■  Submitted or In Preparation

•      ●  Haeseung Lee, Yeajee Kwon, Sera Park, Hyesoo Jung, and Wankyu Kim, "Drug target prediction using a large-scale compound network based on bioactivity similarity”, (in preparation)
•      ●  Jeong-Yoon Choi*, Haeseung Lee*, Eun-Ji Kwon, Ok-Seon Kwon, Hyuk-Jin Cha†, "TGFb promotes YAP dependent AXL induction in mesenchymal lung cancer cells". (Under revision at Molecular Oncology)
•     ●  Gina Ryu and Wankyu Kim, "Application of 3D atom pair map in an attention model for enhanced drug virtual screening". (in preparation)
• 
  

■  2024

     ●  Jihee Kim, Gina Ryu, Jeongmin Seo, Miyeon Go, Gyungmin Kim, Sol Yi, Suwon Kim, Hana Lee, June-Yong Lee, Han SUng Kim, Min-Chan Park, Dong Hae Shin, Hyunbo Shim, Wankyu Kim, Soo Young Lee. "5-aminosalicylic acid suppresses osteoarthritis through the OSCAR-PPARγ axis." Nat Commun. 2024 Feb 3;15(1):1024. doi: 10.1038/s41467-024-45174-6. PMID: 38310093; PMCID: PMC10838344.

■  2023

     ●  Arang Son, Seoyeong Kang, Suha Choi, Sung-Won Shin, Yeeun Kim, Wankyu Kim, Changhoon Choi. "Targeting Na-H exchanger 1 overcomes nuclear factor kappa B-mediated tumor resistance to radiotherapy". Neoplasia.  2023 Jan;35:100862. doi: 10.1016/j.neo.2022.100862. Epub 2022 Dec 9. PMID: 36508876; PMCID: PMC9761853.

     ●  Yeajee Kwon, Sera Park, Jaeok Lee, Jiyeon Kang, Hwa Jeong Lee, Wankyu Kim. "BEAR: A Novel Virtual Screening Method Based on Large-Scale Bioactivity Data." J Chem Inf Model. 2023 Mar 13;63(5):1429-1437. doi: 10.1021/acs.jcim.2c01300. Epub 2023 Feb 23. PMID: 36821004.

   ●  Jeong, Jae Seok, Yeogha Yoon, Wankyu Kim, Hee Jung Kim, Hae Jin Park, Kyung Hwa Park, Kyung Bae Lee. "NecroX Improves Polyhexamethylene Guanidine-induced Lung Injury by Regulating Mitochondrial Oxidative Stress and Endoplasmic Reticulum Stress.". Am J Respir Cell Mol Biol. 2023;69(1):57-72. doi:10.1165/rcmb.2021-0459OC

■  2022

     ●  Jae Seok Jeong, Jin Young Choi, Jong Seung Kim, Seong Ok Park, Wankyu Kim, Yeo-Gha Yoon, Hae Jin Park, Kyung Hwa Park, Doo Hwan Kim, Jung Mo Kim, Gou Young Koh, Seong Kug Eo, Yong Chul Lee, undefined, Jae Seok Jeong, Jin Young Choi, Jong Seung Kim, Seong Ok Park, Wankyu Kim, Yeo-Gha Yoon, Hae Jin Park, Kyung Hwa Park, Doo Hwan Kim, Jung Mo Kim, Gou Young Koh, Seong Kug Eo, Yong Chul Lee, "SARS-CoV-2 infection in severe asthma is associated with worsening of COVID-19 through respiratory NLRP3 inflammasome activation", Allergy. 2023 Jan;78(1):287-290. doi: 10.1111/all.15452. Epub 2022 Aug 5. PMID: 35871401; PMCID: PMC9349818.

■  2021

     ●  Jintae Kim, Sera Park, Dongbo Min, and Wankyu Kim, "Comprehensive Survey of Recent Drug Discovery Using Deep Learning", Int J Mol Sci. 2021 Sep 15;22(18):9983. doi: 10.3390/ijms22189983. PMID: 34576146; PMCID: PMC8470987.

     ●  Miso Park, Ji Won Kim, Kyu Min Kim, Seungmin Kang, Wankyu Kim, Jin-Ki Kim, Youngnam Cho, Hyungjae Lee, Moon Chang Baek, Ju-Hyun Bae, Seung Hyun Lee, Sung Baek Jeong, Sung Chul Lim, Dae Won Jun, Sung Yun Cho, Yeonji Kim, Yong June Choi and Keon Wook Kang, "Circulating Small Extracellular Vesicles Activate TYRO3 to Drive Cancer Metastasis and Chemoresistance", Cancer Res. 2021 Jul 1;81(13):3539-3553. doi: 10.1158/0008-5472.CAN-20-3320. Epub 2021 Apr 28. PMID: 33910929.

     ●  Suntae Kim, Ji Hye Im, Wan Kyu Kim, Young Jae Choi, Ji-Yoon Lee, Sang Kyum Kim, Sun Jo Kim, Sung Won Kwon, Keon Wook Kang, "Enhanced Sensitivity of Nonsmall Cell Lung Cancer with Acquired Resistance to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors to Phenformin: The Roles of a Metabolic Shift to Oxidative Phosphorylation and Redox Balance", Oxid Med Cell Longev. 2021 Jul 29;2021:5428364. doi: 10.1155/2021/5428364. PMID: 34367462; PMCID: PMC8342158.

■  2020

     ●  Ok-Seon Kwon*, Eun-Ji Kwon, Hyeon-Joon Kong, Jeong-Yoon Choi, Yun-Jeong Kim, Eun-Woo Lee, Wankyu Kim, Haeseung Lee†, Hyuk-Jin Cha†, "Systematic identification of a nuclear receptor-enriched predictive signature for erastin-induced ferroptosis", Redox Biology, doi: 10.1016/j.redox.2020.101719, (2020)

     ●  Jimin Jeon*, Hyun-Jin Noh*, Hyemi Lee, Han-Hee Park, Yu-Jin Ha, Seok Hee Park, Haeseung Lee, Seok-Jung Kim, Ho Chul Kang, Soung-il Eyun, Siyoung Yang†, You-Sun Kim†, "TRIM24-RIP3 axis perturbation accelerates osteoarthritis pathogenesis", Annals of the Rheumatic Diseases, 0:1–9, (2020)

     ●  Daehyeon Seong*, Manhyung Jeong, Jinho Seo, Ji-Yoon Lee, Chi Hyun Hwang, Ho-Chul Shin, Jeong Yoon Shin, Young Woo Nam, Jeong Yeon Jo, Haeseung Lee, Hye-Jung Kim, Hwa-Ryeon Kim, Ji Hoon Oh, Sang-Jun Ha, Seung Jun Kim, Jae-Seok Roe, Wankyu Kim, June-Won Cheong, Kwang-Hee Bae, Sang Chul Lee, Andrew Oberst, Peter Vandenabeele, Dong Hoon Shin, Eun-Woo Lee, Jaewhan Song†, "Identification of MYC as an antinecroptotic protein that stifles RIPK1-RIPK3 complex formation", PNAS, 117(33):19982-19993 (2020)

     ●  Keun-Tae Kim*, Ju-Chan Park, Haeseung Lee, Hyeon-Ki Jang, Yang Jin, Wankyu Kim, Jeongmi Lee, Hyongbum Henry Kim, Sangsu Bae, and Hyuk-Jin Cha†, "Safe Scarless Cassette-free Selection of Genome-edited Human Pluripotent Stem Cells Using Temporary Drug Resistance", Biomaterials, doi: 10.1016/j.biomaterials.2020.120295 (2020)

     ●  Doo Ri Park*, Ji Hee Kim, Kyoung Min Kim, Haeseung Lee, Wankyu Kim, Min Chan Park, Hyunbo Shim, Yongwon Choi and Soo Young Lee†, "Osteoclast-associated receptor blockade prevents articular cartilage destruction via chondrocyte apoptosis regulation", Nature Communications, 11(1):4343 (2020)

     ●  Ok-Seon Kwon, Haeseung Lee, Hyeon-Joon Kong, Eun-Ji Kwon, Ji Eun Park, Wooin Lee, Seungmin Kang, Mirang Kim, Wankyu Kim & Hyuk-Jin Cha, "Connectivity map-based drug repositioning of bortezomib to reverse the metastatic effect of GALNT14 in lung cancer", Oncogene, doi: 10.1038/s41388-020-1316-2 (2020)

     ●  Ji Won Hong, Jung Min Kim, Jeong Eun Kim, Hee Cho, Dasol Kim, Wankyu Kim, Jong-Won Oh & Ho Jeong Kwon , "MiR-4435 is an UQCRB-related circulating miRNA in human colorectal cancer", Scientific Reports volume 10, Article number: 2833 (2020)

     ●  Ok-Seon Kwon, Haeseung Lee, Yun-Jeong Kim, Hyuk-Jin Cha, Na-Young Song, and Mi-Ok Lee†, "ERK Dephosphorylation through MKP1 Deacetylation by SIRT1 Attenuates RAS-Driven Tumorigenesis", Cancers, 12(4): 909, (2020)

■  2019

•      ●  Ok-Seon Kwon, Wankyu Kim, Hyuk-Jin Cha, Haeseung Lee, "In silico drug repositioning: from large-scale transcriptome data to therapeutics", Archives of Pharmacal Research, doi: 10.1007/s12272-019-01176-3. (2019)
•      ●  Hanbi Lee and Wankyu Kim, "Comparison of Target Features for Predicting Drug-Target Interactions by Deep Neural Network Based on Large-Scale Drug-Induced Transcriptome Data", Pharmaceutics, 11(8), 377; doi: 10.3390/pharmaceutics11080377. (2019)
•      ●  Young-Hyun Go, Changjin Lim, Ho-Chang Jeong, Ok-Seon Kwon, Sungkyun Chung, Haeseung Lee, Wankyu Kim, Young-Ger Suh, Woo Sung Son, Mi-Ok Lee, Hyuk-Jin Cha and Seok-Ho Kim, "Structure-Activity Relationship Analysis of YM155 for Inducing Selective Cell Death of Human Pluripotent Stem Cells", Frontiers in Chemistry, doi: 10.3389/fchem.2019.00298. (2019)
•      ●  Sera Park, Yeajee Kwon, Hyesoo Jeong, Sukyung Jang, Haeseung Lee, Wankyu kim, "CSgator: an integrated web platform for compound set analysis", Journal of Cheminformatics, 11:17 (2019)
•      ●  Su-Kyeong Jang, Byung-Ha Yoon, Seung Min Kang, Yeo-Gha Yoon, Seon-Young Kim, and Wankyu Kim, "CDRgator: An Integrative Navigator of Cancer Drug Resistance Gene Signatures", Molecules and Cells ,42(), doi:10.14348/molcells.2018.0413. (2019)

■  2018

•      ●  Soon-Ki Hong*, Haeseung Lee*, Ok-Seon Kwon*, Na-Young Song, Hyo-Ju Lee, Seungmin Kan, Jeong-Hwan Kim, Mirang Kim, Wankyu Kim, Hyuk-Jin Cha, "Large-scale pharmacogenomics based drug discovery for ITGB3 dependent chemoresistance in mesenchymal lung cancer", Mol. Cancer 17:175. doi: 10.1186/s12943-018-0924-8. (2018)
•      ●  Seung-Ju Cho, Keun-Tae Kim, Ho-Chang Jeong, Ju-Chan Park, Ok-Seon Kwon, Yun-Ho Song, Joong-Gon Shin, Seungmin Kang, Wankyu Kim, Hyoung Doo Shin, Mi-Ok Lee, Sung-Hwan Moon, Hyuk-Jin Cha, "Selective elimination of culture-adapted human embryonic stem cells with BH3 mimetics", Stem Cell Reports, 11(5): 1244-1256. doi: 10.1016/j.stemcr.2018.09.002. (2018)
•      ●  Jeong Eun Kim, Jiwon Hong, Hannah S. Lee, Wankyu Kim, Jisun Lim, Yoon Shin Cho, and HoJeong Kwon, "Hsa-miR-10a-5p downregulation in mutant UQCRB-expressing cells promotes the cholesterol biosynthesis pathway", Scientific Report 8: 12407. doi: 10.1038/s41598-018-30530-6. (2018)

■  2016

•      ●  Ji Hyun Kim , Bo Bae Lee , Young Mi Oh , Chenchen Zhu , Lars Steinmetz , Yookyeong Lee , Wan Kyu Kim , TaeSoo Kim, "Modulation of mRNA expression dynamics by the Set2/Rpd3S pathway", Nat. Comm. 28;7:13534. doi: 10.1038/ncomms13534. (2016)
•      ●  Haeseung Lee, Seungmin Kang, Wankyu Kim, "Drug Repositioning for Cancer Therapy Based on Large-scale Drug-induced Transcriptional Signatures", PLoS One. 11(3):e0150460. doi: 10.1371/journal.pone.0150460 (2016)

■  2015

•      ●  Xuelian Bai, Juhye Kim, Seungmin Kang, Wankyu Kim, Hyunbo Shim, "A Novel Human scFv Library with Non-Combinatorial Synthetic CDR Diversity", PLOS One, 10(10): e0141045. doi:10.1371/journal.pone.0141045 (2015).
•      ●  Insu Jang, Hyeshik Chang, Yukyung Jun, Seongjin Park, Jin Ok Yang, Byungwook Lee, Wankyu Kim, V. Narry Kim, Sanghyuk Lee*, "miRseqViewer: Multi-panel visualization of sequence, struncture and expression for analysis of microRNA sequencing data", Bioinformatics, 31(4):596-598 (2015).

■  2014

•      ●  Charny Park, Namhee Yu, Ikjung Choi, Wankyu Kim, Sanghyuk Lee, "lncRNAtor: a comprehensive resource for functional investigation of long noncoding RNAs", Bioinformatics, 30(17):2480-5. doi: 10.1093/bioinformatics/btu325. (2014)
•      ●  Daeun Ryu, SeongBeom Cho, Hum Kim, Sanghyuk Lee, and Wankyu Kim, "GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype", Bioinformatics, 30(17):2540-2. doi: 10.1093/bioinformatics/btu240. (2014)
•      ●  Hae Yong Yoo, Min Kyung Sung, Seung Ho Lee, Sangok Kim, Haeseung Lee, Seongjin Park, Sang Cheol Kim, Byungwook Lee, Kyoohyoung Rho, Jong-Eun Lee, Kwang-Hwi Cho, Wankyu Kim, Hyunjung Ju, Jaesang Kim, Seok Jin Kim, Won Seog Kim, Sanghyuk Lee, Young Hyeh Ko, "A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T-cell lymphoma", Nature Genetics, 46(4), 371-375 (2014).
•      ●  Hyunjung Kang, Ikjung Choi, Sooyoung Cho, Daeun Ryu, Sanghyuk Lee, Wankyu Kim, "gsGator: an integrated web platform for cross-species gene set analysis", BMC Bioinformatics. doi:10.1186/1471-2105-15-13. 14 January 2014.

■  2013

•      ●  Sang Cheol Kim, Yeonjoo Jung, Jinah Park, Sooyoung Cho, Chaehwa Seo, Jaesang Kim, Pora Kim, Jehwan Park, Jihae Seo, Jiwoong Kim, Seongjin Park, Insu Jang, Namshin Kim, Jin Ok Yang, Byungwook Lee, Kyoohyoung Rho, Yeonhwa Jung, Juhee Keum, Jinseon Lee, Jungho Han, Sangeun Kang, Sujin Bae, So-Jung Choi, Sujin Kim, Jong-Eun Lee, Wankyu Kim, Jhingook Kim, and Sanghyuk Lee, "A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers", PLoS One, 8(2):e55596.
•      ●  Sooyoung Cho, Insu Jang, Yukyung Jun, Suhyeon Yoon, Minjeong Ko, Yeajee Kwon, Ikjung Choi, Hyeshik Jang, Daeun Ryu, Byungwook Lee, V. Narry Kim, Wankyu Kim, and Sanghyuk Lee, "miRGator v3.0: a microRNA portal for deep sequencing, expression profiling, and mRNA targeting", Nucleic Acids Res. 41, D252-D257 (2013).
•      ●  Yo Na Kim, Sangok Kim, Il-Yong Kim, Jae Hoon Shin, Sooyoung Cho, Sun Shin Yi, Wan Kyu Kim, Kyung-Sub Kim, Sanghyuk Lee, Je Kyung Seong, "Transcriptomic analysis of insulin-sensitive tissues from anti-diabetic drug treated ZDF rats, a T2DM animal model", PLoS One. 8(7):e69624. doi: 10.1371/journal.pone.0069624. 26 July 2013.
•      ●  Taejeong Bae, Kyoohyoung Rho, Jin Woo Choi, Katsuhisa Horimoto, Wankyu Kim, Sunghoon Kim, "Identification of upstream regulators for prognostic expression signature genes in colorectal cancer", BMC System Biology. 7:86. doi: 10.1186/1752-0509-7-86. 4 September 2013.
•      ●  Dong Ju Son, Sandeep Kumar, Wakako Takabe, Chan Woo Kim, Chih-Wen Ni, Noah Alberts-Grill, In-Hwan Jang, Sangok Kim, Wankyu Kim, Sang Won Kang, Andrew H. Baker, Jai Woong Seo, Katherine W. Ferrara, Hanjoong Jo, "The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis", Nature Communication. 4:3000. doi: 10.1038/ncomms4000. 18 December 2013.

■  2012

•      ●  Hoi Jong Jung, Sangok Kim, Yun Jae Kim, Min-Kyu Kim, Sung Gyun Kang, Jung-Hyun Lee, Wankyu Kim, and Sun-Shin Cha, "Dissection of the Dimerization Modes in the DJ-1 Superfamily", Molecules and Cells 33, 1-10
•      ●  Namhee Yu, Jihae Seo, Kyoohyoung Rho, Yeongjun Jang, Jinah Park, Wan Kyu Kim, and Sanghyuk Lee, "hiPathDB: a human-integrated pathway database with facile visualization", Nucleic Acids Res. 40, D797-D802 (2012).

■  2011

•      ●  Yeonjoo Jung, Sanghyuk Lee, Hyung-Seok Choi, Soon-Nam Kim, Eunyoung Lee, Youngah Shin, Jihae Seo, Bumjin Kim, Yeonhwa Jung, Wan Kyu Kim, Ho-Kyung Chun, Woo Yong Lee, and Jaesang Kim, "Clinical validation of colorectal cancer biomarkers identified from bioinformatics analysis of public expression data", Clinical Cancer Research 17(4), 700-709
•      ●  Kyoohyoung Rho, Bumjin Kim, Youngjun Jang, Sanghyun Lee, Taejeong Bae, Jihae Seo, Chaehwa Seo, Jihyun Lee, Hyunjung Kang, Ungsik Yu, Sunghoon Kim, Sanghyuk Lee, and Wan Kyu Kim, "GARNET - gene set analysis with exploration of annotation relations", BMC Bioinformatics 12(Suppl 1):S25
•      ●  Sooyoung Cho, Yukyung Jun, Sanghyun Lee, Hyungseok Chol, Sungchul Jung, Sunyoung Lee, Sangok Kim, Sanghyuk Lee, Wankyu Kim, "miRGator v2.0 : an integrated system for functional investigation of microRNAs", Nucleic Acids Res. 39, D158-162

■  2010

•      ●  Byungwook Lee, In-Sun Chu, Namshin Kim, Jinhyuk Lee, Seon-Yong Kim, Wan Kyu Kim, and Sanghyuk Lee, "Bioinformatics Resources of the Korean Bioinformation Center (KOBIC)", Genomics & Informatics 8(4), 165-169

■  2008

•      ●  W. K. Kim and E. M. Marcotte, "Age-Dependent Evolution of the Yeast Protein Interaction Network", PLoS Comput Biol 4(11): e1000232
•      ●  W. K. Kim, C Krumpelman and E. M. Marcotte, "Inferring mouse gene functions from genomic-scale data using a combined functional network/classifier strategy", Genome Biology 9(Suppl 1):S5
•      ●  F. Roth et al, "A critical assessment of Mus musculus gene function prediction using integrated genomic evidence", Genome Biology 9(Suppl 1):S2

■  2007

•      ●  W. K. Kim, K. W. Kim, E. J. Lee, E. M. Marcotte, H. H. Kim and J. K. Seo, "Identification of Disease Specific Protein Interactions between the Gastric Cancer Causing Pathogen, H. pylori, and Human Hosts using Protein Network Modeling and Gene Chip Analysis", Biochip Journal 1(3): 179-187
•      ●  A. Henschel, C. Winter, W. K. Kim and M. Schroeder., "Using structural motif descriptors for sequence-based binding site prediction", BMC Bioinformatics. 22;8 Suppl 4:S

■  2006

•      ●  W. K. Kim, A. Henschel, C. Winter and M. Schroeder, "The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry", PLOS Computational Biology 2(9): e124
•      ●  C. Winter, A. Henschel, W. K. Kim and M. Schroeder, "SCOPPI: Structural Classification of Protein-Protein Interfaces", Nucleic Acid Research Database Issue 34:D310-D314
•      ●  A. Henschel, W.K. Kim and M. Schroeder, "Equivalent binding sites reveal convergently evolved interaction motifs", Bioinformatics 22(5):550-555

■  2005

•      ●  W. K. Kim and Jon C. Ison, "A survey on the geometric association of domain-domain interfaces", Proteins 61(4):1075-88

■  2004

•      ●  W. K. Kim, Dan M. Bolser and Jong H. Park, "Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map (PSIMAP)", Bioinformatics 20:1138-50

■  2002

•      ●  W. K. Kim, J. Park and J. K. Seo, "Large Scale Statistical Prediction of Protein-Protein Interaction by Potentially Interacting Domain (PID) Pair", Genome Informatics 13:42-50