Journal Publications (peer reviewed) / Book chapter

 

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

      2019:

  1. 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 (accepted for publication)

     

  2. 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
     

  3. 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

     

  4. 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

     

  5. Hein Chun and Sangwoo Kim*
    BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort
    Bioinformatics 2019 (Epub ahead of print)

     

  6. 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

     

  7. 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)
     

  8. 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 

     

  9. 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)

     

  10.  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

    2018:
     

  11. 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

     

  12. 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 https://sourceforge.net/projects/airvf/
     

  13. 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

     

  14. 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

     

  15. 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 https://sourceforge.net/projects/neopepsee/

    - 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.

     

  16. 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

    2017:
     

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

     

  18. 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

     

  19. 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

     

  20. 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

    2016:
     

  21. 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 http://wiki.tgilab.org/isoexpresso/

     

  22. 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 https://sourceforge.net/projects/vecuum/
    - 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.

     

  23. 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

     

  24. 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

     

  25. 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

     

  26. 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


    2015:
     

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

  28. 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

     

  29. 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

     

  30. 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 and Decision Making 2015, 15(Suppl 1):S3

     

  31. 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

     

  32. 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


    2014:
     

  33. 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.


    2013:
     

  34. 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)

     

  35. 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
     

  36. 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
     

  37. 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:
     

  38. 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.

     

  39. 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

     

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

     

  41. 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

     

  42. 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

     

  43. 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

서울특별시 서대문구 연세로 50, 연세대학교 의과대학 신관 613호

#613 Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea  

+82-2-2228-2589

02-2228-2589 (inside Korea)

  • w-facebook
  • Twitter Clean
  • w-googleplus
  • W-Pinterest

© 2014 By Translation Genome Informatics Laboratory, Yonsei University College of Medicine. Proudly created with Wix.com