A practical handbook on single-cell RNA sequencing data quality control and downstream analysis (Jihwan Park - corresponding author, Gyeong Dae Kim, Chaemin Lim - first author)
Gyeong Dae Kim, Chaemin Lim, Jihwan Park. Molecules and Cells.(2024)
Cell Type-and Age-Specific Expression of lncRNAs across Kidney Cell Types (Jihwan Park - corresponding author, Gyeong Dae Kim, So-I Shin - first author)
Gyeong Dae Kim, So-I Shin, Su Woong Jung, Hyunsu An, Sin-Young Choi, Minho Eun, Chang-Duk Jun, Sangho Lee, Jihwan Park.
Journal of the American Society of Nephrology.(2024)
Dynamics of The Γδtcr Repertoires During The Dedifferentiation Process and Pilot Implications for Immunotherapy of Thyroid Cancer (Jihwan Park - corresponding author)
Qing Hao,Ruicen Li, Hancong Li, Shu Rui,Liting You, Lingyun Zhang, Yue Zhao,Peiheng Li, Yuanmin Li, Xinagyu Kong, Haining Chen, Xiuhe Zou, Feng Liu,Xiaofei Wang, Juan Zhou, Weihan Zhang, Libing Huang, Yang Shu, JiaYe Liu, Ronghao Sun, Chao Li, Jingqiang Zhu, Yong Jiang, Tao Wei, Kun Qian, Bing Bai, Yiguo Hu, Yong Peng, Lunzhi Dai, Carlos Caulin, Heng Xu, Zhihui Li, Jihwan Park, Han Luo, Binwu Ying. Advanced Science. (2024)
Single-cell lineage tracing approaches to track kidney cell development and maintenance (Jihwan Park - corresponding author, Baul Yoon - first author)
Baul Yoon, Hayoung Kim, Su woong Jung, Jihwan Park. Kidney International.(2024)
Hedgehog signaling is involved in acquired resistance to KRASG12C inhibitors in lung cancer cells
Chaeyoung Lee, Jawoon Yi, Jihwan Park, Byungyong Ahn, Young-Wook Won, JiHeung Jeon, Byung Ju Lee, Wha Ja Cho, Jeong Woo Park. Cell Death & Disease(2024)
Chromatin accessibility analysis and architectural profiling of human kidneys reveal key cell types and a regulator of diabetic kidney disease (Jihwan Park - corresponding author, Minho Eun - first author)
Minho Eun, Donggun Kim, So-I Shin, Hyun Oh Yang, Kyoung-Dong Kim, Sin Young Choi, Sehoon Park, Dong Ki Kim, Chang Wook Jeong, Kyung Chul Moon, Hajeong Lee, Jihwan Park. Kidney International.(2024)
DRG2 in macrophages is crucial for initial inflammatory response and protection against Listeria monocytogenes infection
Unn Hwa Lee, Sang Jin Park, Seong A. Ju, Sang Chul Lee, Byung Sam Kim, Byungyong Ahn, Jawoon Yi, Jihwan Park, Young-Wook Won, In Seob Han, Byung Ju Lee, Wha Ja Cho, Jeong Woo Park. Clinical Immunology(2023)
Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2
Yunjeong Lee, In Seo Yeo, Namhee Kim, Dong-Keun Lee, Kyung-Tai Kim, Jiyoung Yoon, Jawoon Yi, Young Bin Hong, Byung-Ok Choi, Yoichi Kosodo, Daesoo Kim, Jihwan Park, Mi-Ryoung Song. eLife(2023)
CD40 is expressed in the subsets of endothelial cells undergoing partial endothelial-mesenchymal transition in tumor microenvironment
Kazuki Takahashi, Miho Kobayashi, Hisae Katsumata, Shiori Tokizaki, Tatsuhiko Anzai, Yukinori Ikeda, Daniel M Alcaide, Kentaro Maeda, Makoto Ishihara, Katsutoshi Tahara, Yoshiaki Kubota, Fumiko Itoh, Jihwan Park, Kunihiko Takahashi, Yukiko T Matsunaga, Yasuhiro Yoshimatsu, Katarzyna A Podyma-Inoue, Tetsuro Watabe. Cancer Science.(2023)
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis
Seungchul Lee, Jaemyung Choi, Jihwan Park, Chang Pyo Hong, Daeseok Choi, Soeun Han, Kyuha Choi, Tae-Young Roh, Daehee Hwang & Ildoo Hwang. Genome Biology(2023)
Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia (Jihwan Park - corresponding author, Seo-Gyeong Bae - first author)
Seo-Gyeong Bae, Hyeoung-Joon Kim, Mi Yeon Kim, Dennis Dong Hwan Kim, So-I Shin, Jae-Sook Ahn, Jihwan Park. Molecules and Cells.(2023)
Single cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction (Jihwan Park - corresponding author, Seo-Gyeong Bae - first author)
Seo-Gyeong Bae, Guo Nan Yin, Jiyeon Ock, Jun-Kyu Suh, Ji-Kan Ryu, Jihwan Park. eLife(2023)
Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research
Han-Eol Park, Song Hyun Jo, Rosalind H. Lee, Christian P. Macks, Taeyun Ku, Jihwan Park, Chung Whan Lee, Junho K. Hur, Chang Ho Sohn. Advanced Science.(2023)
BMPR1A Promotes ID2-ZEB1 Interaction to Suppress Excessive Endothelial to Mesenchymal Transition
Heon Woo Lee, Takaomi Adachi, Boryeong Pak, Saejeong Park, Xiaoyue Hu, Woosoung Choi, Piotr S Kowalski, C Hong Chang, Katharine R Clapham, Aram Lee, Irinna Papangeli, Jongmin Kim, Orjin Han, Jihwan Park, Daniel G Anderson, Michael Simons, Suk Won Jin, Hyung J Chun. Cardiovasc Res. (2023)
Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development
Poonam Dhillon, Kelly Ann Mulholland, Hailong Hu, Jihwan Park, Xin Sheng, Amin Abedini, Hongbo Liu, Allison Vassalotti, Junnan Wu, Katalin Susztak. Nat Commun.(2023)
Histamine Signaling Is Essential for Tissue Macrophage Differentiation and Suppression of Bacterial Overgrowth in the Stomach (Jihwan Park - first author)
Kwang H Kim, Jihwan Park, Yejin Cho, Soo Young Cho, Buhyun Lee, Haengdueng Jeong, Yura Lee, Ja-Woon Yi, Yeseul Oh, Jin-Jae Lee, Timothy C Wang, Kyung-Min Lim, Ki Taek Nam. Cell Mol Gastroenterol Hepatol.(2023)
Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment (Jihwan Park - corresponding author)
Han Luo, Xuyang Xia, Li-Bin Huang, Hyunsu An, Minyuan Cao, Gyeong Dae Kim, Hai-Ning Chen, Wei-Han Zhang, Yang Shu, Xiangyu Kong, Zhixiang Ren, Pei-Heng Li, Yang Liu, Huairong Tang, Ronghao Sun, Chao Li, Bing Bai, Weiguo Jia, Yi Liu, Wei Zhang, Li Yang, Yong Peng, Lunzhi Dai, Hongbo Hu, Yong Jiang, Yiguo Hu, Jingqiang Zhu, Hong Jiang, Zhihui Li, Carlos Caulin, Jihwan Park, Heng Xu. Nat Commun.(2022)
Recent developments in application of single-cell RNA sequencing in the tumour immune microenvironment and cancer therapy (Jihwan Park - corresponding author)
Pei-Heng Li, Xiang-Yu Kong, Ya-Zhou He, Yi Liu, Xi Peng, Zhi-Hui Li, Heng Xu, Han Luo, Jihwan Park. Mil Med Res.(2022)
Kidney Decellularized Extracellular Matrix Enhanced the Vascularization and Maturation of Human Kidney Organoids (Jihwan Park - corresponding author, Jawoon Yi - first author)
Jin Won Kim, Sun Ah Nam, Jawoon Yi, Jae Yun Kim, Jong Young Lee, Seo-Yeon Park, Tugce Sen, Yoo-Mi Choi, Jae Yeon Lee, Hong Lim Kim, Hyung Wook Kim, Jihwan Park, Dong-Woo Cho, Yong Kyun Kim. Adv Sci (Weinh).(2022)
Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis
Tomohito Doke, Amin Abedini, Daniel L Aldridge, Ya-Wen Yang, Jihwan Park, Christina M Hernandez, Michael S Balzer, Rojesh Shrestra, Gaia Coppock, Juan M Inclan Rico, Seung Yub Han, Junhyong Kim, Sheng Xin, Adrian M Piliponsky, Marco Angelozzi, Veronique Lefebvre, Mark C Siracusa, Christopher A Hunter, Katalin Susztak. N at Immunol.(2022)
CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins (Jihwan Park - corresponding author, Hyunsu An - first author)
Hyunsu An, Minho Eun, Jawoon Yi, Jihwan Park. Brief Bioinform.(2022)
Transcriptome Analysis Identifies Altered Biological Processes and Novel Markers in Human Immunodeficiency Virus-1 Long-Term Non-Progressors (Jihwan Park - corresponding author, Dayeon Lee - first author)
Dayeon Lee, Cheol-Hee Yoon, Sin Young Choi, Jung-Eun Kim, Young-Keol Cho, Byeong-Sun Cho, Jihwan Park. Infect Chemother.(2021)
Characterizing dedifferentiation of thyroid cancer by integrated analysis (Jihwan Park - corresponding author, Gyeong Dae Kim - first author)
Han Luo, Xuyang Xia, Gyeong Dae Kim, Yang Liu, Zhinan Xue, Lingyun Zhang, Yang Shu, Tian Yang, Yan Chen, Shouyue Zhang, Haining Chen, Weihan Zhang, Ruicen Li, Huairong Tang, Birong Dong, Xianghui Fu, Wei Cheng, Wei Zhang, Li Yang, Yong Peng, Lunzhi Dai, Hongbo Hu, Yong Jiang, Changyang Gong, Yiguo Hu, Jingqiang Zhu, Zhihui Li, Carlos Caulin, Tao Wei, Jihwan Park, Heng Xu. Sci Adv.(2021)
Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney
Amin Abedini, Yuan O Zhu, Shatakshee Chatterjee, Gabor Halasz, Kishor Devalaraja-Narashimha, Rojesh Shrestha, Michael S Balzer, Jihwan Park, Tong Zhou, Ziyuan Ma, Katie Marie Sullivan, Hailong Hu, Xin Sheng, Hongbo Liu, Yi Wei, Carine M Boustany-Kari, Uptal Patel, Salem Almaani, Matthew Palmer, Raymond Townsend, Shira Blady, Jonathan Hogan, Lori Morton, Katalin Susztak; TRIDENT Study Investigators. J Am Soc Nephrol.(2021)
Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity
Xiangchen Gu, Hongliu Yang, Xin Sheng, Yi-An Ko, Chengxiang Qiu, Jihwan Park, Shizheng Huang, Rachel Kember, Renae L Judy, Joseph Park, Scott M Damrauer, Girish Nadkarni, Ruth J F Loos, Vy Thi Ha My, Kumardeep Chaudhary, Erwin P Bottinger, Ishan Paranjpe, Aparna Saha, Christopher Brown, Shreeram Akilesh, Adriana M Hung, Matthew Palmer, Aris Baras, John D Overton, Jeffrey Reid, Marylyn Ritchie, Daniel J Rader, Katalin Susztak. S ci Transl Med.(2021)
The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation (Jihwan Park - corresponding author & first author)
Poonam Dhillon, Jihwan Park, Carmen Hurtado Del Pozo, Lingzhi Li, Tomohito Doke, Shizheng Huang, Juanjuan Zhao, Hyun Mi Kang, Rojesh Shrestra, Michael S Balzer, Shatakshee Chatterjee, Patricia Prado, Seung Yub Han, Hongbo Liu, Xin Sheng, Pieterjan Dierickx, Kirill Batmanov, Juan P Romero, Felipe Prósper, Mingyao Li, Liming Pei, Junhyong Kim, Nuria Montserrat, Katalin Susztak. Cell Metab
Single-cell transcriptomics: a novel precision medicine technique in nephrology (Jihwan Park - corresponding author, Jisoo Kim - first author)
Jisoo Kim, Jihwan Park. Korean J Intern Med.(2020)
Tim-4 functions as a scavenger receptor for phagocytosis of exogenous particles
Chanhyuk Min, Jeongjun Park, Gayoung Kim, Hyunji Moon, Sang-Ah Lee, Deokhwan Kim, Byeongjin Moon, Susumin Yang, Juyeon Lee, Kwanhyeong Kim, Hyeokjin Cho, Jihwan Park, Dae-Hee Lee, Gwangrog Lee, Daeho Park. Cell Death Dis.(2020)
Loss of IL-27Rα Results in Enhanced Tubulointerstitial Fibrosis Associated with Elevated Th17 Responses
Gaia M Coppock, Lillian R Aronson, Jihwan Park, Chengxiang Qiu, Jeongho Park, Jonathan H DeLong, Enrico Radaelli, Katalin Suszták, Christopher A Hunter. J Immunol.(2020)
Single-cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
Leilei Zhong, Lutian Yao, Robert J Tower, Yulong Wei, Zhen Miao, Jihwan Park, Rojesh Shrestha, Luqiang Wang, Wei Yu, Nicholas Holdreith, Xiaobin Huang, Yejia Zhang, Wei Tong, Yanqing Gong, Jaimo Ahn, Katalin Susztak, Nathanial Dyment, Mingyao Li, Fanxin Long, Chider Chen, Patrick Seale, Ling Qin. Elife.(2020)
Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease
Yuting Guan, Hongbo Liu, Ziyuan Ma, Szu-Yuan Li, Jihwan Park, Xin Sheng, Katalin Susztak. J Am Soc Nephrol.(2020)
Inhibition of Endothelial PHD2 Suppresses Post-Ischemic Kidney Inflammation through Hypoxia-Inducible Factor-1
Ganeshkumar Rajendran, Michael P Schonfeld, Ratnakar Tiwari, Shengping Huang, Rafael Torosyan, Timothy Fields, Jihwan Park, Katalin Susztak, Pinelopi P Kapitsinou. J Am Soc Nephrol.(2020)
Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen
Rany M Salem, Jennifer N Tod, Niina Sandholm, Joanne B Cole, Wei-Min Chen, Darrell Andrews, Marcus G Pezzolesi, Paul M McKeigue, Linda T Hiraki, Chengxiang Qiu, Viji Nair, Chen Di Liao, Jing Jing Cao, Erkka Valo, Suna Onengut-Gumuscu, Adam M Smiles, Stuart J McGurnaghan, Jani K Haukka, Valma Harjutsalo, Eoin P Brennan, Natalie van Zuyda, Emma Ahlqvist, Ross Doyle, Tarunveer S Ahluwalia, Maria Lajer, Maria F Hughes, Jihwan Park et al. J Am Soc Nephrol.(2019)
Understanding the kidney one cell at a time (Jihwan Park - first author)
Jihwan Park, Chang Linda Liu, Junhyong Kim, Katalin Susztak. Kidney Int.(2019)
Mitochondrial Damage and Activation of the STING Pathway Lead to Renal Inflammation and Fibrosis
Ki Wung Chung, Poonam Dhillon, Shizheng Huang, Xin Sheng, Rojesh Shrestha, Chengxiang Qiu, Brett A Kaufman, Jihwan Park, Liming Pei, Joseph Baur, Matthew Palmer, Katalin Susztak. Cell Metab.(2019)
Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program
Jacklyn N Hellwege, Digna R Velez Edwards, Ayush Giri, Chengxiang Qiu, Jihwan Park, Eric S Torstenson, Jacob M Keaton, O D Wilson, Cassianne Robinson-Cohen, Cecilia P Chung, Christianne L Roumie, Derek Klarin, Scott M Damrauer, Scott L DuVall, Edward Siew, Elvis A Akwo, Matthias Wuttke, Mathias Gorski, Man Li, Yong Li, J Michael Gaziano, Peter W F Wilson, Philip S Tsao, Christopher J O'Donnel, Csaba P Kovesdy, Cristian Pattaro, Anna Köttgen, Katalin Susztak, Todd L Edwards, Adriana M Hung. Observational Study(2019)
Functional methylome analysis of human diabetic kidney disease (Jihwan Park - first author)
Jihwan Park, Yuting Guan, Xin Sheng, Caroline Gluck, Matthew J Seasock, A. Ari Hakimi, Chengxiang Qiu, James Pullman, Amit Verma, Hongzhe Li, Matthew Palmer, Katalin Susztak. JCI Insight.(2019)
Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease
Caroline Gluck, Chengxiang Qiu, Sang Youb Han, Matthew Palmer, Jihwan Park, Yi-An Ko, Yuting Guan, Xin Sheng, Robert L Hanson, Jing Huang, Yong Chen, Ae Seo Deok Park, Maria Concepcion Izquierdo, Ioannis Mantzaris, Amit Verma, James Pullman, Hongzhe Li, Katalin Susztak. Nat Commun.(2019)
A signature of circulating inflammatory proteins and development of end-stage renal disease in diabetes
Monika A Niewczas, Meda E Pavkov, Jan Skupien, Adam Smiles, Zaipul I Md Dom, Jonathan M Wilson, Jihwan Park, Viji Nair, Andrew Schlafly, Pierre-Jean Saulnier, Eiichiro Satake, Christopher A Simeone, Hetal Shah, Chengxiang Qiu, Helen C Looker, Paolo Fiorina, Carl F Ware, Jennifer K Sun, Alessandro Doria, Matthias Kretzler, Katalin Susztak, Kevin L Duffin, Robert G Nelson, Andrzej S Krolewski. Nat Med.(2019)
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through tranxss-xss-xss-scriptional bursting
Orsolya Symmons, Marcello Chang, Ian A Mellis, Jennifer M Kalish, Jihwan Park, Katalin Suszták, Marisa S Bartolomei, Arjun Raj. PLoS Genet.(2019)
2018
Trans-ethnic association study of blood pressure determinants in over 750,000 individuals (Jihwan Park - first author)
Ayush Giri, Jacklyn N Hellwege, Jacob M keaton, Jihwan Park et al. Nat Genet.(2018)
DNMT1 in Six2 progenitor cells is essential for transposable element silencing and kidney development (Jihwan Park - first author)
Szu-Yuan Li, Jihwan Park, Kiwung Chung, Rojesh Shrestha, Matthew B Palmer, Katalin Susztak. bioRxiv(2018)
Building a single-cell transcriptome atlas of mouse bone marrow mesenchymal lineage cells for analyzing MSC heterogeneity
Robert Tower, Leilei Zhong, Jihwan Park, Luqiang Wang, Rojesh Shrestha, Katalin Susztak, Ling Qin. Journal of Bone and Mineral Research(2018)
Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease
Chengxia, Shizheng Huang, Jihwan Park, Yoson Par, Yi-An Ko, Matthew J Seasock, Joshua S Bryer, Xiang-Xi Xu, Wen-Chao Song, Matthew Palmer, Jon Hill, Paolo Guarnieri, Julie Hawkins, Carine M Boustany-Kari, Steven S Pullen, Christopher D Brown, Katalin Susztak. Nat Med.(2018)
Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming
Shizheng Huang, Jihwan Park, Chengxiang Qiu, Ki Wung Chung, Szu-Yuan Li, Yasemin Sirin, Seung Hyeok Han, Verdon Taylor, Ursula Zimber-Strobl, Katalin Susztak. PLos Biol.(2018)
Single-cell transcriptomic of the mouse kidney reveals potential cellular targets of kidney disease (Jihwan Park - first author)
Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch, Katalin Susztak. Science.(2018)
