Publications

Target Journal list (IF: Version 2024 ) Nature Genetics (IF: 31.7)
Journal of Hematology & Oncology (IF: 29.5)
Molecular Cancer (IF: 27.7)
Nature Cancer (IF: 23.5)
Cancer Communications (IF: 20.1) [1]
Nature Aging (IF: 17.0)
Nucleic Acids Research (IF: 16.6)
ACS Nano (IF: 15.8) [1]
Nature Communications (IF: 14.7)
Nature Structural & Molecular Biology (IF: 12.5)
Science Advances (IF: 11.7)
Journal of Advanced Research (IF: 11.4)
Cell Genomics (IF: 11.1)
Genome Medicine (IF: 10.4)
GENOME BIOLOGY (IF: 10.1)
EXPERIMENTAL AND MOLECULAR MEDICINE (IF: 9.5) [1] [2]
Proceedings of the National Academy of Sciences (PNAS) (IF: 9.4)
Materials Today Bio (IF: 8.7)
Molecular Systems Biology (IF: 8.5)
Aging Cell (IF: 8.0)
Aging and Disease (IF: 7.0)
Briefings in Bioinformatics (IF: 6.8)
BRITISH JOURNAL OF CANCER (IF: 6.4) [1]
Genome Research (IF: 6.2) [OA SNU free]
JOURNAL OF BONE AND MINERAL RESEARCH (IF: 5.8)
Communications Biology (IF: 5.2)
Bioinformatics (IF: 4.4)
BMC BIOINFORMATICS (IF: 2.9)
Research Topics ● Aging (Bone, Brain, Immune)
● Various Cancer (Lung, Head&Neck, Gastric, Colon, Brain, Metastasis, Neoantigen)
● Basic Molecular Biology (Differentiation, Proliferation)
● Basic Dental Medicine
● Complex Disease (OPLL, COPD, MDD)
● Neuroscience (Alzheimer's Disease, Major Depressive Disorder)
● Bioinformatics (Pipelines, Biostatistics, Classical Machine Learning & AI, Algorithm, Packaging and Visualization)
● All of NGS (DNA-seq, Bulk & Single cell RNA-seq, Spatial Transcriptome, Epigenome with ATAC-seq, ChIP-seq, Hi-C, Proteomics, TCR/BCR-seq, Microbiome)

Ongoing Projects

Deciphering 3D Chromatin Architecture via Spatial Density-Based Analysis of Hi-C Data

4DN chromatin structure in differentiation of osteoblast precursor cell line derived from Mus musculus calvaria

A clinical trial integrated, pilot-translational study to discover biomarker for predicting systemic and intraperitoneal chemotherapy response for patient with gastric cancer and peritoneal metastasis (Drafting the manuscript) [Collaborative Research with Korea Univ. and Soon Chun Hyang Medical Center]

Spatial Transcriptome analysis related to recovery capacity of Coll-OMP groups [Collaborative Research with Harvard Univ.]

Spatial Transcriptomic analysis of Aging and Alzheimer's Disease Using the Pin1 KO Model

Identifying the Colorectal Cancer Vaccine through Neoantigen Screening Pipelines [Collaborative Research with Catholic Univ.]

Analysis of Transcriptomic Differences in Peritoneal Cancer Treatment Outcomes [Collaborative Research with Korea Univ.]

Exploring Spatial Transcriptome for Fibroblast-Specific Markers in Gastric Cancer [Collaborative Research with Soon Chun Hyang Medical Center]

Immunological Implications of Microbiome Variations in Organ Transplant Recipients [Collaborative Research with Soon Chun Hyang Medical Center]

Single-Cell Transcriptome Analysis of Pure and Mixed-Type Lung Adenocarcinomas: Unraveling Molecular Insights [Collaborative Research with Chungbuk National University Medical Center]

Building an Automated Comprehensive Tool for Cell Type Labeling with Single-Cell Transcriptome Data using Artifical Intelligence [Collaborative Research with Seoul National Univ. Biomedical Informatics and KOBIC]

Exploring the Genetic Landscape of Head and Neck Cancer Patients through Single-Cell RNA-seq Analysis [Collaborative Research with Seoul National Univ. Biomedical Informatics]

Under reviewing Articles

Rapid-turnaround mRNA-based personalized cancer vaccines targeting major histocompatibility complex-II neoantigens enhance immunotherapeutic efficacy in colorectal cancer.
Seongje Cho, Woori Kwak, Hyunho Yoon, Jisun Lee, Seonghyun Lee, Hyo-Jung Park, Sohee Jo, Yu-Sun Lee, Seo-Hyeon Bae, Subin Yoon, Gahyun Roh, Dahyeon Ha, Ayoung Oh, Eun-Jin Choi, Soo-Yeon Lee, Jungmin Kim, Yeeun Lee, Sowon Lee, Hui-jeong Choi, Sang-In Park, Dae-Keun Kim, Ki-Tae Kim,Kwoneel Kim, Jae-Hwan Nam#
Nature Cancer, 2024, [High Impact J.]

Combinational regenerative inductive effect of bio-adhesive hybrid hydrogels conjugated with hiPSC-derived myofibers and its derived EVs for volumetric muscle regeneration.
Jiseong Kim*, Myung Chul Lee*, Jieun Jeon*, Alejandra Rodríguez-delaRosa, Yori Endo, Andrea Donaxi Madrigal-Salazar1,7, Da-Seul Kim, Jeong Wook Seo, Hyeseon Lee, Ki-Tae Kim, Jae-I Moon, Seung Gwa Park, Mariana Carolina Lopez-Pacheco, Abdulhameed F. Alkhateeb, Nebras Sobahi, Nicole Bassous, Wenpeng Liu, Jaeseo Lee, Seongsoo Kim, Dilara Yilmaz Aykut, Mahmoud Lotfi Nasr, Mohammad Asif Hussain, Soo-Hong Lee, Woo-Jin Kim, Olivier Pourquié, Indranil Sinha# and Su Ryon Shin#
Bioactive Materials, 2024, [High Impact J.]

Decorin as a key marker of desmoplastic cancer-associated fibroblasts mediating first-line immune checkpoint blockade resistance in metastatic gastric cancer.
Ki-Tae Kim, Ph.D.*, Min Hee Lee, M.D.,Ph.D.*, In Cho, M.D., Hee-Kyung Kim, M.D.,Ph.D., Jina Yun, M.D.,Ph.D.#, and Yoon Young Choi, M.D.,Ph.D.#,
Cancer Communications, 2024, [High Impact J.]

Immature Neutrophil Accumulation causes the Decreased Osteopontin Level in Aged Bone Marrow.
Woo-Jin Kim*, Ki-Tae Kim*, Jae-I Moon, Seung Gwa Park, Young-Dan Cho, Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Hyun-Mo Ryoo#,
Experimental & Molecular Medicine, 2024, [High Impact J.]

Spatial Transcriptomic Analysis of Aging-related Changes in Interregional Communication in the Brain.
Ki-Tae Kim*, Woo-Jin Kim* , Jae-I Moon, Seung Gwa Park, Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Young-Dan Cho#, Hyun-Mo Ryoo#,
Communication Biology, 2024

Multi-Omics Analysis Identifies Prognostic Markers and Pathways Linked to Lymphovascular Invasion in Oral Squamous Cell Carcinoma Patients Stratified by Pathologic Lymph Node Stage.
Su Kyung Kuk, Jae Il Lee, Kang Mi Pang, Ki-Tae Kim#,
Oral Oncology , 2024

Unraveling the Dynamics of Osteoblast Differentiation: Transcriptomic Insights into Matrix Mineralization and Cell Proliferation.
Yoon, Heein; Park, Seung Gwa; Shin, Hye-Rim; Kim, Ki-Tae; Cho, Young-Dan; Moon, Jae-I; Kim, Woo-Jin#; Ryoo, Hyun-Mo#,
Journal of Cellular Physiology , 2024

Published Articles

2024

Bone Targeted Lipoplex Loaded Three-Dimensional Bioprinting Bilayer Scaffold Enhanced Bone Regeneration.
Woo-Jin Kim, Jeong-Hyun Ryoo, Ji Won Kim, Ki-Tae Kim, Hye-Rim Shin, Heein Yoon, Hyun-Mo Ryoo, Young-Dan Cho#,
Regenerative Biomaterials , Volume 11, 2024, rbae055, doi: https://doi.org/10.1093/rb/rbae0552024

Deciphering metastatic route-specific signals and their microenvironment interactions in peritoneal metastasis of gastric cancer.
Ki Tae Kim, Ph.D.*,#, Jae Eun Lee, Ph.D.*, Jae-Ho Cheong, M.D., Ph.D., In Cho, M.D., and Yoon Young Choi, M.D., Ph.D.#,
Cancer Communications, 2024, Mar 18 [High Impact J., IF: 20.1] doi: https://doi.org/10.1002/cac2.12533

Prognostic DNA Mutation and mRNA Expression Analysis of Perineural Invasion in Oral Squamous Cell Carcinoma.
Su Kyung Kuk, Ki-Tae Kim, Kang Mi Pang
Scientific Reports , 2024 Jan 29. doi: https://doi.org/10.1038/s41598-024-52745-6

2023

MESIA: Multi-Epigenome Sample Integration Approach for Precise Peak Calling.
Woo-Jin Kim*, Seung Gwa Park, Jae-I Moon, Ki-Tae Kim#, Hyun-Mo Ryoo#,
Scientific Reports, 2023 Nov 27. doi: 10.1038/s41598-023-47948-2

Foci-Xpress: Automated and fast nuclear foci counting tool.
Jae-I Moon, Woo-Jin Kim, Ki-Tae Kim,Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Seung Gwa Park, Min-Sang Park, Young-Dan Cho, Pil-Jong Kim#, Hyun-Mo Ryoo#,
International Journal of Molecular Science, 2023 Sep 23. doi: 10.3390/ijms241914465

Peptidylarginine deiminase 2 plays a key role in osteogenesis by enhancing RUNX2 stability through citrullination.
Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Min-Sang Park, Byung-Gyu Kim, Jae-I Moon, Woo-Jin Kim, Seung Gwa Park, Ki-Tae Kim, Ha-Neui Kim, Je-Yong Choi, Hyun-Mo Ryoo#,
Cell Death & Disease, 2023 Aug 30. doi: 10.1038/s41419-023-06101-7

Nicotinamide enhances osteoblast differentiation through the activation of mitochondrial antioxidant defense system.
Heein Yoon, Seung Gwa Park, Hyun-Jung Kim, Hye-Lim Shin, Ki-Tae Kim, Young-Dan Cho, Jae-I Moon, Min-Sang Park, Woo-Jin Kim#, Hyun-Mo Ryoo#,
Experimental & Molecular Medicine, 2023 Jul 18. doi: 10.1038/s12276-023-01041-w

Genomic and evolutionary characteristics of metastatic gastric cancer by routes.
Ki Tae Kim*, Jae Eun Lee*, Su-Jin Shin, Jae-Ho Cheong# and Yoon Young Choi#,
British Journal of Cancer, 2023 Jul 08. doi: 10.1038/s41416-023-02338-3

The cumulative survival rate of sandblasted, large-grit, acid-etched dental implants: a retrospective analysis.
Haeji Yum, Hee-seung Han, Ki Tae Kim, Sungtae Kim and Young-Dan Cho#,
J Periodontal Implant Sci., 2023 Jun 15. doi: 10.5051/jpis.2301440072

2022

Prognostic Genomic Markers of Pathological Stage in Oral Squamous Cell Carcinoma.
Su Kyung Kuk, Jae Il Lee, Kitae Kim#,
Head Neck Pathol., 2022 Dec 31. doi: 10.1007/s12105-022-01516-8

Dental implant proximity to adjacent teeth: A retrospective study.
Ki Tae Kim, Ph.D.*, Hee-seung Han D.D.S*,Pil-Jong Kim D.D.S*, Sungtae Kim D.D.S, Ph.D., Young Ku D.D.S, Ph.D., Young-Dan Cho D.D.S, Ph.D.#,
Clinical Implant Dentistry and Related Research., 2022 Dec;24(6):733-739 doi: 10.1111/cid.13132

Clinico-pathologic and genomic characteristics of mucinous gastric adenocarcinoma.
Yoon Young Choi, M.D., Ph.D.* , Jae Eun Lee, Ph.D., Ji Yeong An, M.D., Ph.D., Ki Tae Kim, Ph.D., Su Jin Shin, M.D., Ph.D., Jae-Ho Cheong, M.D., Ph.D.#,
Gastric Cancer, 2022 Jul;25(4):697-711 doi: 10.1007/s10120-022-01295-9

Nanofibrous topography-driven altered responsiveness to Wnt5a mediates the three-dimensional polarization of odontoblasts.
Kim, W. J.; S. U. Rahman; Chung, S. H.; Woo, K. M.#,
Materials Today Bio, 2022 Nov 2;17:100479. doi: 10.1016/j.mtbio.2022.100479

The worldwide patent landscape of dental implant technology.
Kim, W. J.; Kim, B. S.; Kim, H. J.; Cho, Y. D.; Shin, H. L.; Yoon, H. I.; Lee, Y. S.; Baek, J. H.; Woo, K. M.; Ryoo, H. M.#,
Biomaterials Research, 2022 Oct 23;26(1):59. doi: 10.1186/s40824-022-00307-0

2021

Septal chondrocyte hypertrophy contributes to midface deformity in a mouse model of Apert syndrome.
Kim, B.S.; Shin, H. R.; Kim, H. J.; Yoon, H. I.; Cho, Y. D.; Choi, K. Y.; Choi, J. Y.; Kim, W. J.#; Ryoo, H. M.#,
Scientific Reports, 2021 Apr 12;11(1):7979. doi: 10.1038/s41598-021-87260-5

Genetic differences between physical injury patients with and without post-traumatic syndrome: Focus on secondary findings and potential variants revealed by whole-exome sequencing.
Hee-Ju Kang, Ho-Yeon Lee, Ki-Tae Kim, Ju-Wan Kim, Ju-Yeon Lee, Sung-Wan Kim, Jung-Chul Kim, Il-Seon Shin, Namshin Kim, Jae-Min Kim#,
Clin Psychopharmacol Neurosci., 2021 Nov 30;19(4):683-694. doi: 10.9758/cpn.2021.19.4.683

Unveiling the genetic variation of severe continuous/mixed-type ossification of the posterior longitudinal ligament by whole-exome sequencing and bioinformatic analysis.
Ki Tae Kim*, Chang-Hyun Lee*, Chi Heon Kim, Eun Young Lee, Sang Gu Lee, Myung-Eui Seo, Ju Han Kim# and Chun Kee Chung#,
Spine J. , 2021 Nov;21(11):1847-1856. doi: 10.1016/j.spinee.2021.07.005

Genetic markers for depressive disorders with earlier age at onset.
Ki Tae Kim*, Hee-Ju Kang*, Kyoung-Hoon Yoo, Yoomi Park, Ju-Wan Kim, Sung-Wan Kim, Il-Seon Shin, Ju Han Kim#, Jae-Min Kim#,
Progress in Neuro-psychoparmacology & Biological psychiatry , 2021 Jun 8;108:110176. doi: 10.1016/j.pnpbp.2020.110176

Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives.
Cho, Y. D., Kim, W. J.; Ryoo, H. M.; Kim, H. K.; Ku, Y; Seoul. Y. J.#,
Clin Epigenetics. , 2021 Apr 26;13(1):92. doi: 10.1186/s13148-021-01074-w

2020

Intratesticular Peptidyl Prolyl Isomerase 1 Protein Delivery Using Cationic Lipid Coated Fibroin Nanoparticle Complexes Rescues Male Infertility in Mice.
Kim, W. J.; Kim, B. S.; Kim, H. J.; Cho, Y. D.; Shin, H. L.; Yoon, H. I.; Lee, Y. S.; Baek, J. H.; Woo, K. M.; Ryoo, H. M.#,
ACS Nano., 2020 Oct 27;14(10):13217-13231. doi: 10.1021/acsnano.0c04936

RUNX2-modifying enzymes: therapeutic targets for bone disease.
Kim, W. J.; Shin, H. L.; Kim, B. S.; Kim, H. J.; Ryoo, H. M.#,
Experimental & Molecular Medicine, 2020 Aug;52(8):1178-1184. doi: 10.1038/s12276-020-0471-4

Sex differences in the genetic architecture of depression.
Hee-Ju Kang, Yoomi Park, Kyoung-Hoon Yoo, Ki-Tae Kim, Eun-Song Kim, Ju-Wan Kim, Sung-Wan Kim, Il-Seon Shin, Jin-Sang Yoon, Ju Han Kim#, Jae-Min Kim#,
Scientific Reports , 2020 Jun 18;10(1):9927. doi: 10.1038/s41598-020-66672-9

Genetic markers for later remission in response to early improvement of antidepressants.
Ki Tae Kim*, Hee-Ju Kang*, Kyoung-Hoon Yoo, Yoomi Park, Ju-Wan Kim, Sung-Wan Kim, Il-Seon Shin, Ju Han Kim#, Jae-Min Kim#,
Int J Mol Sci. , 2020 Jul 10;21(14):4884. doi: 10.3390/ijms21144884

Post-Translational Regulations of Transcriptional Activity of RUNX2.
Kim, H. J.; Kim, W. J.; Ryoo, H. M.#,
Mol Cells. , 2020 Feb 29;43(2):160-167. doi: 10.14348/molcells.2019.0247

Histone acetylation together with DNA demethylation empowers higher plasticity in adipocytes to differentiate into osteoblasts.
Cho, Y. D.; Kim, B. S. Kim, W. J.; Kim, H. J.; Baek J. H.; Woo, K. M.; Seol, Y. J.; Ku, Y.; Ryoo H. M.#,
Gene , 2020 Apr 5;733:144274. doi: 10.1016/j.gene.2019.144274

Aggregate removal of particulate matter by selective protein-rich fraction of Moringa oleifera extract.
Cho, Y.W.; Yun, J.H.; Kwon, S.H.; Eom, Y.J.; Kim, W. J.#,
Journal of Industrial Engineering Chemistry , 2020 Jan 25(81):161-166. doi: 10.1016/j.jiec.2019.09.004

~ 2019

Is NF2 a key player in the differentially expressed gene of spinal cord ependymoma compared with the intracranial ependymoma?
Ki Tae Kim*, Chang-Hyun Lee*, Chun Kee Chung#, Ju Han Kim#,
World Neurosurgery , 2018 Oct;118:e906-e917. doi: 10.1016/j.wneu.2018.07.096

Predicting Treatable traits for Long-Acting Bronchodilators in Patients with Stable COPD.
Ki Tae Kim*, Jieun Kang*, Ji-Hyun Lee, Eun Kyung Kim, Tae-Hyung Kim, Kwang Ha Yoo, Jae Seung Lee, Woo Jin Kim, Ju Han Kim#, Yeon-Mok Oh#,
Int J Chron Obstruct Pulmon Dis. , 2017 Dec 12;12:3557-3565. doi: 10.2147/COPD.S151909

Fibroin particle-supported cationic lipid layers for highly efficient intracellular protein delivery.
Kim, W. J.; Kim, B. S.; Cho, Y. D.; Yoon, W. J.; Baek, J. H.; Woo, K. M.; Ryoo, H. M.#,
Biomaterials, 2017 Apr;122:154-162. doi: 10.1016/j.biomaterials.2017.01.019

Direct Delivery of Recombinant Pin1 Protein Rescued Osteoblast Differentiation of Pin1-Deficient Cells.
Kim, W. J., Islam, R.; Kim, B. S.; Cho, Y. D.; Yoon, W. J.; Baek, J. H.; Woo, K. M.; Ryoo, H. M.#,
Journal of Cellular Physiology , 2017 Oct;232(10):2798-2805. doi: 10.1002/jcp.25673

Blood-testis barrier integrity depends on Pin1 expression in Sertoli cells.
Islam, R.; Yoon, H. I.; Kim, B. S.; Bae, H. S.; Shin, H. R., Kim, W. J.; Yoon, W. J.; Lee, Y. S.; Woo, K. M.; Baek, J. H.; Ryoo, H. M#,
Sci Rep. , 2017 Aug 1;7(1):6977. doi: 10.1038/s41598-017-07229-1

Association of FAT1 mutation with overall survival in patients with human papillomavirus-negative head and neck squamous cell carcinoma.
Ki Tae Kim*, Bo-Sung Kim*, Ju Han Kim#,
Head & Neck , 2016 Apr;38 Suppl 1(Suppl 1):E2021-9. doi: 10.1002/hed.24372

Epigenetic modifications and canonical wingless/int-1 class (WNT) signaling enable trans-differentiation of nonosteogenic cells into osteoblasts.
Cho, Y. D.; Yoon, W. J.; Kim, W. J.; Woo, K. M.; Baek, J. H.; Lee, G.; Ku, Y.; van Wijnen, A. J.; Ryoo, H. M.#,
J Biol Chem. , 2014 Jul 18;289(29):20120-8. doi: 10.1074/jbc.M114.558064

Prolyl isomerase Pin1-mediated conformational change and subnuclear focal accumulation of Runx2 are crucial for fibroblast growth factor 2 (FGF2)-induced osteoblast differentiation.
Yoon, W. J.; Cho, Y. D.; Kim, W. J.; Woo, K. M.; Baek, J. H.; Lee, G.; Ku, Y.; van Wijnen, A. J.; Ryoo, H. M.#,
J Biol Chem. , 2014 Mar 28;289(13):8828-38. doi: 10.1074/jbc.M113.516237

Wnt3a stimulates Mepe, matrix extracellular phosphoglycoprotein, expression directly by the activation of the canonical Wnt signaling pathway and indirectly through the stimulation of autocrine Bmp-2 expression.
Cho, Y. D.; Kim, W. J.; Yoon, W. J.; Woo, K. M.; Baek, J. H.; Lee, G.; Kim, G. S.; Ryoo, H. M.#,
J Cell Physiol. , 2012 Jun;227(6):2287-96. doi: 10.1002/jcp.24038

Conferences

Frequent clonotypes and its corresponding epitopes in mCD4+ and mCD8+ T-cells.
Ki-Tae Kim, Yunjung Cho
LMCE 2021 (Laboratory Medicine Congress & Exhibition) & KSLM 62nd Annual Meeting, 2021

Prediction model of fitness of clonotypes in mCD4+ and mCD8+ T-cells.
Ki-Tae Kim, Yunjung Cho
Korean Society of Diagnostic Immunology, 2021

Comprehensive analysis of shared clonotypes between memory CD4+ and CD8+ T-cells with TCR Repertoire and scRNA sequencing.
Ki-Tae Kim, Yunjung Cho
KAI International Virtual Meeting, 2020

Patents

Analysis pipeline of shared clonotypes between CD4+ and CD8+ T-cells for precision medicine.
Patent ID: 10-2021-0074968 Ki-Tae Kim, Yunjung Cho

Composition for diagnostics and the uses compromising SPP1 for immature neutrophil deposition of aging bone marrow.
Patent ID: 10-2022-0151288 Ki-Tae Kim, Woo-jin Kim, Hyun-Mo Ryoo

Method for screening biomarkers for diagnosis of ovarian metastatic gastric cancer and biomarkers selected by the method.
Patent ID: 10-2022-173056 Ki-Tae Kim, Yoon Young Choi, Jae Eun Lee

Method for screening biomarkers for diagnosis of peritoneal metastatic gastric cancer and biomarkers selected by the method.
Patent ID: 10-2022-173051 Ki-Tae Kim, Yoon Young Choi, Jae Eun Lee

Method for screening biomarkers for predicting prognosis and metastasis of gastric cancer and biomarkers selected by the method.
Patent ID: 10-2023-0073634 Ki-Tae Kim, Yoon Young Choi

Composition for predicting resistance to anti-PD-1 immune checkpoint inhibitor.
Patent ID: 10-2024-0062963 Ki-Tae Kim, Yoon Young Choi, Jina Yun, Min Hee Lee