Publications

2022

1. Zachary Jackson^, Changjin Hong^, Robert Schauner, Boro Dropulic, Paolo F Caimi, Marcos JG de Lima, Kalpana Gupta, Jane Reese, Tae Hyun Hwang*, David Wald*, “Sequential Single Cell Transcriptional and Protein Marker Profiling Reveals TIGIT As a Marker of CD19 CAR-T Cell Dysfunction in Patients with Non-Hodgkin's Lymphoma“, Cancer Discovery, 2022 June 16; https://doi.org/10.1158/2159-8290.CD-21-1586 (^co-first authors, *co-corresponding authors)

2. Hongming Xu, Sunho Park, Jean René Clemenceau, Jinhwan Choi, Sung Hak Lee, Tae Hyun Hwang, “Spatial heterogeneity and organization of tumor mutation burden with immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer“, Journal of Pathology Informatics, 2022 May 21; https://doi.org/10.1016/j.jpi.2022.100105. *equal contribution

3. Hongming Xu, Yoon Jin Cha, Jean R Clemenceau, Jinhwan Choi, Sung Hak Lee, Jeonghyun Kang, Tae Hyun Hwang, “Spatial analysis of tumor-infiltrating lymphocytes in histological sections using deep learning techniques predicts survival in colorectal carcinoma“, The Journal of Pathology: Clinical Research, 2022 April 28; https://doi.org/10.1002/cjp2.273

4. John D Karalis, Lynn Y Yoon, Suntrea TG Hammer, Changjin Hong, Min Zhu, Ibrahim Nassour, Michelle R Ju, Shu Xiao, Esther C Castro-Dubon, Deepak Agrawal, Jorge Suarez, Scott I Reznik, John C Mansour, Patricio M Polanco, Adam C Yopp, Herbert J Zeh, Tae Hyun Hwang, Hao Zhu, Matthew R Porembka, Sam C Wang, “Lenvatinib inhibits the growth of gastric cancer patient-derived xenografts generated from a heterogeneous population“, Journal of Translational Medicine, 2021 March 07; 20(1) 1-13; https://doi.org/10.1186/s12967-022-03317-7

5. Chan Hyuk Park, Changjin Hong, A-reum Lee, Jaeyun Sung, Tae Hyun Hwang, “Multi-omics reveals microbiome, host gene expression, and immune landscape in gastric carcinogenesis“, iScience, 2022 February 19, 103956; https://doi.org/10.1016/j.isci.2022.103956

6. Jae-Ho Cheong, Sam C Wang, Sunho Park, Matthew R Porembka, Alana L Christie, Hyunki Kim, Hyo Song Kim, Hong Zhu, Woo Jin Hyung, Sung Hoon Noh, Bo Hu, Changjin Hong, John D Karalis, In-Ho Kim, Sung Hak Lee, Tae Hyun Hwang, “Development and validation of a prognostic and predictive 32-gene signature for gastric cancer“, Nature Communications, 2022 February 9; 12(1) 1-9; https://doi.org/10.1038/s41467-022-28437-y

2021

1. Hongming Xu, Fengyu Cong, Tae Hyun Hwang, “Machine Learning and Artificial Intelligence–driven Spatial Analysis of the Tumor Immune Microenvironment in Pathology Slides“, Europe Urology Focus, 2021 Aug 2;S2405-4569(21)00186-3.

   doi: 10.1016/j.euf.2021.07.006.

2. Jessica Minnier, Mark R Emmett, Ruby Perez, Liang-Hao Ding, Brooke L Barnette, Rianna E Larios, Changjin Hong, Tae Hyun Hwang, Yongjia Yu, Christina M Fallgren, Michael D Story, Michael M Weil, Jacob Raber, “Associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following 28Si ion irradiation“, Scientific Reports, 2021 July 21;11(1), 1-30; https://doi.org/10.1038/s41598-021-93869-3

3. LC Stetson, Dheepa Balasubramanian, Susan Pereira Ribeiro, Tammy Stefan, Kalpana Gupta, Xuan Xu, Slim Fourati, Anne Roe, Zachary Jackson, Robert Schauner, Ashish Sharma, Banumathi Tamilselvan, Samuel Li, Marcos de Lima, Tae Hyun Hwang, Robert Balderas, Yogen Saunthararajah, Jaroslaw Maciejewski, Thomas LaFramboise, Jill S Barnholtz-Sloan, Rafick-Pierre Sekaly, David N Wald, “Single cell RNA sequencing of AML initiating cells reveals RNA-based evolution during disease progression“, Leukemia, 2021 July 9; 35(10) 2799-2812; doi: 10.1038/s41375-021-01338-7

4. Chihyun Park^, Jean R. Clemenceau^, Anna Seballos, Sara Crawford, Rocio Lopez, Tyler Coy, Gowtham Atluri, Tae Hyun Hwang*, “A Spatiotemporal Analysis of Opioid Poisoning Mortality in Ohio from 2010 to 2016”, Scientific Report, 11, Article number: 4692 (2021) (^co-first authors)

5. Jeonghyun Kang, Jae-soon Lee, Hye Sun Lee, Eun-Suk Cho, Eun Jung Park, Seung Hyuk Bank, Kang Young Lee, Chihyun Park, Yunku Yeu, Jean R Clemenceau, Sunho Park, Hongming Xu, Changjin Hong, Tae Hyun Hwang, “Radiomics Features of 18F-Fluorodeoxyglucose Positron-Emission Tomography as a Novel Prognostic Signature in Colorectal Cancer”, Cancers, 2021, 13(3), 392; https://doi.org/10.3390/cancers13030392

6. Samaneh K. Sarvestani, Steven Signs, Bo Hu, Yunku Yeu, Hao Feng, Ying Ni, David R. Hill, Robert C. Fisher, Sylvain Ferrandon, Reece K. DeHaan, Jennifer Stiene, Michael Cruise, Tae Hyun Hwang, Xiling Shen, Jason R. Spence & Emina H. Huang, “Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity”, Nature Communication, January 11, 262 (2021). https://doi.org/10.1038/s41467-020-20351-5

2020

1. Khandakar Tanvir Ahmed, Sunho Park, Qibing Jiang, Yunku Yeu, TaeHyun Hwang, Wei Zhang, “Network-based drug sensitivity prediction”, BMC Medical Genomics, 2020 December 28;13(Suppl 11):193.doi: 10.1186/s12920-020-00829-3

2. Vishal Nanavaty, Elizabeth W Abrash, Changjin Hong*, Sunho Park, Emily E Fink, Zhuangyue Li, Thomas J Sweet, Jeffrey M Bhasin, Srinidhi Singuri, Byron H Lee, Tae Hyun Hwang, Angela H Ting, “DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex”, Molecular Cell, 2020 April 24. doi.org/10.1016/j.molcel.2020.03.024 (*co-first author)

3. Defne Bayik, Yadi Zhou, Chihyun Park, Changjin Hong, Daniel Vail, Daniel J Silver, Adam J Lauko, Gustavo A Roversi, Dionysios C Watson, Alice Lo, Tyler J Alban, Mary McGraw, Mia D Sorensen, Matthew M Grabowski, Balint Otvos, Michael A Vogelbaum, Craig M Horbinski, Bjarne W Kristensen, Ahmad M Khalil, Tae Hyun Hwang, Manmeet S Ahluwalia, Feixiong Cheng, Justin Lathia, Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner, Cancer Discovery, 2020 April 16. doi:10.1158/2159-8290.CD-19-1355

4. Sam C Wang*, Yunku Yeu (co-first author), Suntrea T G Hammer, Shu Xiao, Min Zhu, Changjin Hong, Jean Clemenceau, Lynn Y Yoon Ibrahim Nassour, Jeanne Shen, Deepak Agarwal, Scott I Reznik, John C Mansour, Adam C Yopp, Hao Zhu, Tae Hyun Hwang*, Matthew R Porembka, Hispanic/Latino gastric adenocarcinoma patients have distinct molecular profiles including a high rate of germline CDHI mutations, Cancer Research, 2020 April doi: 10.1158/0008-5472.CAN-19-2918 (*co-corresponding author)

5. Sunho Park, Nabhonil Kar, Jae-Ho Cheong, Tae Hyun Hwang*, Bayesian Semi-nonnegative Matrix Tri-factorization to Identify Pathways associated with Cancer Phenotypes,Pacific Symposium on Biocomputing (PSB), 2020, doi:10.1101/739110

6. Yingming Li, Rendong Yang, Christine M Henzler, Yeung Ho, Courtney Passow, Benjamin Auch, Suzanne Carreira, Daniel Nava Rodrigues, Claudia Bertan, Tae Hyun Hwang, David A Quigley, Ha X. Dang, Colm Morrissey, Michael Fraser, Stephen R Plymate, Christopher A Maher, Felix Y. Feng, Johann S. de Bono and Scott M. Dehm, Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer, Clinical Cancer Research, 2020 January 13, doi: 10.1158/1078-0432.CCR-19-3023

2019

1. Hongming Xu, Sunho Park, Tae Hyun Hwang, Computerized Classification of Prostate Cancer Gleason Scores from Whole Slide Images,
   IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019 September, doi: 10.1109/TCBB.2019.2941195.

2. Rubina Tuladhar, Yunku Yeu, John Tyler Piazza, Zhen Tan, Jean R. Clemenceau, Xiaofeng Wu, Quinn Barrett, Jeremiah Herbert, David H Matthews, James Kim, Tae Hyun Hwang*, Lawrence Lum*, CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation,
   Nature Communications, 2019 September 6;10:4056. doi: 10.1038 (*co-corresponding author)

3. Hongming Xu, Tae Hyun Hwang, Statistical Local Binary Patterns (SLBP): Application to Prostate Cancer Gleason Score Prediction from Whole Slide Pathology Images,
   2019 IEEE 16th International Symposium on Biomedical Imaging, 2019 April, 2019;895-899 doi: 10.1109/ISBI.2019.8759406

2018

1. Emily Kunce Stroup, Yunku Yeu, Albert Budhipramono, Tae Hyun Hwang, Dinesh Rakheja, Anat Erdreich-Epstein, Theodore W. Laetsch, James F. Amatruda, Kenneth S. Chen, WT-CLS1 is a rhabdoid tumor cell line and can be inhibited by miR-16,
   Cancer Reports, 2018 July 11, doi: 10.1002/cnr2.1110

2. Mohammad Alyamani, Hamid Emamekhoo, Sunho Park, Jennifer Taylor, Nima Almassi, Sunil Upadhyay, Allison Tyler, Michael P. Berk, Bo Hu, Tae Hyun Hwang, William Douglas Figg, Cody J. Peer, Caly Chien, Vadim S. Koshkin, Prateek Mendiratta, Petros Grivas, Brian Rini, Jorge Garcia, Richard J. Auchus, and Nima Sharifi, HSD3B1(1245A>C) variant regulates dueling abiraterone metabolite effects in prostate cancer,
   The Journal of Clinical Investigation, 2018 August, 2018;128(8):3333–3340. doi: 10.1172/JCI98319

3. Elizabeth A. McMillan, Caroline H. Diep, Saurabh Mendiratta, Myung-Jeon Ryu, Jean R. Clemenceau, Rachel M. Vaden, Kyle R. Covington, Michael Peyton, Kenneth Huffman, Xiaofeng Wu, Luc Girard, Ju-Hwa Kim, Yeojin Sung, Pei-Hsaun Chen, Joo Young Lee, Jordan Hanson, Yunku Yeu, Sunho Park, Jessica Sudderth, Christopher DeSevo,Donna M. Muzny, HarshaVardhan Doddapaneni, Richard A. Gibbs, Tae Hyun Hwang, John V. Heymach, Ignacio Wistuba, Kevin R. Coombes, Noelle S. Williams, David A. Wheeler, John B. MacMillan, John D. Minna, Ralph J. Deberardinis, Michael G. Roth, Bruce A. Posner, Hyunseok Kim, Michael A. White, Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer,
   Cell, 2018 May 3; 173(4):864-878. doi: 10.1016/j.cell.2018.03.028. [Impact factor: 30.41]

2014

1. Sunho Park, Tae Hyun Hwang, and Seungjin Choi,
   Convex Optimization for Binary Classifier Aggregation in Multiclass Problems,
   SIAM International Conference on Data Mining (SDM), April 2014.

2. Sean Landman Tae Hyun Hwang*, Kevin Silverstein, Yingming Li, Scott Dehm, Michael Steinbach, and Vipin Kumar,
   SHEAR: sample heterogeneity estimation and assembly by reference,
   BMC Genomics. 2014 Jan 29;15(1):84. [Impact Factor: 3.99]
   (*corresponding author)
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   ↳ SHEAR is the first tool that accounts for heterogeneous variants by estimating their representative percentages and allowing for selective assembly of sample subpopulations.

2013

1. Donghyeon Yu, MinSoo Kim, Guanghua Xiao and Tae Hyun Hwang*,
   Review of Biological Network Data and its Applications,
   Genomics & Informatics, 2013 Dec;11(4):200-210.
   (*corresponding author)

2. Michael D. Nyquista, Yingming Li, Tae Hyun Hwang, Luke S. Manlovea, Robert L. Vessellad, Kevin A. T. Silversteina, Daniel F. Voytasg, and Scott M. Dehma,
   TALEN-Engineered AR Gene Rearrangements Reveal Endocrine Uncoupling of Androgen Receptor in Prostate Cancer,
   Proceedings of the National Academy of Sciences (PNAS), October 7, 2013, doi:10.1073/pnas.1308587110 [Impact Factor: 9.809]
   ↳ This study describes the discovery of AR gene rearrangements in clinical prostate cancer tissues, and the first use of genome engineering in prostate cancer with TAL effector nucleases (TALENs) to functionally classify these gene rearrangements as drivers of resistance. This new knowledge is expected to lead to better patient management and enable the development of more effective therapies for advanced prostate cance.

3. Tae Hyun Hwang*, Gowtham Atluri, Rui Kuang, Timothy Starr, Kevin AT Silverstein, Peter Haverty, Zemin Zhang, and Jinfeng Liu*,
   Large-scale Integrative Network-based analysis Identifies Common Pathways Disrupted by Copy Number Alterations across Cancers,
   BMC Genomics, 2013 14:440. DOI: 10.1186/1471-2164-14-440 [Impact Factor: 3.986]
   (*corresponding author)
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   ↳ We applied our approach to a data set of 2172 cancer patients across 16 different types of cancers, and found a set of commonly disrupted pathways across cancers, along with a set of pathways disrupted in a specific type(s) of cancers.

4. Yingming Li, Siu Chiu Chan, Lucas J Brand, Tae Hyun Hwang, Kevin Silverstein, and Scott Dehm.,
   Androgen Receptor Splice Variants Mediate Enzalutamide Resistance in Castration-Resistant Prostate Cancer Cell Lines,
   Cancer Research, 2013 Jan 15;73(2):483-9. doi: 10.1158/0008-5472.CAN-12-3630. Epub 2012 Nov 1. [Impact Factor: 9.329] [PMid: 23117885]
   ↳ This study is the first to characterize rearrangement-driven expression of activated androgen receptor splice variants important in dvance prostate cancer as a mechanism of resistance to the next-generation of anti-androgen drug.
   ↳ *The most highly-cited paper in the prostate cancer field from 2012-present

2012

1. Tae Hyun Hwang, Maoqiang Xie, Gowtham Atluri, Sanjoy Dey, Changjin Hong, Vipin Kumar, and Rui Kuang.,
   Co-clustering Phenome-genome for Phenotype Classification and Disease Gene Discovery,
   Nucleic Acids Research, June 2012., doi: 10.1093/nar/gks615. [Impact factor: 8.026] [PMid: 22735708]
   ↳ This is the first computational approach for phenotype classification as well as disease gene, and pathway discovery by integrating phenome-genome-interactome data.

2. Young-Mi Kim, Matthew Stone, Tae Hyun Hwang, Yeon-Gil Kim, Timothy J. Griffin, and Do-Hyung Kim,
   SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1,
   Molecular Cell, May 2012., doi:10.1016/j.molcel.2012.04.007. [Impact factor: 14.194] [PMid:22575674]

3. Yingming Li*, Tae Hyun Hwang*, LeAnn Oseth, Betsy Hirsch, Robert Vessella, Kenny Beckman, Kevin Silverstein, and Scott Dehm,
   AR intragenic deletions linked to Androgen Receptor Splice Variant Expression and Activity in Models of Prostate Cancer Progression,
   Oncogene, January 2012., doi:10.1038/onc.2011.637. [Impact factor: 7.414] [PMid:22266865]
   (*Joint first authors)
   ↳ We use paired-end AR gene re-sequencing to identify a novel intragenic deletion linked to increased AR splice variant expression and a selective growth advantage during androgen deprivation.

4. Seung-Jun Kim, Tae Hyun Hwang, and Georgios B. Giannakis,
   Sparse Robust Matrix Tri-factorization with Application to Cancer Genomics,
   International Workshop on Cognitive Information Processing (CIP), 2012.

2011

1. Tae Hyun Hwang, Wei Zhang, Maoqiang Xie, Jinfeng Liu, and Rui Kuang,
   Inferring Disease and Gene Set Associations with Rank Coherence in Networks,
   Bioinformatics 2011 1;27(19):2692-9. Epub August 8, 2011. [PMid: 21824970]
   Website 🌐

2. Tae Hyun Hwang,
   Network-based learning algorithms for understanding human disease,
   Ph.D Thesis (University of Minnesota, Twin Cities), 2011

2010

1. Tae Hyun Hwang, and Rui Kuang.,
   A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery,
   SIAM International Conference on Data Mining (SDM), April 2010.
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