PUBLICATIONS

(#: co-first authors; *: (co-)corresponding authors)

2023

Jin X*,Wang Y, Xu J, Li Y, Cheng F, Luo Y, Zhou H, Lin S, Xiao F, Zhang L, Lin Y, Zhang Z, Jin Y, Zheng F, Chen W, Zhu A, Tao Y, Zhao J, Kuo T, Li Y, Li L, Wen L, Ou R, Li F, Lin L, Zhang Y, Sun J, Yuan H, Zhuang Z, Sun H, Chen Z, Li J, Zhuo J, Chen D, Zhang S, Sun Y, Wei P, Yuan J, Xu T, Yang H, Wang J, Xu X, Zhong N, Xu Y*, Sun K*, Zhao J*. Plasma cell-free DNA promise monitoring and tissue injury assessment of COVID-19. Mol Genet Genomics. 2023 Jul; 298(4):823-836. PubMed

An Y, Zhao X, Zhang Z, Xia Z, Yang M, Ma L, Zhao Y, Xu G, Du S, Wu X, Zhang S, Hong X, Jin X*, Sun K*. DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun. 2023 Jan 18; 14(1):287. PubMed

Chen Q, Zeng Y, Kang J, Hu M, Li N,

Sun K

, Zhao Y. Enhancer RNAs in transcriptional regulation: recent insights. Front Cell Dev Biol. 2023 May 17; 11:1205540. PubMed

Du J, Li A, Shi D, Chen X, Wang Q, Liu Z,

Sun K

, Guo T. Association of APOE4, osteoarthritis, β-amyloid, and tau accumulation in primary motor and somatosensory regions in Alzheimer's Disease. Neurology 2023 May 15; 10.1212/WNL.0000000000207369. PubMed

Liu Y, Sun K, Gan Y, Liu H, Yu J, Xu W, Zhang L, Chen D. RNA-sequencing reveals gene expression and pathway signatures in umbilical cord blood affected by birth delivery mode. Phenomics 2023 Apr 8; 3(3):228-242. PubMed

Cai Y, Du J, Li A, Zhu Y, Xu L, Sun K, Ma S, Guo T, Alzheimer's Disease Neuroimaging Initiative. Initial levels of β-amyloid and tau deposition have distinct effects on longitudinal tau accumulation in Alzheimer's disease. Alzheimers Res Ther 2023 Feb 7; 15(1):30. PubMed

2022

Ju J, Sun K*. Plasma cell-free DNA analysis for COVID-19 and beyond. Clin Transl Discov. 2022 Sep; 2(3):e122. PubMed

Li L, An Y, Ma L, Yang M, Yuan P, Liu X, Jin X, Zhao Y, Zhang S*, Hong X*, Sun K*. Msuite2: all-in-one DNA methylation data analysis toolkit with enhanced usability and performance. Comput Struct Biotechnol J. 2022 Mar 10; 20:1271-1276. PubMed

Peng Q, Huang Z,

Sun K

, Liu Y, Yoon CW, Harrison RES, Schmitt DL, Zhu L, Wu Y, Tasan I, Zhao H, Zhang J, Zhong S, Chien S, Wang Y. Engineering inducible biomolecular assemblies for genome imaging and manipulation in live cells. Nat Commun 2022 Dec 24; 13(1):7933. PubMed

Wang Y, Li J, Zhang L, Sun HX, Zhang Z, Xu J, Xu Y, Lin Y, Zhu A, Luo Y, Zhou H, Wu Y, Lin S, Sun Y, Xiao F, Chen R, Wen L, Chen W, Li F, Ou R, Zhang Y, Kuo T, Li Y, Li L, Sun J,

Sun K

, Zhuang Z, Lu H, Chen Z, Mai G, Zhuo J, Qian P, Chen J, Yang H, Wang J, Xu X, Zhong N, Zhao J, Li J, Zhao J, Jin X. Plasma cell-free RNA characteristics in COVID-19 patients. Genome Res. 2022 Feb; 32(2):228-241. PubMed

2021

An Y, Fan F, Jiang X*, Sun K*. Recent advances in liquid biopsy of brain cancers. Front. Genet. 2021 Sep 17; 12:720270. PubMed

Li LS, Guo XY, Sun K*. Recent advances in blood-based and artificial intelligence-enhanced approaches for gastrointestinal cancer diagnosis. World J Gastroenterol 2021 Sep 14; 27(34):5666-5681. PubMed

Sun K

*, Wang H, Sun H*. NAMS webserver: coding potential assessment and functional annotation of plant transcripts. Brief Bioinform 2021 May 20; 22(3):bbaa200. PubMed

Sun K

*, Gu L, Ma L, Duan Y*. Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. Heliyon 2021 Jan; 7(1):e05850. PubMed

Chen X, Wu T, Li L, Lin Y, Ma Z, Xu J, Li H, Cheng F, Chen R, Sun K, Luo Y, Zhang C, Chen F, Wang J, Kuo T, Li X, Geng C, Lin F, Huang C, Hu J, Yin J, Liu M, Tao Y, Zhang J, Ou R, Zheng F, Jin Y, Yang H, Wang J, Xu X, Fu S, Jiang H, Jin X, Zhang H. Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients. Front Genet 2021 May 28; 12:663098. PubMed

2020

Sun K

*, Li L, Ma L, Zhao Y, Deng L, Wang H, Sun H. Msuite: a high-performance and versatile DNA methylation data-analysis toolkit. Patterns (N Y) 2020 Oct 15; 1(8):100127. PubMed

Fan F, Chen D, Zhao Y, Wang H, Sun H, Sun K*. Rapid preliminary purity evaluation of tumor biopsies using deep learning approach. Comput Struct Biotechnol J 2020 Jun 16; 18:1746-1753. PubMed

Sun K

*. Ktrim: an extra-fast and accurate quality- and adapter-trimmer for sequencing data. Bioinformatics 2020 Jun 1; 36(11):3561-3562. PubMed

Jiang P#, Sun K#, Peng W#, Cheng SH, Ni M, Yeung PC, Heung MMS, Xie T, Shang H, Zhou Z, Chan RWY, Wong J, Wong VWS, Poon LC, Leung TY, Lam WKJ, Chan JYK, Chan HLY, Chan KCA, Chiu RWK, Lo YMD. Plasma DNA end motif profiling as a fragmentomic marker in cancer, pregnancy and transplantation. Cancer Discov 2020 May; 10(5):664-673. PubMed

2019

Sun K

*. Clonal hematopoiesis: background player in plasma cell-free DNA variants. Ann Transl Med 2019 Dec; 7(Suppl 8):S384. PubMed

Sun K

*, Jiang P, Cheng SH, Cheng THT, Wong J, Wong VWS, Ng SSM, Ma BBY, Leung TY, Chan SL, Mok TSK, Lai PBS, Chan HLY, Sun H, Chan KCA, Chiu RWK, Lo YMD*. Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin. Genome Res 2019 Mar; 29(3):418-427. PubMed

Gai W, Sun K*. Epigenetic biomarkers in cell-free DNA and applications in liquid biopsy. Genes (Basel) 2019 Jan 9; 10(1):32. PubMed

Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban MA, Sun H, Wang H. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun 2019 Dec 19; 10(1):5787. PubMed

Serpas L, Chan RWY, Jiang P, Ni M, Sun K, Rashidfarrokhi A, Soni C, Sisirak V, Lee WS, Cheng SH, Peng W, Chan KCA, Chiu RWK, Reizis B, Lo YMD. Dnase1l3 deletion causes aberrations in length and end motif frequencies in plasma DNA. Proc Natl Acad Sci U S A 2019 Jan 8; 116(2):641-649. PubMed

2018

Sun K

*, Wang J, Wang H, Sun H*. GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. Bioinformatics 2018 Dec 1; 34(23):4129-4130. PubMed

Jiang P#, Sun K#, Tong YK, Cheng SH, Cheng THT, Heung MMS, Wong J, Wong VWS, Chan HLY, Chan KCA, Lo YMD, Chiu RWK. Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma. Proc Natl Acad Sci U S A 2018 Nov 13; 115(46):E10925-E10933. PubMed

Sun K

, Jiang P, Wong AIC, Cheng YKY, Cheng SH, Zhang H, Chan KCA, Leung TY, Chiu RWK, Lo YMD. Size-tagged preferred ends in maternal plasma DNA shed light on production mechanism and show utility in noninvasive prenatal testing. Proc Natl Acad Sci U S A 2018 May 29; 115(22):E5106-E5114. PubMed

Sun K, Lun FMF, Leung TY, Chiu RWK, Lo YMD, Sun H. Noninvasive reconstruction of placental methylome from maternal plasma DNA: potential for prenatal testing and monitoring. Prenat Diagn 2018 Feb; 38(3):196-203. PubMed Issue cover article

Gai W, Ji L, Lam WKJ, Sun K, Jiang P, Chan AWH, Wong J, Lai PBS, Ng SSM, Ma BBY, Wong GLH, Wong V, Chan HLY, Chiu RWK, Lo YMD, Chan KCA. Liver- and colon-specific DNA methylation markers in plasma for investigation of colorectal cancers with or without liver metastases. Clin Chem 2018 Aug; 64(8):1239-1249. PubMed

2017

Sun K

, Lun FMF, Jiang P, Sun H. BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data. Bioinformatics 2017 Nov 1; 33(21):3495-3496. PubMed

Lam WKJ#, Gai W#, Sun K#, Wong RSM, Chan RWY, Jiang P, Chan NPH, Hui WWI, Chan AWH, Szeto CC, Ng SC, Law MF, Chan KCA, Chiu RWK, Lo YMD. DNA of erythroid origin is present in human plasma and informs the types of anemia. Clin Chem 2017 Oct; 63(10):1614-1623. PubMed

Sun K

, Wang H, Sun H. mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors. Sci Rep 2017 Jun 8; 7(1):3022. PubMed

Sun K, Chan KCA, Hudecova I, Chiu RWK, Lo YMD, Jiang P. COFFEE: control-free noninvasive fetal chromosomal examination using maternal plasma DNA. Prenat Diagn 2017 Apr; 37(4):336-340. PubMed Issue cover article

Certified as "Top Downloaded Article 2017-2018 in Prenatal Diagnosis" by Wiley

An Y*, Wang G*, Diao Y*, Long Y, Fu X, Weng M, Zhou L, Sun K, Cheung TH, Ip NY, Sun H, Wang H, Wu Z. A Molecular Switch Regulating the Cell Fate Choice Between Muscle Progenitor Cells and Brown Adipocytes. Dev Cell 2017 May 22; 41(4):382-391.e5. PubMed

Chen X, He L, Zhao Y, Li Y, Zhang S, Sun K, So K, Chen F, Zhou L, Lu L, Wang L, Zhu X, Bao X, Esteban MA, Nakagawa S, Prasanth KV, Wu Z, Sun H, Wang H. Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity. Cell Discov 2017 Mar 14; 3:17002. PubMed

Jiang P, Tong YK,

Sun K

, Cheng SH, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Gestational age assessment by methylation and size profiling of maternal plasma DNA: a feasibility study. Clin Chem 2017 Feb; 63(2):606-608. PubMed

2016

Chan KCA#, Jiang P#, Sun K#, Cheng YKY, Tong YK, Cheng SH, Wong AIC, Hudecova I, Leung TY, Chiu RWK, Lo YMD. Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance and preferred DNA ends. Proc Natl Acad Sci U S A 2016 Dec 13; 113(50):E8159-8168. PubMed

Sun K

, Zhou L, Zhao Y, Wang H, Sun H. Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis. Genom Data 2016 Feb 2; 7:247-9. PubMed

Wong FCK,

Sun K

, Jiang P, Cheng YKY, Chan KCA, Leung TY, Chiu RWK, Lo YMD. Cell-free DNA in maternal plasma and serum: A comparison of quantity, quality and tissue origin using genomic and epigenomic approaches. Clinical Biochemistry 2016 Dec; 49(18):1379-1386. PubMed

Jiang P*, Peng X*, Su X,

Sun K

, Yu SC, Chu WI, Leung TK, Sun H, Chiu RWK, Lo YMD, Chan KCA. FetalQuant-SD: Accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA. npj Genomic Medicine 2016 May 11; 1:16013. PubMed

2015

Zhou L#, Sun K#, Zhao Y#, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang L, Tang LY, Esteban MA, Wang R, Jauch R, Sun H, Wang H. Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1. Nat Commun 2015 Dec 11; 6:10026. PubMed

Sun K

, Jiang P, Chan KCA. The impact of digital DNA counting technologies on noninvasive prenatal testing. Expert Rev Mol Diagn 2015; 15(10):1261-1268. PubMed

Cheng SH, Jiang P,

Sun K

, Cheng KY, Chan KCA, Leung TK, Chiu RWK, Lo YMD. Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: feasibility assessment. Clin Chem 2015 Oct; 61(10):1305-6. PubMed

Fu X, Xiao J, Wei Y, Li S, Liu Y, Yin J,

Sun K

, Sun H, Wang H, Zhang Z, Zhang BT, Sheng C, Wang H, Hu P. Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. Cell Res 2015 Jun; 25(6):655-73. PubMed

Wang L, Zhao Y, Bao X, Zhu X, Kwok YK, Sun K, Chen X, Huang Y, Jauch R, Esteban MA, Sun H, Wang H. LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res 2015 Mar; 25(3):335-50. PubMed

Li L, Zhang Y, Fan Y, Sun K, Su X, Du Z, Tsao SW, Loh TK, Sun H, Chan AT, Zeng YX, Chan WY, Chan FK, Tao Q. Characterization of the nasopharyngeal carcinoma methylome identifies aberrant disruption of key signaling pathways and methylated tumor suppressor genes. Epigenomics 2015; 7(2):155-73. PubMed

2014

Sun K

, Yuen YP, Wang H, Sun H. Online Diagnosis System: a webserver for analysis of Sanger sequencing-based genetic testing data. Methods 2014 Oct 1; 69(3):230-236. PubMed

Sun K

, Lu L, Wang H, Sun H. Genome-wide profiling of YY1 binding in skeletal muscle cells. Genom Data 2014 May 23; 2:89-91. PubMed

Sun K

, Zhao Y, Wang H, Sun H. Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs):- Application in Human Skeletal Muscle Cells. PLoS ONE 2014 Jan 6; 9(1):e84500. PubMed

Zhao Y*, Yang Y*, Trovik J,

Sun K

, Zhou L, Jiang P, Lau TS, Hoivik EA, Salvesen HB, Sun H, Wang H. A Novel Wnt Regulatory Axis in Endometrioid Endometrial Cancer. Cancer Research 2014 Sep 15; 74(18):5103-17. PubMed

Jiang P, Sun K, Lun FMF, Guo AM, Wang H, Chan KCA, Chiu RWK, Lo YMD, Sun H. Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS ONE 2014 Jun 19; 9(6):e100360. PubMed

Sun K

, Yuen YP, Wang H, and Sun H: The Online Diagnosis System for Sanger sequencing based genetic testing. In: Big Data and Smart Computing (BIGCOMP), 2014 IEEE International Conference on. 2014: 47-51. IEEEXplore

2013

Lu L#, Sun K#, Chen X, Zhao Y, Wang L, Zhou L, Sun H, Wang H. Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. EMBO J 2013 Oct 2; 32(19):2575-88. PubMed

Sun K

, Chen X, Jiang P, Song X, Wang H, Sun H. iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 2013; 14(Suppl 2):S7. PubMed

Chan KCA*, Jiang P*, Chan CW*,

Sun K

, Wong J, Hui EP, Chan SL, Chan WC, Hui DS, Ng SS, Chan HL, Wong CS, Ma BB, Chan AT, Lai PB, Sun H, Chiu RW, Lo YMD. Noninvasive detection of cancer-associated genomewide hypomethylation and copy number aberrations using massively parallel bisulfite sequencing of plasma DNA. Proc Natl Acad Sci U S A 2013 Nov 19; 110(47):18761-8. PubMed

Lun FMF*, Chiu RWK*,

Sun K

, Leung TY, Jiang P, Chan KCA, Sun H, Lo YMD. Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA. Clin Chem 2013 Nov; 59(11):1583-94. PubMed

Guo AM,

Sun K

, Su X, Wang H, Sun H. YY1TargetDB: an integral information resource for Yin Yang 1 target loci. Database (Oxford) 2013 Feb 14; 2013:bat007. PubMed

2012

Lu L, Zhou L, Chen EZ, Sun K, Jiang P, Wang L, Su X, Sun H, Wang H. A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS ONE 2012; 7(2):e27596. PubMed

Diao Y, Guo X, Li Y,

Sun K

, Lu L, Jiang L, Fu X, Zhu H, Sun H, Wang H, Wu Z. Pax3/7BP is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Cell Stem Cell 2012, Aug 3; 11(2):231-241. PubMed

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