH, Hagemann AR, Powell MA, Mutch DG, Khabele D, Longmore GD, Mardis ER, Maher CA, Miller CA, Fuh KC. Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival. Commun Biol. 2023 
• Sawant M, Wilson A, Sridaran D, Mahajan K, O’Conor CJ, Hagemann IS, Luo J, Weimholt C, Li T, Roa JC, Pandey A, Wu X, Mahajan NP. Epigenetic reprogramming of cell cycle genes by ACK1 promotes breast cancer resistance to CDK4/6 inhibitor. Oncogene. 2023
• Nguyen T, Sridaran D, Chouhan S, Weimholt C, Wilson A, Luo J, Li T, Koomen J, Fang B, Putluri N, Sreekumar A, Feng FY, Mahajan K, Mahajan NP. Histone H2A Lys130 acetylation epigenetically regulates androgen production in prostate cancer. Nat Commun. 2023 
• Matsiukevich D, Kovacs A, Li T, Kokkonen-Simon K, Matkovich SJ, Oladipupo SS, Ornitz DM.
  Characterization of a robust mouse model of heart failure with preserved ejection fraction. Am J Physiol Heart Circ Physiol. 2023 
• Ren Z, Zhao S, Li T, Wedner HJ, Atkinson JP. Insights into the pathogenesis of hereditary angioedema using genetic sequencing and recombinant protein expression analyses. J Allergy Clin Immunol. 2023 
• 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

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
• Avraham O, Le J, Leahy K, Li T, Zhao G, Cavalli V. Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration. Front Mol Neurosci. 2022
• Zhang CR, Ostrander EL, Kukhar O, Mallaney C, Sun J, Haussler E, Celik H, Koh WK, King KY, Gontarz P, Challen GA. Txnip Enhances Fitness of Dnmt3a-Mutant Hematopoietic Stem Cells via p21. Blood Cancer Discov. 2022 
• 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 

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 DAC, Fowles JS, Wong TN, Stubbs MC, Koblish HK, Oh ST, Challen GA. A Humanized Animal Model Predicts Clonal Evolution and Therapeutic Vulnerabilities in Myeloproliferative Neoplasms. Cancer Discov. 2021 
• 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
• Ou T, Huang G, Wilson B, Gontarz P, Skeath JB, Johnson AN. A genetic screen for regulators of muscle morphogenesis in Drosophila. G3 (Bethesda). 2021 
• 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

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).
• Troutwine BR, Gontarz P, Konjikusic MJ, Minowa R, Monstad-Rios A, Sepich DS, Kwon RY, Solnica-Krezel L, Gray RS. The Reissner Fiber Is Highly Dynamic In Vivo and Controls Morphogenesis of the Spine. Curr Biol. 2020 
• Bohnert KL, Hastings MK, Sinacore DR, Johnson JE, Klein SE, McCormick JJ, Gontarz P, Meyer GA. Skeletal Muscle Regeneration in Advanced Diabetic Peripheral Neuropathy. Foot Ankle Int. 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. Development.  2020 147: dev181032 doi: 10.1242/dev.181032
• 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 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 
• 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 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

• NPT Huynh, B Zhang, F Guilak.High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis.The FASEB Journal, fj. 201800534R
• 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
• 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 (3), 225
• Arpana Agrawal, Yi-Ling Chou, Caitlin E Carey, David AA Baranger, Bo Zhang, Richard Sherva, Leah Wetherill, Manav Kapoor, Jen-Chyong Wang, Sarah Bertelsen, Andrey P Anokhin, Victor Hesselbrock, John Kramer, Michael T Lynskey, Jacquelyn L Meyers, John I Nurnberger, John P Rice, Jay Tischfield, Laura J Bierut, Louisa Degenhardt, Lindsay A Farrer, Joel Gelernter, Ahmad R Hariri, Andrew C Heath, Henry R Kranzler, Pamela AF Madden, Nicholas G Martin, Grant W Montgomery, Bernice Porjesz, Ting Wang, John B Whitfield, Howard J Edenberg, Tatiana Foroud, Alison M Goate, Ryan Bogdan, Elliot C Nelson. Genome-wide association study identifies a novel locus for cannabis dependence. Molecular psychiatry 23 (5), 1293
• RH Brophy, B Zhang, L Cai, RW Wright, LJ Sandell, MF Rai. Transcriptome comparison of 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
• 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 57, 14-20

2017

• Kesavan Meganathan, Emily MA Lewis, Paul Gontarz, Shaopeng Liu, Edouard G Stanley, Andrew G Elefanty, James E Huettner, Bo Zhang, Kristen L Krol. Regulatory networks specifying cortical interneurons from human embryonic stem cells reveal roles for CHD2 in interneuron development. Proceedings of the National Academy of Sciences. 114 (52), E11180-E11189
• Bo Zhang, Pamela Madden, Junchen Gu, Xiaoyun Xing, Savita Sankar, Jennifer Flynn, Kristen Kroll, Ting Wang. Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. BMC genomics 18 (1), 439
• 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
• 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

2016

• JA Cox, B Zhang, HM Pope, MM Voigt. PloS one 11 (2), e0148726. Transcriptome Analysis of Chemically-Induced Sensory Neuron Ablation in Zebrafish
• MF Rai, LJ Sandell, B Zhang, RW Wright, RH Brophy. PloS one 11 (5), e0155373. RNA microarray analysis of macroscopically normal articular cartilage from knees undergoing partial medial meniscectomy: potential prediction of the risk for developing osteoarthritis
• CJ Huh, B Zhang, MB Victor, S Dahiya, LFZ Batista, S Horvath, AS Yoo. eLife 5, e18648. Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts
• S Sankar, D Yellajoshyula, B Zhang, B Teets, N Rockweiler, KL Kroll. Scientific Reports 6. Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1