Publications

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. 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