Cancer liquid biopsy:

1. Gong F^#, Pan Y^#, Lin H^#, An Y, Yang M, Liu X, Bai Y, Zhang Z, Tang B, Zhang K, Zhao X, Zhao Y, Du C, Shen X*, Sun K*. Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics. Nature Communications 2026 Jul 18; 17:8801.

2. Zhang Z^#, An Y^#, Yang M, Pan Y, Liu X, Gong F, Lin H, Tang B, Bai Y, Zhao X, Zhao Y, Du C, Sun K*. Cancer-like fragmentomic characteristics of somatic variants in cell-free DNA. Advanced Science 2026 Mar; 13(16):e14819.

3. Ju J^#, Zhao X^#, An Y^#, Yang M^#, Zhang Z^#, Liu X, Hu D, Wang W, Pan Y, Xia Z, Fan F, Shen X, Sun K*. Cell-free DNA end characteristics enable accurate and sensitive cancer diagnosis. Cell Reports Methods 2024 Oct 21; 4(10):100877.

4. 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. Nature Communications 2023 Jan 18; 14(1):287.

5. 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 Discovery 2020 May; 10(5):664-673.

6. 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 Research 2019 Mar; 29(3):418-427.

7. Sun K^#, Jiang P^#, Chan KCA^#, Wong J, Cheng YK, Liang RH, Chan WK, Ma ES, Chan SL, Cheng SH, Chan RW, Tong YK, Ng SS, Mong RSM, Hui DS, Leung TN, Leung TY, Lai PBS, Chiu RWK, Lo YMD. Plasma DNA tissue mapping by genomewide methylation sequencing for noninvasive prenatal, cancer and transplantation assessments. Proc Natl Acad Sci U S A 2015 Oct 6; 112(40):E5503-12.

Cancer metastasis and lncRNA:

1. Wang W*, Yang M, Gong F, Zhang Z, Ma Y, Li H, Zhao Y, Du C, Li N, He G*, Sun K*. Candida albicans drives colorectal cancer progression by inducing hypoxia signaling. eLife 2025 Nov 26; 14:RP108665.

2. 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, a novel functional long non-coding RNA in myogenic differentiation and muscle regeneration. Nat Commun. 2015 Dec 11; 6:10026.

3. 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.

Muti-omics and computational biology:

1. Hu D^#, Wang W^#, Zhao X^#, An Y, Liu X, Yang M, Pan Y, Lin H, Gong F, Tang B, Sheng Y, Zhou W, Zhang K, Zhang Z, Wu Y, Zhao Y, Hu H*, Du C*, Sun K*. Expression pattern of glutaminase informs the dynamics of glutamine metabolism. The Innovation Life 2025 May 26; 3(2):100128.

2. Hu D^#, Zhang Z^#, Liu X^#, Wu Y^#, An Y, Wang W, Yang M, Pan Y, Qiao K, Du C, Zhao Y, Li Y, Bao J, Qin T, Pan Y, Xia Z*, Zhao X*, Sun K*. Generalizable transcriptome-based tumor malignant level evaluation and molecular subtyping towards precision oncology. J Transl Med. 2024 May 28; 22:512.

3. 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.

4. 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 Nov 13; 1(8):100127.

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