Hwang Laboratory
Hwang Lab
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Publications


  1. Sunho Park, Hongming Xu, Tae Hyun Hwang, Gaussian Process Based Heteroscedastic Noise Modeling for Tumor Mutation Burden Prediction from Whole Slide Images, bioRxiv, 2019 February 19. doi: 10.1101/554261

  2. Hongming Xu, Sunho Park, Sung Hak Lee, Tae Hyun Hwang , Using transfer learning on whole slide images to predict tumor mutational burden in bladder cancer patients, bioRxiv, 2019 February 19. doi: 10.1101/554527

  3. Hongming Xu and Tae Hyun Hwang, Automatic Skin Lesion Segmentation Using Deep Fully Convolutional Networks, arXiv, 2018 July 17. doi: 1807.06466

  4. Hongming Xu, Sunho Park, Tae Hyun Hwang, Automatic Classification of Prostate Cancer Gleason Scores from Digitized Whole Slide Tissue Biopsies,
    bioRxiv, 2018 May 9. doi: 10.1101/315648

  5. Zabi Wardak, Sunho Park, Hong Zhu, Kevin S. Choe, Tae Hyun Hwang, Molecular Subtypes of Anaplastic Gliomas Identified with Somatic-Mutation and Pathway Based Gene Signature,
    bioRxiv, 2018 May 4. doi: 10.1101/3139244.

  6. Changjin Hong, Jean R Clemenceau, Yunku Yeu, Tae Hyun Hwang, Divine: Prioritizing Genes for Rare Mendelian Disease in Whole Exome Sequencing Data,

    bioRxiv, 2018 January 1. doi: https://doi.org/10.1101/396655

  7. Sunho Park, Tae Hyun Hwang, Bayesian Semi-nonnegative Tri-matrix Factorization to Identify Pathways Associated with Cancer Types,
    arXiv, 2017December 1. arXiv:1712.00520

Pre-Print


  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]

2018


  1. Xuxu Sun, Sam C. Wang, Yonglong Wei, Xin Luo, Yuemeng Jia, Lin Li, Purva Gopal, Min Zhu, Ibrahim Nassour, Jen-Chieh Chuang, Thomas Maples, Cemre Celen, Liem H. Nguyen, Linwei Wu, Shunjun Fu, Weiping Li, Lijian Hui, Feng Tian, Yuan Ji, Shuyuan Zhang, Mahsa Sorouri, Tae Hyun Hwang, Lynda Letzig, Laura James, Zixi Wang, Adam C. Yopp, Amit G. Singal, Hao Zhu, Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer,
    Cancer Cell, 2017 November 13;32(5):574-589.e6., doi: 10.1016/j.ccell.2017.12.011, [Impact factor: 23.214].

  2. Kristina Y Aguilera, Huocong Huang, Wenting Du, Moriah M Hagopian, Zhen Wang, Stefan Hinz, Tae Hyun Hwang, Huamin Wang, Jason B. Fleming, Diego H Castrillon, Xiaomei Ren, Ke Ding and Rolf A Brekken, "Inhibition of discoidin domain receptor 1 reduces collagen-mediated tumorigenicity in pancreatic ductal adenocarcinoma",
    Molecular Cancer Therapeutics, 2017 September 1; doi: 10.1158/1535-7163.MCT-16-0834

  3. Muthahar Syed, Tae Hyun Hwang, Jinoh Kim, Scalable Gene Sequence Analysis on Spark,
    Big Data and Visual Analytics, 2017. p:97-113

  4. Xiuxing Wang, Kailin Yang, Qi Xie, Qiulian Wu, Stephen C Mack, Yu Shi, Leo J Y Kim, Briana C Prager, William A Flavahan, Xiaojing Liu, Meromit Singer, Christopher G Hubert, Tyler E Miller, Wenchao Zhou, Zhi Huang, Xiaoguang Fang, Aviv Regev, Mario L Suvà, Tae Hyun Hwang, Jason W Locasale, Shideng Bao & Jeremy N Ric.,
    Purine synthesis promotes maintenance of brain tumor initiating cells in glioma,
    Nature Neuroscience, 2017 Mar 27. doi: 10.1038/nn.4537 [Impact Factor: 16.724].

  5. Vural Tagal, Shuguang Wei, Wei Zhang, Rolf A. Brekken, Bruce A. Posner, Michael Peyton, Luc Girard, Tae Hyun Hwang, David A. Wheeler, John D. Minna, Michael A. White, Adi F. Gazdar, and Michael G. Roth.,
    SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers,
    Nature Communication, 2017 January 19;8:14098. doi: 10.1038/ncomms14098 [Impact Factor: 11.329].

  6. Xiaorong Zhou, Barrett L. Updegraff, Yabin Guo, Michael Peyton, Luc Girard, Jill E. Larsen, Xian-Jin Xie, Yunyun Zhou, Tae Hyun Hwang, Yang Xie, Jaime Rodriguez-Canales, Pamela Villalobos, Carmen Behrens, Ignacio I Wistuba, John Minna andKathryn A. O'Donnell.,
    PROTOCADHERIN 7 acts through SET and PP2A to potentiate MAPK signaling by EGFR and KRAS during lung tumorigenesis,
    Cancer Research, 2017 January 1;77(1):187-197. doi: 10.1158/0008-5472.CAN-16-1267-T. Epub 2016 Nov 7. [Impact Factor: 9.329].

2017


  1. Christine Henzler, Yingming Li, Rendong Yang, Terri McBride, Yeung Ho, Cynthia Sprenger, Gang Liu, Ilsa Coleman, Bryce Lakely, Rui Li, Shihong Ma, Sean R. Landman, Vipin Kumar, Tae Hyun Hwang, Ganesh V. Raj, Celestia S. Higano, Colm Morrissey, Peter S. Nelson, Stephen R. Plymate & Scott M. Dehm.,
    Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer tumorigenesis,
    Nature Communication, 2016 November 29, doi:10.1038/ncomms13668 [Impact Factor: 11.329]

  2. Raphael Petegrosso, Sunho Park, Tae Hyun Hwang, Rui Kuang.,
    Transfer Learning across Ontologies for Phenome-Genome Association Prediction,
    Bioinformatics, 2016 October 22. doi:10.1093/bioinformatics/btw649
    Download 🡇

  3. Wenfang Chen, Haley Hill, Alana Christie, Min Soo Kim, Eboni Holloman, Andrea Pavia-Jimenez, Farrah Homayoun, Yuanqing Ma, Nirav Patel, Paul Yell, Guiyang Hao, Qurratulain Yousuf, Allison Joyce, Ivan Pedrosa, Heather Geiger, He Zhang, Jenny Chang, Kevin H. Gardner, Richard K. Bruick, Catherine Reeves, Tae Hyun Hwang, Kevin Courtney, Eugene Frenkel, Xiankai Sun, Naseem Zojwalla, Tai Wong, James P. Rizzi, Eli M. Wallace, John A. Josey, Yang Xie, Xian-Jin Xie, Payal Kapur, Renée M. McKay & James Brugarolas.,
    Targeting Renal Cell Carcinoma with a HIF-2 antagonist,
    Nature, 2016 September 5. doi: 10.1038/nature19796. [Impact Factor:38.138]

  4. Kenneth Chen, Woo Sun Kwon, Jiwoong Kim, Su Jin Heo, Hyo Song Kim, Hyo Ki Kim, Soo Hee Kim, Won Suk Lee, Hyun Cheol Chung, Sun Young Rha, and Tae Hyun Hwang*.,
    A novel TP53-KPNA3 translocation defines a de novo treatment-resistant clone in osteosarcoma,
    Molecular Case Studies, 2016 September;2(5):a000992. doi: 10.1101/mcs.a000992.
    (*corresponding author)

  5. Lee J, Kee HJ, Min S, Park KC, Park S, Hwang TH, Ryu DH, Hwang GS Cheong JH.,
    Integrated omics-analysis reveals WNT-mediated NAD+ metabolic reprogramming in cancer stem-like cells,
    Oncotarget, 2016 Jul 6. doi: 10.18632/oncotarget.10432. [Impact Factor:6.359]

2016


  1. Yabin Guo, Barrett L. Updegraff, Sunho Park, Deniz Durakoglugil, Victoria Burton,Sarah Maddux, Tae Hyun Hwang, and Kathryn A. O'Donnell.,
    Comprehensive ex vivo transposon mutagenesis identifies genes that promote growth factor independence and leukemogenesis,
    Cancer Research, 2015 December 16, doi:10.1158/0008-5472.CAN-15-1697 [Impact Factor: 9.329].

  2. Sunho Park, Seung-Jun Kim, Donghyeon Yu, Samuel Pena-Llopis, Jianjiong Gao,J in Suk Park, Beibei Chen, Jessie Norris, Xinlei Wang, Min Chen, Minsoo Kim,Jeongsik Yong, Zabi Wardak, Kevin Choe, Michael Story, Timothy Starr, Jae-Ho Cheong and Tae Hyun Hwang*.,
    An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types,
    Bioinformatics, 2016 Jun 1; 3(11): 1643-1651. doi: 10.1093/bioinformatics/btv692 [Impact Factor: 4.981]
    (*corresponding author)
    Download 🡇 Learn More ►
    ↳ We develop a novel algorithm called NTriPath to integrate somatic mutation with biological prior knowledge to identify cancer-type specific and commonly altered pathways by somatic mutation across cancers.

  3. Jae-Woong Chang, Wei Zhang, Hsin-Sung Yeh, Ebbing P. de Jong, Semo Jun, Kwan- Hyun Kim, Sun Sik Bae, Kenneth Beckman, Tae-Hyun Hwang, Kye-Seong Kim, Do-Hyung Kim, Timothy J. Griffin, Rui Kuang, and Jeongsik Yong.,
    mRNA 3’UTR shortening is a molecular signature of mTORC1 activation,
    Nature Communications, 2015 Jun 15;6:7218. doi: 10.1038/ncomms8218. [Impact Factor: 11.410]

  4. MaoQiang Xie, YingJie Xu, YaoGong Zhang, Tae Hyun Hwang and Rui Kuang.,
    Network-based Phenome-Genome Association Prediction by Bi-Random Walk,
    PLOS One, 2015 May 1;10(5):e0125138. doi: 10.1371/journal.pone.012513 [Impact Factor: 3.234]

  5. Changjin Hong, Jason Wang, Chao Xing, Tae Hyun Hwang, and Jason Y. Park.,
    Intersection of DNA Privacy and Whole-Genome Sequencing,
    Clinical Chemistry, February 5, 2015, doi:10.1373/clinchem.2014.235499 [Impact Factor: 7.911]

2015


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)
    Download 🡇
    ↳ 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 understading 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.
    Download 🡇


2009

  1. Ze Tian*, Tae Hyun Hwang*, and Rui Kuang.,
    A Hypergraph-based Learning Algorithm for Classifying Gene Expression and arrayCGH data with Prior Knowledge,
    Bioinformatics, Vol. 25, No. 21, pages 2831-2838, 2009. [Impact factor: 4.328] [PMid: 19648139]
    (*Joint first authors)
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  2. Ze Tian, Tae Hyun Hwang, and Rui Kuang.,
    A Hypergraph-based Learning Algorithm for Classifying ArrayCGH Data with Spatial Prior,
    Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009


2008

  1. Tae Hyun Hwang*, Ze Tian*, Jean-Pierre Kocher, and Rui Kuang.,
    Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction,
    Proc. of the 8th IEEE International Conference on Data Mining (ICDM), December 2008.
    (*Joint first authors)

  2. Tae Hyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Dennis A. Wigle, Jean-Pierre Kocher, Vipin Kumar and Rui Kuang.,
    Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs,
    Bioinformatics, Vol. 24, No. 18, pages 2023-2029, 2008. [Impact factor: 5.039] [PMid: 18653521]

  3. Tae Hyun Hwang, Rui Kuang.,
    A Comparative Study of Breast Cancer Microarray Gene Expression Profiles using Label Propagation,
    Proc. of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining (SDM), 2008.


2007

  1. Jaehoon Jeong, Tae Hyun Hwang, Tian He, and David Du.,
    MCTA: Target Tracking Algorithm based on Minimal Contour in Wireless Sensor Networks,
    Proc. of 26th IEEE INFOCOM 2007 Minisymposia (INFOCOM), August 2007.