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Journal Publications (peer reviewed) / Book chapter


† Equal contributors
* Corresponding Author(s)
Names in bold: TGIL members


  1. Young-soo Chung, Seungseok Kang, Jisu Kim, Sangbo Lee, and Sangwoo Kim*
    CLEMENT: Genomic Decomposition and Reconstruction of Non-tumor Subclones
    Nucleic Acids Research (accepted for publication)


  2. Il Bin Kim, Myeong-Heui Kim, Saehoon Jung, Woo Kyeong Kim, Junehawk Lee, Young Seok Ju, Maree J. Webster, Sanghyeon Kim, Ja Hye Kim, Hyun Jung Kim, Junho Kim*, Sangwoo Kim*, Jeong Ho Lee*
    Low-level brain somatic mutations in exonic regions are collectively implicated in autism with germline mutations in autism risk genes
    Experimental & Moleculear Medicine (accepted for publication)


  3. Jiyun Hong, Eunwoo Choi, Dahee Kim, Mi-kyoung Seo, Hyundeok Kang, BeumJin Park, and Sangwoo Kim*
    Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment
    npj Precision Oncology 2024 8, Article number 15



  4. Yoo-Jin Ha, Seungseok Kang, Jisoo Kim, Junhan Kim, Se-Young Jo, and Sangwoo Kim*
    Comprehensive benchmarking and guidelines of mosaic variant calling strategies
    Nature Methods 2023, 20:2058-2067
    - Media covered in BRIC (한빛사)
    - Media covered in SeoulEconomy, KyungHyang, MedicalTodayDailyMedi, eNewsToday and 7 more news outlets


  5. In Seok Yang, Insu Jang, Jin Ok Yang, Jinhyuk Choi, Min-Seo Kim, Ka-Kyung Kim, Byung-Joon Seung, Jae-Ho Cheong, Jung-Hyang Sur, Hojung Nam, Byungwook Lee*, Junho Kim*, and Sangwoo Kim*
    CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)
    BMC Genomics 2023, 24(613)
    - Database available at:


  6. Eun-Jin Yun, Dongwhi Kim, Sangwoo Kim, Jer-Tsong Hsieh, and Seung Tae Baek*
    Targeting Wnt/β-catenin-mediated upregulation of oncogenic NLGN3 suppresses cancer stem cells in glioblastoma
    Cell Death & Disease 2023, 14, article number 423


  7. Bhumsuk Keam, Min Hee Hong, Seong Hoon Shin, Seong Gu Heo, Ji Eun Kim, Hee Kyung Ahn, Yun-Gyoo Lee, Keon-Uk Park, Tak Yun, Keun-Wook Lee, Sung-Bae Kim, Sang-Cheol Lee, Min Kyung Kim, Sang Hee Cho, So Yeon Oh, Sang-Gon Park, Shinwon Hwang, Byung-Ho Nam, Sangwoo Kim*, Hye Ryun Kim*, Hwan-Jung Yun*
    Personalized biomarker-based umbrella trial for patients with recurrent or metastatic head and neck squamous cell carcinoma: KCSG HN 15-16 TRIUMPH trial
    Journal of Clinical Oncology 2023 (ePub ahead of print)
    - Media covered in BRIC (한빛사)
    - Media covered in Medipana, Korea Healthlog, kMedInfo, and MedicalObserver


  8. Min Hwan Kim, Gun Min Kim, Jin Mo Ahn, Won-Ji Ryu, Seul-Gi Kim, Jee Hung Kim, Tae Yeong Kim, Hyun Ju Han, Jee Ye Kim, Hyung Seok Park, Seho Park, Byeong Woo Park, Seung Il Kim, Joon Jeong, Jieun Lee, Soonmyung Paik, Sangwoo Kim, Kyung Hae Jung, Eun Hae Cho*, Joohyuk Sohn*
    Copy number aberrations in ctDNA enables prognosis prediction and molecular characterization of breast cancer
    Journal of the National Cancer Institute 2023, 115(9), 1036-1049


  9. Se Hee Kim, Soon Sung Kwon, Mi Ri Park, Hyeon Ah Lee, Ji Hun Kim, JiHoon Cha, Sangwoo Kim, Seung Tae Baek, Se Hoon Kim, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung-Tae Lee, Hoon-Chul Kang
    Detecting low-variant allele frequency mosaic pathogenic variants of NF1, TSC2, and AKT3 genes from blood in patients with neurodevelopmental disorders
    The Journal of Molecular Diagnostics 2023, 25(8), 583-591


  10. Se-Young Jo, Namki Hong, Seunghyun Lee, Jong Ju Jeong, Jeongsoo Won, Jiho Park, Gi Jeong Kim, Sang Kyum Kim, Sangwoo Kim*, Yumie Rhee*,
    Genomic and transcriptomic profiling reveal molecular characteristics of parathyroid carcinoma
    Experimental & Moleculear Medicine 2023, 55, 886-897 
    - Media covered in BRIC (한빛사)



  11. Ja Hye Kim, Shinwon Hwang, Hyeonju Son, Dongsun Kim, Il Bin Kim, Myeong-Heui Kim, Nam Suk Sim, Dong-Seok Kim, Yoo-Jin Ha, Junehawk Lee, Hoon-Chul Kang, Jeong Ho Lee*, and Sangwoo Kim*
    Analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development
    PLoS Genetics 2022, 18(9):e1010404


  12. Hyundeok Kang, Mi-Kyoung Seo, BeumJin Park, Sun Och Yoon, Yoon Woo Koh, Dahee Kim*, and Sangwoo Kim*
    Characterizing intrinsic molecular features of the immune subtypes of salivary mucoepidermoid carcinoma
    Translational Oncology 2022, 24, 101496


  13. BeumJin Park, Seok-Jae Heo, Yong Joon Lee, Mi-Kyoung Seo, Jiyun Hong, Eui-Cheol Shin, Inkyung Jung, and Sangwoo Kim*
    HLA-I-restricted CD8+ T cell immunity may accelerate tumorigenesis in conjunction with VHL inactivation
    iScience 2022, 25;6, 104467


  14. Yun-Ji Cha, Sae-Bom Jeon, Jaewon Oh, Seung-Tae Lee, Sangwoo Kim, Hyoeun Kim, Jungyoon Choi, Hyo-Kyoung Choi, Dongju Won, Jong Rak Choi, Seok-Jun Kim, Sahng Wook Park*, Seok Min Kang*, and Seung-Hyun Lee*
    Derivation of YCMi005-A, a human-induced pluripotent stem cell line, from a patient with dilated cardiomyopathy carrying missense variant in TPM1 (p. Glu192Lys)
    Stem Cell Research 2022, 60, 102707


  15. Songyeon Lee, Byung-Joon Seung, In Seok Yang, Jueun Lee, Taewoong Ha, Hee-Myung Park, Jae-Ho Cheong, Sangwoo Kim, Jung-Hyang Sur, Geum-Sook Hwang* & Hojung Nam* 
    1H NMR based urinary metabolites profiling dataset of canine mammary tumors
    Scientific Data 2022, 9, article number 132


  16. Mi-Kyoung Seo, Hyundeok Kang, and Sangwoo Kim*
    Tumor microenvironment-aware, single-transcriptome prediction of microsatellite instability in colorectal cancer using meta-analysis
    Scientific Reports 2022, 12, article number 6238


  17. Yoo-Jin Ha, Myung Joon Oh, Junhan Kim, Jisoo Kim, Seungseok Kang, John D. Minna, Hyun Seok Kim* and Sangwoo Kim*
    Establishment of reference standards for multifaceted mosaic variant analysis
    Scientific Data 2022, 9, article number 35
    - Reference standard data available at GitHub page


  18. Yohan Yang, Eunyoung Kim, Taek Chung and Sangwoo Kim*
    Insignificant effects of loss of heterozygosity in human leukocyte antigen on the efficacy of immune checkpoint blockade treatment
    Genes and Genomics 2022, 44, 595-515


  19. Seong Jin Choi, Dong-Uk Kim, Ji Yun Noh, Sangwoo Kim, Se-Hyung Park, Hye Won Jeong, and Eui-Cheol Shin
    T cell epiotpes in SARS-CoV-2 proteins are substantially conserved in the Omicron variant
    Cellular & Molecular Immunology 2022, 19, 447-448



  20. Jung Ho Kim†, Mi-Kyoung Seo†, Ji Ae Lee, Seung-Yeon Yoo, Hyeon Jeong Oh, Hyundeok Kang, Nam-Yun Cho, Jeong Mo Bae, Gyeong Hoon Kang* and Sangwoo Kim*
    Genomic and transcriptomic characterization of heterogeneous immune subgroups of microsatellite instability-high colorectal cancers
    Journal for immunotherapy of cancer 2021;9;e003414
    - Media covered in BRIC (한빛사)
    - Media covered in Donga Science, Herald Economy, Asia Economy, News1, Digital Times, and 4 others.


  21. Jaewon Oh, Sun-Ho Lee, Jungyoon Choi, Jong Rak Choi, Sangwoo Kim, Yun-Ji Cha, Hyo-Kyoung Choi, Dongju Won, Ho-Geun Yoon, Sahng Wook Park, Seok-Min Kang*, Seung-Tae Lee*, Seung-Hyun Lee*
    Establishment of a novel human iPSC line (YCMi003-A) from a patient with dilated cardiomyopathy carrying genetic variant LMNA p.Asp364His
    Stem Cell Research 2021, 56, 102508


  22. Jung Ho Kim*, Jeong Hoon Hong, Yoon-La Choi*, Ji Ae Lee, Mi-kyoung Seo, Mi-Sook Lee, Sung Bin An, Min Jung Sung, Nam-Yun Cho, Sung-Su Kim, Young Kee Shin, Sangwoo Kim, Gyeong Hoon Kang
    NTRK oncogenic fusions are exclusively associated with the serrated neoplasia pathway in the colorectum and begin to occur in sessile serrated lesions
    The Journal of Pathology 2021, 255(4):399-411


  23. Kyung Won Kim, Dong Yun Kim, Dankyu Yoon, Ka-Kyung Kim, Haerin Jang, Nathan Schoettler, Eun Gyul Kim, Mi Na Kim, Jung Yeon Hong, Jeom-Kyu Lee, Sangwoo Kim, Carole Ober, Heon Yung Gee*, and Myung Hyun Sohn*
    Genome-wide association study identifies TNFSF15 associated with childhood asthma
    Allergy 2021, 00:1-12


  24. Bhumsuk Keam, Jin Young Park, Jinpyo Kim, Gun Do Kim, Yunsuk Yu, Sang Hee Cho, Sangwoo Kim, Hee Kyung Ahn, Sang Hoon Chun, Jung Hye Kwon, Tak Yun, Ji-Won Kim, Ji Eun Kim, Myung-Ju Ahn, Joo-Hang Kim, and Hwan Jung Yun*
    Comprehensive Analysis of Mutation-Based and Expressed Genes-Based Pathways in Head and Neck Squamous Cell Carcinoma
    Processes 2021, 9(5), 792


  25. Sun Min Lim†, Eunyoung Kim†, Kyung Hae Jung†, Sora Kim, Ja Seung Koo, Seung Il Kim, Seho Park, Hyung Seok Park, Byoung Woo Park, Young Up Cho, Ji Ye Kim, Soonmyung Paik, Nak-Jung Kwon, Gun Min Kim, Ji Hyoung Kim, Min Hwan Kim, Min Kyung Jeon, Sangwoo Kim*, Joohyuk Sohn*
    Genomic landscape of extraordinary responses in metastatic breast cancer
    Communications Biology 2021, 4, Article number 449


  26. In Seok Yang†, Sang Won Bae†, BeumJin Park,  and Sangwoo Kim*
    Development of a program for in silico optimized selection of oligonucleotide-based molecular barcodes 
    PLoS ONE 2021, 16(2):e0246354


  27. Hee Seung Lee, Eunyoung Kim†, Jinyoung Lee, Seung Joon Park, Ho Kyoung Hwang, Chan Hee Park, Se-Young Jo, Chang Moo Kang, Seung-Mo Hong, Huapyong Kang, Jung Hyun Jo, In Rae Cho, Moon Jae Chung, Jeong Youp Park, Seung Woo Park, Si Young Song, Jung Min Han, Sangwoo Kim*, and Seungmin Bang* 
    Profiling of conditionally reprogrammed cell lines for in vitro chemotherapy response prediction of pancreatic cancer
    EBioMedicine 2021, 65:103218



  28. Mi-kyoung Seo, Soongmyung Paik* and Sangwoo Kim*
    An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier
    Cancers 2020,12(12), 3506


  29. Eun-Jin Yun, Sangwoo Kim, Jer-Tsong Hsieh, and Seung Tae Baek,
    Wnt/β-catenin signaling pathway induces autophagy-mediated temozolomide-resistance in human glioblastoma
    Cell Death & Disease 2020, 11. article number 771


  30. Tae-Min Kim, In Seok Yang, Byung-Joon Seung, Sejoon Lee, Dohyun Kim, Yoo-Jin Ha, Mi-kyoung Seo, Ka-Kyung Kim, Hyun Seok Kim, Jae-Ho Cheong, Jung-Hyang Sur, Hojung Nam, and Sangwoo Kim*
    Cross-species Oncogenic Signatures of Breast Cancer in Canine Mammary Tumors
    Nature Communications 2020 11, article number 3616
    - Media covered in BRIC (한빛사)
    - Covered in 14 major media (online collection) (2020/07/17)


  31. Hyun Chang, Yun-Gyoo Lee, Yoon Ho Ko, Jang Ho Cho, Jong-Kwon Choi, Keon Uk Park, Eun Joo Kang, Keun-Wook Lee, Sun Min Lim, Jin-Soo Kim, Hyun Woo Lee, Min Kyoung Kim, In Gyu Hwang, Sangwoo Kim, Byung-Ho Nam, Hye Ryun Kim*
    Prognostic value of CD200R1 mRNA expression in head and neck squamous cell carcinoma
    Cancers 2020, 12(7), 1777


  32. Min Hwan Kim, Jae-Hwan Kim, Ji Min Lee, Jae Woo Choi, Dongmin Jung, Hojin Cho, Hyundeok Kang, Min Hee Hong, Su Jin Heo, Se Heon Kim, Eun Chang Choi, Da Hee Kim, Young Min Park, Sangwoo Kim, Sun Och Yoon, Yoon Woo Koh, Byoung Chul Cho, and Hye Ryun Kim
    Molecular subtypes of oropharyngeal cancer show distinct immune microenvironment related with immune checkpoint blockade response
    British Journal of Cancer 2020, 122:1649-1660


  33. Yeomin Yun, Sung-Ah Hong, Ka-Kyung Kim, Daye Baek, Dongsu Lee, Ashwini M. Londhe, Minhyung Lee, Jihyeon Yu, Zachary T. Mceachin, Robert Bowser, Sung-Rae Cho, Janghwan Kim, Ae Nim Pae, Eunji Cheong, Sangwoo Kim, Nicholas M. Boulis, Sangsu Bae*, Yoon Ha*
    CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual sequencing
    Communications Biology 2020, 3, Article number 33 


  34. Bo Min Kim, Sae Rom Hong, Hein Chun, Sangwoo Kim, and Kyoung-Jin Shin*
    Comparison of whole mitochondrial genome variants between hair shafts and reference samples using massively parallel sequencing
    International Journal of Legal Medicine 2020, 134:853–861



  35. You Jin Chun, Jae Woo Choi, Min Hee Hong, Dongmin Jung, Hyeonju Son, Eun Kyung Cho, Young Joo Min, Sang-We Kim, Keunchil Park, Sung Sook Lee, Sangwoo Kim*, Hye Ryun Kim*, and Byung Chul Cho*
    Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing
    PLoS ONE 2019 14(11):e0224379


  36. Se-Young Jo†, Eunyoung Kim†, and Sangwoo Kim*
    Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis
    Genome Biology 2019 (20):231
    - Product available at GitHub and Zenodo
    - Media covered in BRIC (한빛사)
    - Media covered in: Daily Economy, Newsis, Asian EconomyMedical Today, iNews, Nocut News (2019/11/12)


  37. Ka-Kyung Kim†, Byung-Joon Seung, Dohyun Kim, Hee-Myung Park, Sejoon Lee, Doo-Won Song, Gunho Lee, Jae-Ho Cheong, Hojung Nam*, Jung-Hyang Sur*, Sangwoo Kim*
    Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors
    Scientific Data 2019, 6:147


  38. Jun Sung Park, Junehawk Lee, Eun Sun Jung, Myeong-heui Kim, Il Bin Kim, Hyeonju Son, Sangwoo Kim, Sanghyeon Kim, Young Mok Park, Inhee Mook-Jung, Seok Jong Yu*, and Jeong Ho Lee*
    Brain somatic mutations observed in Alzheimer's disease associated with aging and dysregulation of tau phosphorylation
    Nature Communications 2019,  10, Article number 3090


  39. Hein Chun and Sangwoo Kim*
    BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort
    Bioinformatics 2019, 35(22):4806-4808


  40. Won-Ji Ryu, Jae Eun Lee, Yong-Hee Cho, Gunho LeeMi-kyoung Seo, Sang-Kyu Lee, Jeong-Ha Hwang, Do Sik Min, Sung Hoon Noh, Soonmyung Paik, Sangwoo Kim, Jae-Ho Cheong*, and Kang-Yell Choi*
    A therapeutic Strategy for chemotherapy-resistant gastric cancer via destabilization of both b-catenin and RAS
    Cancers, 2019(11):4, 496


  41. Junho Kim, Dachan Kim, Jae Seok Lim, Ju Heon Maeng, Hyeonju Son, Hoon-Chul Kang, Hojung Nam, Jeong Ho Lee* and Sangwoo Kim*
    The use of technical replication for detection of low-level somatic mutations in next-generation sequencing
    Nature Communications 2019, 10, Article number 1047
    - Software available at SourceForge
    - Media covered in BRIC (한빛사)
    - Media covered in: Medical Tribune, Bridge Economy, Medipana News (2019/03/18)
    - Selected as Top 5 Biomedical Research of Korea in 2019


  42. Eun Kyung Kim, Kyung A. Kim, Chang Young Lee, Sangwoo Kim, Sunhee Chang, Byoung Chul Cho, Hyo Sup Shim
    Molecular Diagnostic Assays and Clinicopathologic Implication of MET Exon 14 Skipping Mutation in Non-small-cell Lung Cancer
    Clinical Lung Cancer, 2019, 20(1):e123-32 


  43. Gunho Lee†, Hyang Joo Ryu, Ji Woon Choi, Hyundeok Kang, Woo Ick Yang, In Seok Yang, Mi-Kyoung Seo, Sangwoo Kim* and Sun Och Yoon*
    Characteristic gene alterations in primary gastrointestinal T and NK cell lymphomas
    Leukemia 2019, 33, 1797-1832
    - Media covered in BRIC (한빛사)


  44.  Sun Min Lim, Sang Hee Cho, In Gyu Hwang, Jae Woo Choi, Hyun Chang, Myung-Ju Ahn, Keon Uk Park, Ji-Won Kim, Yoon Ho Ko, Hee Kyung Ahn, Byoung Chul Cho, Byung-Ho Nam, Sang Hoon Chun, Ji Hyung Hong, Jung Hye Kwon, Jong Gwon Choi, Eun Joo Kang, Tak Yun, Keun-Wook Lee, Joo-Hang Kim, Jin Soo Kim, Hyun Woo Lee, Min Kyoung Kim, Dongmin Jung, Ji Eun Kim, Bhumsuk Keam, Hwan Jung Yun*, Sangwoo Kim* and Hye Ryun Kim* 
    Investigating the feasibility of targeted next-generation sequencing to guide the treatment of head and neck squamous cell carcinoma
    Cancer Research and Treatment 2019:51(1):300-312



  45. Nam Suk Sim, Youngsuk Seo, Jae Seok Lim, Woo Kyeong Kim, Hyeonju Son, Heung Dong Kim, Sangwoo Kim, Hyun Joo An, Hoon-Chul Kang, Se Hoon Kim, Dong-Seok Kim, Jeong Ho Lee
    Brain somatic mutations in SLC35A2 cause intractable epilepsy with aberrant N-glycosylation
    Neurology Genetics 2018, 4:e294


  46. Sunguk Shin, Hanna Lee, Hyeonju Son, Soonmyung Paik and Sangwoo Kim*
    AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
    Bioinformatics 2018, 34(7):1232-1234
    - Software available at


  47. Soo-jin Ann, Ka-Kyung Kim†, Eun Jeong Cheon, Hye-Min Noh, Sungha Park, Seok-Min Kang, Sangwoo Kim*, Sang-Hak Lee*
    Palmitate and Minimally-Oxidized Low-Density Lipoprotein Additively Promotes Macrophage Activation via TLR4-Dependent and -Independent Pathways
    PLoS ONE 2018,13(3): e0193649


  48. Ara Ko, Song Ee Youn, Se Hee Kim, Joon Soo Lee, Sangwoo Kim, Jong Rak Choi, Heung Dong Kim, Seung-Tae Lee, Hoon-Chul Kang
    Targeted gene panel and genotype-phenotype correlation in children with developmental and epileptic encephalopathy
    Epilepsy Research 2018, 141:48-55


  49. Sora Kim†, Han Sang Kim, Eunyoung Kim, Min Goo Lee, Eui-Cheol ShinSoonmyung Paik and Sangwoo Kim*
    Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information
    Annals of Oncology 2018, 29(4):1030-1036
    - Media covered in BRIC (한빛사)
    - Software available at

    - Media covered in: Yonhap News, Daily Economy, Chosun Biz, Digital Times, Medical Today, Nocut News (2018/02/12)
    - Discussed in Editorial:
      A C Ekulund and Z Szallasi, "
    Computational prediction of neoantigens: do we need more data or new approaches?", Annals of Oncology 2018.


  50. In Seok Yang and Sangwoo Kim*,
    Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients
    BMC Bioinformatics 2018, 19(Supp l1):40



  51. Hyeonju Son, Hyundeok Kang, Hyun Seok Kim and Sangwoo Kim*
    Somatic mutation driven codon transition bias in human cancer
    Scientific Reports 2017, 7:14204


  52. Choong-kun Lee†, Sora Kim†, Jae Seok Lee, Jeong Eun Lee, Sung Moo Kim, In Seok Yang, Hye Ryun Kim, Jeong Ho Lee, Sangwoo Kim*, and Byoung Chul Cho*,
    Next-generation sequencing reveals novel resistance mechanisms and molecular heterogeneity in EGFR-mutant non-small cell lung cancer with acquired resistance to EGFR-TKIs
    Lung Cancer 2017, 113:106-114


  53. Sangwoo Kim and Hojung Nam*, 
    In Silico Simulation of Signal Cascades in Biomedical Networks Based on the Production Rule System
    Lecture Notes in Computer Science,  vol 10330. Springer, Cham


  54. Jae Seok Lim, Ramu Gopalappa, Se Hoon Kim, Suresh Ramakrishna, Minji Lee, Woo-il Kim, Junho Kim, Sang Min Park, Junehawk Lee, Jung-Hwa Oh, Heung Dong Kim, Chang-Hwan Park, Joon Soo Lee, Sangwoo Kim, Dong Seok Kim, Jung Min Han, Hoon-Chul Kang*, Hyongbum Kim* & Jeong Ho Lee*, 
    Somatic Mutations in TSC1 and TSC2 cause focal cortical dysplasia
    The American Journal of Human Genetics 2017, 100(3):454-472



  55. In Seok Yang, Hyeonju Son, Sora Kim and Sangwoo Kim*,
    ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer,
    BMC Genomics 2016, 17(1):1-14
    - Database available at


  56. Junho Kim, Ju Heon Maeng, Jae Seok Lim, Hyeonju Son, Junehawk Lee, Jeong Ho Lee and Sangwoo Kim*,
    Vecuum: identification and filtration of false somatic variants caused by vector contamination,
    Bioinformatics 2016, 32(20):3072-3080
    - Software available at
    - Media covered in BRIC (한빛사)
    - Article recommended  by F1000
    - This is a very interesting paper that presents software to identify vector-contamination by inserts that are variable, not just the usual contamination by known vectors of fixed sequence. The background is that when a vector gets integrated into a sequence and linearized, the fixed vector part may be adjacent to a variable sequence segment that was put (with different mutations) into the cloning vector. Such variations may be misinterpreted as bona fide low frequency mutations, especially in the setting of cancer sequencing studies that look for low-frequency somatic mutations in bulk samples. Thus, the authors' method can be used to distinguish somatic mutations in the host DNA from variation in the sequencing reagents that get sequenced along with the sample DNA. The general idea of the method is to identify sequence matches to known vectors, using BWA, and then look at the exon junction patterns in the adjacent sequences to see if they are skewed. In this paper, Figure 1 is "worth more than a thousand words" and readers should start at Figure 1 to understand the innovative problem formulation done by the authors.


  57. Hyung Soon Park, Sun Min Lim, Sora Kim, Sangwoo Kim, Hye Ryun Kim, KyuBum Kwack, Min Goo Lee, Joo-Hang Kim, Yong Wha Moon*,
    Pilot Study of a Next-Generation Sequencing-Based Targeted Anticancer Therapy in Refractory Solid Tumor at a Korean Institution,
    PLoS ONE 2016, 11(4):e0154133


  58. Yoon Young Choi, Jae Eun Lee, Hyunki Kim, Moon Hee Sim, Ka-Kyung Kim, Gunho Lee, Hyoung-Il Kim, Ji Yeong An, Woo Jin Hyung, Choong-Bai Kim, Sung Hoon Noh, Sangwoo Kim & Jae-Ho Cheong*,
    Establishment and characterisation of patient-derived xenografts as paraclinical models for gastric cancer
    Scientific Reports 2016,6:22172


  59. Kie Kyon Huang, Kang Won Jang, Sangwoo Kim, Han Sang Kim, Sung-Moo Kim, Hyeong Ju Kwon, Hye Ryun Kim, Hwan Jung Yun, Myung Ju Ahn, Keon Uk Park, Kalpana Ramnarayanan, John R. McPherson, Shenli Zhang, Je-Keun Rhee, André L. Vettore, Kakoli Das, Takatsugu Ishimoto, Joo Hang Kim, Yoon Woo Koh, Se Hun Kim, Eun Chang Choi, Bin Tean Teh, Steven G. Rozen, Tae-Min Kim, Patrick Tan & Byoung Chul Cho,
    Exome sequencing reveals recurrent REV3L mutations in cisplatin-resistant squamous cell carcinoma of head and neck,
    Scientific Reports 2016, 6:19552


  60. Sun Min Lim, Hyung Soon Park, Sangwoo Kim, Sora Kim, Siraj. M. Ali, Joel. R. Greenbowe, In Seok Yang, Nak-Jung Kwon, Jae Lyun Lee, Min-Hee Ryu, Jin-Hee Ahn, Jeeyun Lee, Min Goo Lee, Hyo Song Kim, Hyunki Kim, Hye Ryun Kim, Yong Wha Moon, Hyun Cheol Chung, Joo-Hang Kim, Yoon-Koo Kang and Byoung Chul Cho,
    Next-generation sequencing reveals somatic mutations that confer exceptional response to everolimus,
    Oncotarget 2016, 7(9), 10547-56



  61. In Seok Yang and Sangwoo Kim*,
    Analysis of Whole Transcriptome Sequencing Data: Workflow and Software,
    Genomics & Informatics 2015, 13(4) 119-125


  62. Seung Tae Baek, Brett Copeland, Eun-jin Yun, Seok-Kyu Kwon, Alicia, Guemez-Gamboa, Sangwoo Kim, Hoon-Chul Kang, Saera Song, Gary Mathern and Joseph G. Gleeson
    An AKT-FOXG1-Reelin Network Underlies Defective Migration in Human Focal Malformations of Cortical Development,
    Nature Medicine 2015, 1445-1454


  63. Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim* and Doheon Lee*,
    SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data,
    Bioinformatics 2015, 31(19) 3105-3113


  64. Seyeol Yoon, Junmyung Jung, Hasun Yu, Mijin Kwon, Sungji Choo, Kyunghyun Park, Dongjin Jang, Sangwoo Kim* and Doheon Lee*, Context-based resolution of semantic conflicts in biological pathways,
    BMC Medical Informatics an
    d Decision Making 2015, 15(Suppl 1):S3


  65. Seunghwan Jung, Sejoon Lee, Sangwoo Kim and Hojung Nam*, 
    Identification of Genomic Features in the Classification of Loss- and Gain-of-Function Mutation,
    BMC Medical Informatics and Decision Making 2015, 15(Suppl 1):S6


  66. Jae Seok Lim, Woo-il Kim, Hoon-Chul Kang, Se Hoon Kim, Ah Hyung Park, Eun Kyung Park, Young-Wook Cho, Sangwoo Kim, Ho Min Kim, Jeong A Kim, Junho Kim, Hwanseok Rhee, Seok-Gu Kang, Heung Dong Kim, Daesoo Kim, Dong-Seok Kim* & Jeong Ho Lee*, 
    Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy
    Nature Medicine 2015, 21 395-400



  67. Hojung Nam*, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Bernhard O. Palsson*,
    A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks
    PLoS Computational Biology 2014, 10(9): e1003837.



  68. Sangwoo Kim†*, Kyowon Jeong†, Kunal Bhutani, Jeong Ho Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G. Gleeson and Vineet Bafna*,
    Virmid: accurate detection of somatic mutations with sample impurity inference, 
    Genome Biology
     2013, 14:R90
    -  Software available at 
    SourceForge Site
    -  Media covered in BRIC (한빛사)


  69. Sangwoo Kim*, Paul Medvedev, Tara A. Paton and Vineet Bafna*,
    REPREVER: Resolving low-copy duplicated sequences using template driven assembly, 
    Nucleic Acids Research
     2013, 41(12):e128
    -  S
    oftware available at SourceForge Site


  70. Sangwoo Kim*, Kyowon Jeong and Vineet Bafna*,
    Wessim: A whole exome sequencing simulator based on in silico exome capture
    Bioinformatics 2013, 29(8) pp.1076~1077.
    Software available at GitHub Site


  71. Christine Lo*, Sangwoo Kim, Shay Zakov and Vineet Bafna,
    Evaluating genome architecture of a complex region via generalized bipartite matching
    BMC Bioinformatics 2013, 14(Suppl 5):S13.

    ~ 2012:


  72. Jeong Ho Lee, Jennifer L. Sillhavy, My Huynh, Sangwoo Kim, Tracy Dixon-Salazar, Andrew Heiberg, Eric Scott, Vineet Bafna, Kiley J. Hill, Adrienne Collazo, Vincent Funary, Carsten Russ, Stacey B. Gabriel, Gary W. Mathern*, Joseph G. Gleeson*,
    De novo somatic mutations of the PI3K-AKT3-mTOR pathway in hemimegalencephaly, 
    Nature Genetics 2012, 44(8), 941-945.


  73. Sangwoo Kim, Hojung Nam and Doheon Lee*,
    Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer
    BMC Systems Biology 2011, 5(Suppl 2):S4


  74. Sohyun Hwang, Sangwoo Kim, Heesung Shin and Doheon Lee*,
    Context-dependent transcriptional regulations between signal transduction pathways
    BMC Bioinformatics 2011, 12:19


  75. Sangwoo Kim and Doheon Lee*,
    Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases
    BMC Bioinformatics 2009, 10(Suppl 3):S2


  76. Hojung nam, Taewoo Ryu, KiYoung Lee, Sangwoo Kim, and Doheon Lee*,
    Computational Identification of Significantly Regulated Metabolic Reactions by Integration of Data on Enzyme Activity and Gene Expression
    Biochemistry and Molecular Biology reports, 2008.08.31; 41(8) pp. 609~614


  77. Doheon Lee*, Sangwoo Kim and Younghoon Kim,
    BioCAD: an information fusion platform for bio-network inference and analysis
    BMC Bioinformatics 2007,8(Suppl 9):S2

Conference Proceedings and Presentations (peer reviewed)

  1. Junehawk Lee, Junho Kim, Minho Lee and Sangwoo Kim*, Machine learning based genetic variant filtration for detecting low-frequency somatic mutations, The 15th European Conference on Computational Biology (ECCB 2016), Hague, Netherlands, Sep 3-7, 2016 (poster)

  2. Hyeonju Son and Sangwoo Kim*, Significant mutation bias events of cancer mutations, The 10th International Workshops on Biomedical Informatics (DTMBIO 16), Indianapolis, IN, USA, Oct 28, 2016 (poster)

  3. Sun Min Lim* , Hyung Soon Park*, Sora Kim, Nak-Jung Kwon, Jae-Lyun Lee, Min-Hee Ryu, Jin-Hee Ahn, Jeeyun Lee, Hyo Song Kim, Hyun Ki Kim, Hye Ryun Kim, Hyun Cheol Chung, Joo-Hang Kim, Sangwoo Kim, Yoon-Koo Kang, Byoung Chul Cho, Next-generation sequencing reveals somatic mutations that confer sensitivity to everolimus, American Society of Clinical Oncology, Chicago, 2015 

  4. Jinmyung Jung, Hasun Yu, Seyeol Yoon, Mijin Kwon, Sungji Choo, Sangwoo Kim* and Doheon Lee*, Construction of Multi-level Networks Incorporating Molecule, Cell, Organ and Phenotype Properties for Drug-induced Phenotype Prediction, Proceedings of the 8th International Workshop on Data and Text Mining in Biomedical Informatics p.47

  5. Seyeol Yoon, Junmyung Jung, Hasun Yu, Mijin Kwon, Sungji Choo, Kyunghyun Park, Dongjin Jang, Sangwoo Kim* and Doheon Lee*, Systematic Identification of Context-Dependent Conflicting Information in Biological Pathways, Data and Text Mining in Bioinformatics, Shanghai, China, Nov 7, 2014

  6. J. S. Lim, W. I. Kim, H. C. Kang, S. H. Kim, A. H. Park, Sangwoo Kim, D. Kim4 D. S. Kim, J. H. Lee, Brain somatic mutations cause focal cortical dysplasia typeII in human and mouse, Americal Society of Human Genetics 2014, San Diego, Oct 18-22, 2014

  7. Sangwoo Kim and Vineet Bafna, Computational identification of genomic repetitive sequences and its applications, KSEA US-Korea Conference (UKC 2013), New Jersey, Aug 08-10, 2013

  8. Sangwoo Kim†, Kyowon Jeong†, Kunal Bhutani†, Hayan Lee, and Vineet Bafna, Computational Identification of Within Individual Contamination for Higher Sensitivity in Somatic Mutation Profiling, Conference on High Throughput Sequencing Methods and Applications (ISMB-HiTSeq 2012), Long Beach, Jul 13-14 2012.

  9. Sangwoo Kim, Paul Medvedev and Vineet Bafna, Systematic Identification of Interspersed Duplication using Paired End Sequencing, The 2nd RECOMB Satellite Workshop On Massively Parallel Sequencing (RECOMB-seq), Barcelona, Spain, Apr 19-20, 2012

  10. Sangwoo Kim, Hojung Nam and Doheon Lee, Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer, The 22nd international Conference on Genome Informatics, Busan, Dec 5-7, 2011

  11. Sangwoo Kim, Paul Medvedev and Vineet Bafna, Systematic Identification of Interspersed Duplication using Paired End Sequencing, the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor, NY, Nov 2-5, 2011

  12. Sangwoo Kim and Doheon Lee, Mining metastasis related genes by primary-secondary tumor comparisons from large-scale database, the 2nd International Workshop on Data and Text Mining in Bioinformatics in conjunction with CIKM (DTMBio 2008), Napa Valley (USA) October 2008

  13. Sungwon Jung, Hyun Chul Jung, Nam Jin Koo, Sangwoo Kim, Kwang H. Lee and Doheon Lee, Bio-Network Reverse Engineering Platform with Loosely Coupled Architecture, the 8th International Conference of Korean Society for Bioinformatics, p.68-73 Daejeon (Korea) November 2007

  14. Sangwoo Kim, Sungwon Jung, Nam Jin Koo, Hyun Chul Jung, Kwang H. Lee and Doheon Lee, Integration of heterogeneous biological data in syntactic and semantic way, the 8th International Symposium on Advanced Intelligent Systems (ISIS2007), Sokcho (Korea) September 2007

  15. Sungwon Jung, Sangwoo Kim and Doheon Lee Loosely Coupled Architecture for Bio-Network Reverse Engineering, the International Symposium on Optimization and Systems Biology, Beijing (China) August 2007

  16. Doheon Lee, Sangwoo Kim and Younghoon Kim, BioCAD: an information fusion platform for bio-network inference and analysis, the 1st international workshop on Text mining in bioinformatics (TMBio2006), Arlington, VA (USA), November 2006

  17. Sangwoo Kim, Kiryong Ha, and Doheon Lee, BioCAD: Web service based integration system for inferring genetic regulatory circuits, the 7th International conference on Systems Biology (ISCB2006), Yokohama (Japan), October 2006

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