Last modified at
Last modified at 2024-03-12T15:33:57+09:00
Co-first authors†Co-corresponding authors*
2024
Kim H†, Jang J†, Choi JH†, Song JH†, Lee SH, Park J, Ryoo SK, Lee EM, Jeong HO, Kim S, Lee SH, Lee KH, Lee KT, Kim KM, Jang KT, Lee H*, Lee S*, Lee JK*, Park JK*. Establishment of a patient-specific avatar organoid model derived from endoscopic ultrasonography-guided fine needle biopsy for timely clinical application in pancreatic ductal adenocarcinoma. Gastrointest Endosc. 2024 Mar 4:S0016-5107(24)00132-9. doi: 10.1016/j.gie.2024.02.021.
2023
Yang HW, Lee S, Berry BC, Yang D, Zheng S, Carroll RS, Park PJ, Johnson MD. A role for mutations in AK9 and other genes affecting ependymal cells in idiopathic normal pressure hydrocephalus. Proc Natl Acad Sci U S A. 2023 Dec 19;120(51):e2300681120. doi: 10.1073/pnas.2300681120. Epub 2023 Dec 15. PMID: 38100419.
Hong YM†, Lee J†, Cho DH†, Jeon JH, Kang J†, Kim MG†*, Lee S†*, Kim JK†*. Predicting preterm birth using machine learning techniques in oral microbiome. Scientific Reports. 2023 Nov 30;13(1):21105. doi: 10.1038/s41598-023-48466-x. PMID: 38036587. PMCID: PMC10689490
Jang J†, Kim H†, Park SS†, Kim M†, Min YK, Jeong HO, Kim S, Hwang T, Choi DW, Kim, HJ, Song S, Kim DO, Lee S*, Lee CH*, Lee JW*, 2023. Single-cell RNA Sequencing Reveals Novel Cellular Factors for Response to Immunosuppressive Therapy in Aplastic Anemia. HemaSphere, 2023 Oct 28. doi: 10.1097/HS9.0000000000000977. PMID: 37908861. PMCID: PMC10615405
Kim JY†, Park S†, Cho EY†, Lee JE†, Jung HH, Chae BJ, Kim SW, Nam SJ, Cho SY, Park YH, Ahn JS, Lee S*, Im YH*. Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer. Exp Mol Med. 2023 Jul 3. doi: 10.1038/s12276-023-01030-z. PMID: 37394589.
Ivanov D, Hwang T, Sitko LK, Lee S, Gartner A. Experimental systems for the analysis of mutational signatures: no 'one-size-fits-all' solution. Biochem Soc Trans. 2023 Jun 28;51(3):1307-1317. doi: 10.1042/BST20221482. PMID: 37283472; PMCID: PMC10317150.
Lim JH†, Lee S†, Ryu JS. Prediction of Treatment Response to Chemoimmunotherapy: Concerted Effort Needed. J Thorac Oncol. 2023 Jun;18(6):682-685. doi: 10.1016/j.jtho.2023.03.005. PMID: 37210177.
Shin U†, Choi Y†, Ko HS, Myung K, Lee S*, Cheon CK*, Lee Y*. A heterozygous mutation in UBE2H in a patient with developmental delay leads to an aberrant brain development in zebrafish. Hum Genomics. 2023 May 19;17(1):44. doi: 10.1186/s40246-023-00491-7. PMID: 37208785; PMCID: PMC10199504.
Lee YJ, Shin KJ, Jang HJ, Ryu JS, Lee CY, Yoon JH, Seo JK, Park S, Lee S, Je AR, Huh YH, Kong SY, Kwon T, Suh PG, Chae YC. GPR143 controls ESCRT-dependent exosome biogenesis and promotes cancer metastasis. Dev Cell. 2023 Feb 27;58(4):320-334.e8. doi: 10.1016/j.devcel.2023.01.006. Epub 2023 Feb 16. PMID: 36800996.
Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S; Focal Cortical Dysplasia Neurogenetics Consortium; Brain Somatic Mosaicism Network (Lee S); Gleeson JG. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet. 2023 Feb;55(2):209-220. doi: 10.1038/s41588-022-01276-9. Epub 2023 Jan 12. PMID: 36635388; PMCID: PMC9961399.
Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL; NIMH Brain Somatic Mosaicism Network (Lee S); Gleeson JG. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol. 2023 Jun;41(6):870-877. doi: 10.1038/s41587-022-01559-w. Epub 2023 Jan 2. PMID: 36593400; PMCID: PMC10314968.
Lee K†, Cho D†, Jang J†, Choi K, Jeong HO, Seo J*, Jeong WK*, Lee S*. RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction. Brief Bioinform. 2023 Jan 19;24(1):bbac504. doi: 10.1093/bib/bbac504. PMID: 36460623.
2022
Jeong HO†, Lee H†, Kim H†, Jang J, Kim S, Hwang T, Choi DW, Kim HS, Lee N, Lee YM, Park S, Jung HA, Sun JM, Ahn JS, Ahn MJ, Park K, Lee S*, Lee SH*. Cellular plasticity and immune microenvironment of malignant pleural effusion are associated with EGFR-TKI resistance in non-small-cell lung carcinoma. iScience. 2022 Oct 13;25(11):105358. doi: 10.1016/j.isci.2022.105358. PMID: 36339256; PMCID: PMC9626676.
Yoon M†, Lee HK†, Park EY, Kim JH, Lee JH, Kim YS, Kim HJ, Kim H, Yoo CW, Lee S, Hong EK, Kim TH, Kim TS, Seo SS, Kang S, Chang SJ, Shin HJ, Uong TNT, Lee S*, Kim JY*. Randomized multicenter phase II trial of prophylactic irradiation of para-aortic lymph nodes in advanced cervical cancer according to tumor hypoxia: Korean Radiation Oncology Group (KROG 07-01) study. Int J Cancer. 2022 Dec 15;151(12):2182-2194. doi: 10.1002/ijc.34190. Epub 2022 Jul 11. PMID: 35751421.
Ju MK†, Lee JR†, Choi Y†, Park SY†, Sul HJ†, Chung HJ, An S, Lee S, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y*, Kim H*, Zang DY*. PWWP2B promotes DNA end resection and homologous recombination. EMBO Rep. 2022 Jul 5;23(7):e53492. doi: 10.15252/embr.202153492. Epub 2022 May 18. PMID: 35582821; PMCID: PMC9253748.
Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y; NIMH Brain Somatic Mosaicism Network (Lee S); Glass CK, Gleeson JG. Somatic mosaicism reveals clonal distributions of neocortical development. Nature. 2022 Apr;604(7907):689-696. doi: 10.1038/s41586-022-04602-7. Epub 2022 Apr 20. PMID: 35444276; PMCID: PMC9436791.
Li J, Lu H, Ng PK, Pantazi A, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric- Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. A functional genomic approach to actionable gene fusions for precision oncology. Sci Adv. 2022 Feb 11;8(6):eabm2382. doi: 10.1126/sciadv.abm2382. Epub 2022 Feb 9. PMID: 35138907; PMCID: PMC8827659.
Her AY, Bhak Y, Jun EJ, Yuan SL, Garg S, Lee S, Bhak J, Shin ES. Sex-specific difference of in-hospital mortality from COVID-19 in South Korea. PLoS One. 2022 Jan 24;17(1):e0262861. doi: 10.1371/journal.pone.0262861. PMID: 35073365; PMCID: PMC8786158.
Kee KM, Kim SH, Yang SY, Shin JU, Nam YW, Jang EJ, Kim HT, Lee SM, Park SH, Kim DW. Comparison of 3-month cytogenetic and molecular assays for early assessment of long-term clinical impact after BCR-ABL1 tyrosine kinase inhibitor treatment in chronic myeloid leukemia. Leuk Res. 2022 Jan;112:106754. doi: 10.1016/j.leukres.2021.106754. Epub 2021 Nov 22. PMID: 34906861.
2021
Lim M, Park S, Jeong HO, Park SH, Kumar S, Jang A, Lee S, Kim DU, Cho YK. Circulating Tumor Cell Clusters Are Cloaked with Platelets and Correlate with Poor Prognosis in Unresectable Pancreatic Cancer. Cancers (Basel). 2021 Oct 20;13(21):5272. doi: 10.3390/cancers13215272. PMID: 34771436; PMCID: PMC8582483.
Lee E†, Park S†, Um S, Kim S, Lee J, Jang J, Jeong HO, Shin J, Kang J, Lee S*, Jeong T*. Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience. Diagnostics (Basel). 2021 Jul 23;11(8):1324. doi: 10.3390/diagnostics11081324. PMID: 34441259; PMCID: PMC8393408.
Kim M†, Min YK†, Jang J†, Park H, Lee S*, Lee CH*. Single-cell RNA sequencing reveals distinct cellular factors for response to immunotherapy targeting CD73 and PD-1 in colorectal cancer. J Immunother Cancer. 2021 Jul;9(7):e002503. doi: 10.1136/jitc-2021-002503. PMID: 34253638; PMCID: PMC8276303.
Park J, Yeu SY, Paik S, Kim H, Choi SY, Lee J, Jang J, Lee S, Koh Y, Lee H. Loss of BubR1 acetylation provokes replication stress and leads to complex chromosomal rearrangements. FEBS J. 2021 Oct;288(20):5925-5942. doi: 10.1111/febs.15912. Epub 2021 May 21. PMID: 33955658.
Her AY, Bhak Y, Jun EJ, Yuan SL, Garg S, Lee S, Bhak J, Shin ES. A Clinical Risk Score to Predict In-hospital Mortality from COVID-19 in South Korea. J Korean Med Sci. 2021 Apr 19;36(15):e108. doi: 10.3346/jkms.2021.36.e108. PMID: 33876588; PMCID: PMC8055508.
Jeon Y, Jeon S, Blazyte A, Kim YJ, Lee JJ, Bhak Y, Cho YS, Park Y, Noh EK, Manica A, Edwards JS, Bolser D, Kim S, Lee Y, Yoon C, Lee S, Kim BC, Park NH, Bhak J. Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling. Front Genet. 2021 Feb 9;12:633731. doi: 10.3389/fgene.2021.633731. PMID: 33633791; PMCID: PMC7900555.
Bhak Y, Jeon Y, Jeon S, Yoon C, Kim M, Blazyte A, Kim Y, Kang Y, Kim C, Lee SY, Bae JW, Kim W, Kim YJ, Shim J, Kim N, Chun S, Kim BC, Kim BC, Lee S, Bhak J, Shin ES. Polygenic risk score validation using Korean genomes of 265 early-onset acute myocardial infarction patients and 636 healthy controls. PLoS One. 2021 Feb 4;16(2):e0246538. doi: 10.1371/journal.pone.0246538. PMID: 33539413; PMCID: PMC7861392.
Yang HW, Lee S, Yang D, Dai H, Zhang Y, Han L, Zhao S, Zhang S, Ma Y, Johnson MF, Rattray AK, Johnson TA, Wang G, Zheng S, Carroll RS, Park PJ, Johnson MD. Deletions in CWH43 cause idiopathic normal pressure hydrocephalus. EMBO Mol Med. 2021 Mar 5;13(3):e13249. doi: 10.15252/emmm.202013249. Epub 2021 Jan 18. PMID: 33459505; PMCID: PMC7933959.
2020
Kim JY†, Jeong HO†, Heo DS, Keam B, Moon KC, Kwak C, Jang J, Kim S, Kim JI, Lee S*, Lee SH*. Treatment strategy for papillary renal cell carcinoma type 2: a case series of seven patients treated based on next generation sequencing data. Ann Transl Med. 2020 Nov;8(21):1389. doi: 10.21037/atm-20-3466. PMID: 33313134; PMCID: PMC7723617.
Kim EH†, Kim S†, Kim HJ†, Jeong HO, Lee J, Jang J, Joo JY, Shin Y, Kang J, Park AK, Lee JY*, Lee S*. Prediction of Chronic Periodontitis Severity Using Machine Learning Models Based On Salivary Bacterial Copy Number. Front Cell Infect Microbiol. 2020 Nov 16;10:571515. doi: 10.3389/fcimb.2020.571515. PMID: 33304856; PMCID: PMC7701273.
Cheon CK, Lee YJ, Yoo S, Lee JH, Lee JE, Kim HJ, Choi IJ, Choi Y, Lee S, Yoon JY. Delineation of the genetic and clinical spectrum, including candidate genes, of monogenic diabetes: a multicenter study in South Korea. J Pediatr Endocrinol Metab. 2020 Oct 8;33(12):1539-1550. doi: 10.1515/jpem-2020-0336. PMID: 33031055.
Hwang T, Reh S, Dunbayev Y, Zhong Y, Takata Y, Shen J, McBride KM, Murnane JP, Bhak J, Lee S, Wood RD, Takata KI. Defining the mutation signatures of DNA polymerase θ in cancer genomes. NAR Cancer. 2020 Sep;2(3):zcaa017. doi: 10.1093/narcan/zcaa017. Epub 2020 Aug 27. PMID: 32885167; PMCID: PMC7454005.
Jeon S†, Bhak Y†, Choi Y†, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G*, Lee S*, Bhak J*. Korean Genome Project: 1094 Korean personal genomes with clinical information. Sci Adv. 2020 May 27;6(22):eaaz7835. doi: 10.1126/sciadv.aaz7835. PMID: 32766443; PMCID: PMC7385432.
Weber JA, Park SG, Luria V, Jeon S, Kim HM, Jeon Y, Bhak Y, Jun JH, Kim SW, Hong WH, Lee S, Cho YS, Karger A, Cain JW, Manica A, Kim S, Kim JH, Edwards JS, Bhak J, Church GM. The whale shark genome reveals how genomic and physiological properties scale with body size. Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20662-20671. doi: 10.1073/pnas.1922576117. Epub 2020 Aug 4. PMID: 32753383; PMCID: PMC7456109.
Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res. 2020 Jul 27;48(13):7218-7238. doi: 10.1093/nar/gkaa501. PMID: 32542338; PMCID: PMC7367208.
Choi SS, Lee SK, Kim JK, Park HK, Lee E, Jang J, Lee YH, Khim KW, Hyun JM, Eom HJ, Lee S, Kang BH, Chae YC, Myung K, Myung SJ, Park CY, Choi JH. Flightless-1 inhibits ER stress-induced apoptosis in colorectal cancer cells by regulating Ca2+ homeostasis. Exp Mol Med. 2020 Jun;52(6):940-950. doi: 10.1038/s12276-020-0448-3. Epub 2020 Jun 5. PMID: 32504039; PMCID: PMC7338537.
Lim M, Park J, Lowe AC, Jeong HO, Lee S, Park HC, Lee K, Kim GH, Kim MH, Cho YK. A lab-on-a-disc platform enables serial monitoring of individual CTCs associated with tumor progression during EGFR-targeted therapy for patients with NSCLC. Theranostics. 2020 Apr 6;10(12):5181-5194. doi: 10.7150/thno.44693. PMID: 32373206; PMCID: PMC7196290.
Seidualy M, Blazyte A, Jeon S, Bhak Y, Jeon Y, Kim J, Eriksson A, Bolser D, Yoon C, Manica A, Lee S, Bhak J. Decoding a highly mixed Kazakh genome. Hum Genet. 2020 May;139(5):557-568. doi: 10.1007/s00439-020-02132-8. Epub 2020 Feb 19. PMID: 32076829; PMCID: PMC7170836.
Lee YG, Nam Y, Shin KJ, Yoon S, Park WS, Joung JY, Seo JK, Jang J, Lee S, Nam D, Caino MC, Suh PG, Chan Chae Y. Androgen-induced expression of DRP1 regulates mitochondrial metabolic reprogramming in prostate cancer. Cancer Lett. 2020 Feb 28;471:72-87. doi: 10.1016/j.canlet.2019.12.017. Epub 2019 Dec 12. PMID: 31838085.
2019
Kim HS†, Jeon S†, Kim C, Kim YK, Cho YS, Kim J, Blazyte A, Manica A, Lee S*, Bhak J*. Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. Gigascience. 2019 Dec 1;8(12):giz125. doi: 10.1093/gigascience/giz125. PMID: 31794015; PMCID: PMC6889754.
Lee K†, Jeong HO†, Lee S*, Jeong WK*. CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network. Sci Rep. 2019 Nov 15;9(1):16927. doi: 10.1038/s41598-019-53034-3. PMID: 31729414; PMCID: PMC6858312.
Bhak Y†, Jeong HO†, Cho YS, Jeon S, Cho J, Gim JA, Jeon Y, Blazyte A, Park SG, Kim HM, Shin ES, Paik JW, Lee HW, Kang W, Kim A, Kim Y, Kim BC, Ham BJ, Bhak J*, Lee S*. Depression and suicide risk prediction models using blood-derived multi- omics data. Transl Psychiatry. 2019 Oct 17;9(1):262. doi: 10.1038/s41398-019-0595-2. PMID: 31624227; PMCID: PMC6797735.
Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 Oct 15;20(1):209. doi: 10.1186/s13059-019-1818-9. PMID: 31610796; PMCID: PMC6792267.
Yang L, Wang S, Lee JJ, Lee S, Lee E, Shinbrot E, Wheeler DA, Kucherlapati R, Park PJ. An enhanced genetic model of colorectal cancer progression history. Genome Biol. 2019 Aug 15;20(1):168. doi: 10.1186/s13059-019-1782-4. PMID: 31416464; PMCID: PMC6694562.
2018
Park JE†, Jang J†, Lee EJ, Kim SJ, Yoo HJ, Lee S*, Kang MJ*. Potential involvement of Drosophila flightless-1 in carbohydrate metabolism. BMB Rep. 2018 Sep;51(9):462-467. doi: 10.5483/BMBRep.2018.51.9.153. PMID: 30060781; PMCID: PMC6177503.
Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJ. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 Jul 10;24(2):515-527. doi: 10.1016/j.celrep.2018.06.025. PMID: 29996110; PMCID: PMC6092947.
Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Res. 2018 Aug;28(8):1217-1227. doi: 10.1101/gr.228080.117. Epub 2018 Jun 13. PMID: 29898899; PMCID: PMC6071640.
Phi JH†, Park AK†, Lee S†, Choi SA, Baek IP, Kim P, Kim EH, Park HC, Kim BC, Bhak J, Park SH, Lee JY, Wang KC, Kim DS, Shim KW, Kim SH, Kim CY, Kim SK. Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas. Acta Neuropathol. 2018 Jun;135(6):939-953. doi: 10.1007/s00401-018-1845-8. Epub 2018 Apr 11. PMID: 29644394.
Kim J, Weber JA, Jho S, Jang J, Jun J, Cho YS, Kim HM, Kim H, Kim Y, Chung O, Kim CG, Lee H, Kim BC, Han K, Koh I, Chae KS, Lee S, Edwards JS, Bhak J. KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses. Sci Rep. 2018 Apr 4;8(1):5677. doi: 10.1038/s41598-018-23837-x. PMID: 29618732; PMCID: PMC5885007.
2017
Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J. Corrigendum: An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nat Commun. 2017 Oct 9;8:16168. doi: 10.1038/ncomms16168. Erratum for: Nat Commun. 2016 Nov 24;7:13637. PMID: 28991236; PMCID: PMC5635174.
Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network (Lee S); Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. Erratum in: Cancer Cell. 2018 Jan 8;33(1):151. PMID: 28810145; PMCID: PMC5619925.
Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 Jun 12;31(6):820-832.e3. doi: 10.1016/j.ccell.2017.04.013. Epub 2017 May 18. PMID: 28528867; PMCID: PMC5502825.
Cancer Genome Atlas Research Network (Lee S). Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384. doi: 10.1038/nature21386. Epub 2017 Jan 23. PMID: 28112728; PMCID: PMC5354998.
Cancer Genome Atlas Research Network (Lee S). Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175. doi: 10.1038/nature20805. Epub 2017 Jan 4. PMID: 28052061; PMCID: PMC5651175.
2016
Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, ,Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nat Commun. 2016 Nov 24;7:13637. doi: 10.1038/ncomms13637. Erratum in: Nat Commun. 2017 Oct 09;8:16168. PMID: 27882922; PMCID: PMC5123046.
Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, An J, Bae CH, Bhak Y, Jeon S, Yoon H, Kim Y, Jun J, Lee H, Cho S, Uphyrkina O, Kostyria A, Goodrich J, Miquelle D, Roelke M, Lewis J, Yurchenko A, Bankevich A, Cho J, Lee S, Edwards JS, Weber JA, Cook J, Kim S, Lee H, Manica A, Lee I, O'Brien SJ, Bhak J, Yeo JH. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome Biol. 2016 Oct 11;17(1):211. doi: 10.1186/s13059-016-1071-4. PMID: 27802837; PMCID: PMC5090899.
Xi R, Lee S, Xia Y, Kim TM, Park PJ. Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res. 2016 Jul 27;44(13):6274-86. doi: 10.1093/nar/gkw491. Epub 2016 Jun 3. PMID: 27260798; PMCID: PMC5772337.
Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network (Lee S); Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28;164(3):550-63. doi: 10.1016/j.cell.2015.12.028. PMID: 26824661; PMCID: PMC4754110.
Nam JY, Kim NK, Kim SC, Joung JG, Xi R, Lee S, Park PJ, Park WY. Evaluation of somatic copy number estimation tools for whole-exome sequencing data. Brief Bioinform. 2016 Mar;17(2):185-92. doi: 10.1093/bib/bbv055. Epub 2015 Jul 25. PMID: 26210357; PMCID: PMC6283367.
2015
De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQ. Corrigendum: Failure to replicate the STAP cell phenomenon. Nature. 2016 Mar 17;531(7594):400. doi: 10.1038/nature16479. Epub 2015 Dec 16. Erratum for: Nature. 2015 Sep 24;525(7570):E6-9. PMID: 26675720.
Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001. PMID: 26647970; PMCID: PMC4682041.
Cancer Genome Atlas Research Network (Lee S). The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025. PMID: 26544944; PMCID: PMC4695400.
Lodato MA†, Woodworth MB†, Lee S†, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ*, Walsh CA*. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 2;350(6256):94-98. doi: 10.1126/science.aab1785. PMID: 26430121; PMCID: PMC4664477.
De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQ. Failure to replicate the STAP cell phenomenon. Nature. 2015 Sep 24;525(7570):E6-9. doi: 10.1038/nature15513. Erratum in: Nature. 2016 Mar 17;531(7594):400. PMID: 26399835.
Cancer Genome Atlas Network (Lee S). Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. doi: 10.1016/j.cell.2015.05.044. PMID: 26091043; PMCID: PMC4580370.
Cancer Genome Atlas Research Network (Lee S). Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10. PMID: 26061751; PMCID: PMC4530011.
Kapanidou M, Lee S, Bolanos-Garcia VM. BubR1 kinase: protection against aneuploidy and premature aging. Trends Mol Med. 2015 Jun;21(6):364-72. doi: 10.1016/j.molmed.2015.04.003. Epub 2015 May 8. PMID: 25964054.
Cancer Genome Atlas Network (Lee S). Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129. PMID: 25631445; PMCID: PMC4311405.
2014
Cancer Genome Atlas Research Network (Lee S). Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050. PMID: 25417114; PMCID: PMC4243044.
Lee S, Bolanos-Garcia VM. The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation. Front Physiol. 2014 Sep 29;5:368. doi: 10.3389/fphys.2014.00368. PMID: 25324779; PMCID: PMC4179342.
Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13. PMID: 25313082; PMCID: PMC4217452.
Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network (Lee S); Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21. PMID: 25155756; PMCID: PMC4160352.
Cancer Genome Atlas Research Network (Lee S). Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. Erratum in: Nature. 2014 Oct 9;514(7521):262. Rogers, K [corrected to Rodgers, K]. Erratum in: Nature. 2018 Jul;559(7715):E12. PMID: 25079552; PMCID: PMC4231481.
Cancer Genome Atlas Research Network (Lee S). Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. doi: 10.1038/nature13480. Epub 2014 Jul 23. PMID: 25079317; PMCID: PMC4170219.
Cancer Genome Atlas Research Network (Lee S). Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-22. doi: 10.1038/nature12965. Epub 2014 Jan 29. PMID: 24476821; PMCID: PMC3962515.
2013
Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network (Lee S). The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Erratum in: Cell. 2014 Apr 24;157(3):753. PMID: 24120142; PMCID: PMC3910500.
Cancer Genome Atlas Research Network (Lee S); Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. PMID: 24071849; PMCID: PMC3919969.
Cancer Genome Atlas Research Network (Lee S); Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113. Erratum in: Nature. 2013 Aug 8;500(7461):242. PMID: 23636398; PMCID: PMC3704730.
2012
Xi R, Lee S, Park PJ. A survey of copy-number variation detection tools based on high-throughput sequencing data. Curr Protoc Hum Genet. 2012 Oct;Chapter 7:Unit7.19. doi: 10.1002/0471142905.hg0719s75. PMID: 23074071.
Cancer Genome Atlas Research Network (Lee S). Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404. Epub 2012 Sep 9. Erratum in: Nature. 2012 Nov 8;491(7423):288. Rogers, Kristen [corrected to Rodgers, Kristen]. PMID: 22960745; PMCID: PMC3466113.
Cancer Genome Atlas Network (Lee S). Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. PMID: 22810696; PMCID: PMC3401966.
2011
Lee S, Thebault P, Freschi L, Beaufils S, Blundell TL, Landry CR, Bolanos- Garcia VM, Elowe S. Characterization of spindle checkpoint kinase Mps1 reveals domain with functional and structural similarities to tetratricopeptide repeat motifs of Bub1 and BubR1 checkpoint kinases. J Biol Chem. 2012 Feb 17;287(8):5988-6001. doi: 10.1074/jbc.M111.307355. Epub 2011 Dec 20. PMID: 22187426; PMCID: PMC3285366.
2009
Lee S†, Brown A†, Pitt WR†, Higueruelo AP, Gong S, Bickerton GR, Schreyer A, Tanramluk D, Baylay A, Blundell TL. Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics. Mol Biosyst. 2009 Dec;5(12):1456-72. doi: 10.1039/B906402h. Epub 2009 Aug 6. PMID: 19763326.
Gong S, Worth CL, Bickerton GR, Lee S, Tanramluk D, Blundell TL. Structural and functional restraints in the evolution of protein families and superfamilies. Biochem Soc Trans. 2009 Aug;37(Pt 4):727-33. doi: 10.1042/BST0370727. PMID: 19614584.
Lee S, Blundell TL. Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinformatics. 2009 Aug 1;25(15):1976-7. doi: 10.1093/bioinformatics/btp300. Epub 2009 May 5. PMID: 19417059; PMCID: PMC2712337.
Lee S, Blundell TL. BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinformatics. 2009 Jun 15;25(12):1559-60. doi: 10.1093/bioinformatics/btp243. Epub 2009 Apr 8. PMID: 19357098.
2007
Worth CL, Bickerton GR, Schreyer A, Forman JR, Cheng TM, Lee S, Gong S, Burke DF, Blundell TL. A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease. J Bioinform Comput Biol. 2007 Dec;5(6):1297-318. doi: 10.1142/s0219720007003120. PMID: 18172930.
2005
Park D†, Lee S†, Bolser D, Schroeder M, Lappe M, Oh D, Bhak J. Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics. 2005 Aug 1;21(15):3234-40. doi: 10.1093/bioinformatics/bti512. Epub 2005 May 24. PMID: 15914543.