Publications

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Machine Learning and Oncology Radiomics

Michael Baine, Justin Burr, Qian Du, Chi Zhang, Xiaoying Liang, Luke Krajewski, Laura Zima, Gerard Rux, Dandan Zheng. The Potential Use of Radiomics with Pre-Radiation Therapy MR Imaging in Predicting Risk of Pseudoprogression in Glioblastoma Patients. Journal of Imaging, Feb 2021. doi.org/10.3390/jimaging7020017

Yu Shi, Ethan Wahle, Qian Du, Luke Krajewski, Xiaoying Liang, Sumin Zhou, Chi Zhang, Michael Baine, Dandan Zheng. Associations between Statin/Omega3 Usage and MRI-Based Radiomics Signatures in Prostate Cancer. Diagnostics, Jan 2021. doi.org/10.3390/diagnostics11010085

Elsa Parr [1], Qian Du [1], Chi Zhang, Chi Lin, Ahsan Kamal, Josiah McAlister, Xiaoying Liang, Kyle Bavitz, Gerard Rux, Michael Hollingsworth, Michael Baine, Dandan Zheng Radiomics-Based Outcome Prediction for Pancreatic Cancer Following Stereotactic Body Radiotherapy Cancers, April 2020. doi.org/10.3390/cancers12041051

Qian Du, Michael Baine, Kyle Bavitz, Josiah McAllister, Xiaoying Liang, Hongfeng Yu, Jeffrey Ryckman, Lina Yu, Hengle Jiang, Sumin Zhou, Chi Zhang, Dandan Zheng. Radiomic feature stability across 4D respiratory phases and its impact on lung tumor prognosis prediction PLOS One, May 2019. doi.org/10.1371/journal.pone.0216480

Qian Du, Chi Zhang, Xiaofeng Zhu, Xiaoying Liang, Chi Zhang, Vivek Verma, Kenneth Follet, Shuo Wang, Qiyong Fan, Rongtao Ma, Sumin Zhou, Dandan Zheng. Application of statistical and computational methodology to predict brainstem dosimetry for trigeminal neuralgia stereotactic radiosurgery. Medical physics, May 2018. doi.org/10.1002/mp.12852

Statistical Genetics and Salinity Tolerance

Malachy T Campbell, Qian Du, Kan Liu, Sandeep Sharma, Chi Zhang, Harkamal Walia. Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). BMC genomics, December 2020. doi.org/10.1186/s12864-020-06786-6

Gleb Moisseyev, Kiyoul Park, Alix Cui, Daniel Freitas, Divith Rajagopal, Anji Reddy Konda, Madalayne Martin-Olenski, Mackenzie Mcham, Kan Liu, Qian Du, James C Schnable, Etsuko N Moriyama, Edgar B Cahoon, Chi Zhang. Database, Jan 2020. doi.org/10.1093/database/baaa038

Qian Du, Malachy Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang. Network‐based feature selection reveals substructures of gene modules responding to salt stress in rice. Plant direct, August 2019. doi.org/10.1002/pld3.154

Laetitia Virlouvet, Thomas J Avenson, Qian Du, Chi Zhang, Ning Liu, Michael Fromm, Zoya Avramova, Sabrina E Russo. Dehydration stress memory: gene networks linked to physiological responses during repeated stresses of Zea mays. Frontiers in plant science, July 2018.doi.org/10.3389/fpls.2018.01058

Malachy T Campbell, Qian Du, Kan Liu, Chris J Brien, Bettina Berger, Chi Zhang, Harkamal Walia. A Comprehensive Image‐based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa). The Plant Genome, July 2017. doi: 10.3835/plantgenome2016.07.0064

Malachy T Campbell, Nonoy Bandillo, Fouad Razzaq A Al Shiblawi, Sandeep Sharma, Kan Liu, Qian Du, Aaron J Schmitz, Chi Zhang, Anne-Aliénor Véry, Aaron J Lorenz, Harkamal Walia. Allelic variants of OsHKT1; 1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PLoS genetics, June 2017. doi.org/10.1371/journal.pgen.1006823

Statistics, Bioinformatics, NGS

Huihui Yu, Qian Du, Malachy Campbell, Bin Yu, Harkamal Walia, Chi Zhang. R package: VaSP. New Phytologist, Jan 2021.doi.org/10.1111/nph.17189

Kan Liu, Shangang Jia, Qian Du, Chi Zhang. NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. BIBM, November 2017. doi.org/10.1109/BIBM.2017.8217937

Kan Liu, Qian Du, Guodong Ren, Bin Yu, Chi Zhang. Identification of differential alternative splicing events with an adjusted beta-distribution model. 2017 IEEE International Conference on Electro Information Technology, May 2017. doi.org/10.1109/EIT.2017.8053369

Yongchao Dou, Shengjun Li, Weilong Yang, Kan Liu, Qian Du, Guodong Ren, Bin Yu, Chi Zhang. Genome-wide discovery of circular RNAs in the leaf and seedling tissues of Arabidopsis thaliana. Current genomics, August 2017. doi.org/10.2174/1389202918666170307161124

Bioinformatics and Bioengineering

Zhanqi Wang, Fuxing Zuo, Qing Liu, Xuesheng Wu, Qian Du, Yuguo Lei, Zhangmin Wu, Haishuang Lin. Comparative Study of Human Pluripotent Stem Cell-Derived Endothelial Cells in Hydrogel-Based Culture Systems ACS omega, Mar 2021. doi.org/10.1021/acsomega.0c06187

Haishuang Lin, Xuefeng Qiu, Qian Du, Qiang Li, Ou Wang, Leonard Akert, Zhanqi Wang, Dirk Anderson, Kan Liu, Linxia Gu, Chi Zhang, Yuguo Lei. Engineered microenvironment for manufacturing human pluripotent stem cell-derived vascular smooth muscle cells. Stem cell reports, Jan 2019. doi.org/10.1016/j.stemcr.2018.11.009

Haishuang Lin, Qian Du, Qiang Li, Ou Wang, Zhanqi Wang, Kan Liu, Leonard Akert, Chi Zhang, Soonkyu Chung, Bin Duan, Yuguo Lei. Differentiating human pluripotent stem cells into vascular smooth muscle cells in three dimensional thermoreversible hydrogels. Biomaterials science, https://doi.org/10.1039/C8BM01128A

Haishuang Lin, Qian Du, Qiang Li, Ou Wang, Zhanqi Wang, Christian Elowsky, Kan Liu, Chi Zhang, Soonkyu Chung, Bin Duan, Yuguo Lei. Manufacturing human pluripotent stem cell derived endothelial cells in scalable and cell-friendly microenvironments. Biomaterials science, doi.org/10.1039/C8BM01095A

Haishuang Lin, Qiang Li, Qian Du, Ou Wang, Zhanqi Wang, Leonard Akert, Mark A Carlson, Chi Zhang, Anuradha Subramanian, Matthew Lunning, Ming Li, Yuguo Lei. Biomaterials. Jan 2019. doi.org/10.1016/j.biomaterials.2018.10.027

Haishuang Lin, Qian Du, Qiang Li, Ou Wang, Zhanqi Wang, Neety Sahu, Christian Elowsky, Kan Liu, Chi Zhang, Soonkyu Chung, Bin Duan, Yuguo Lei. A scalable and efficient bioprocess for manufacturing human pluripotent stem cell-derived endothelial cells. Stem cell reports, August 2018. doi.org/10.1016/j.stemcr.2018.07.001

Haishuang Lin [1], Qian Du [1], Qiang Li, Ou Wang, Zhanqi Wang, Kan Liu, Christian Elowsky, Chi Zhang, Yuguo Lei. Hydrogel-Based Bioprocess for Scalable Manufacturing of Human Pluripotent Stem Cell-Derived Neural Stem Cells. ACS applied materials & interfaces, August 2018. doi.org/10.1021/acsami.8b05780

Qiang Li, Haishuang Lin, Qian Du, Kan Liu, Ou Wang, Catelyn Evans, Hannah Christian, Chi Zhang, Yuguo Lei. Scalable and physiologically relevant microenvironments for human pluripotent stem cell expansion and differentiation. Biofabrication, Feb 2018. doi.org/10.1088/1758-5090/aaa6b5

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