Education:

2009-2012 Ph.D. in Biomedical Sciences, Ohio State University

2001-2005 B.Sc. in Biotechnology, Ocean University of China

Professional Positions:

2017– Assistant/Associate Professor, Department of Basic Medical Sciences, THU School of Medicine

2012–2017 Postdoctoral research associate, Department of Genetics, Stanford University (Moved from U Chicago in 2013) Advised by Dr. Jonathan K. Pritchard

Research Areas:

Our lab is dedicated to developing next-generation sequencing technologies and computational algorithms to uncover new biological insights. Our primary objectives include investigating cell differentiation dynamics under normal and disease conditions, and understanding the interaction between tumor neoantigens and T cell receptors. To achieve these goals, we utilize high-throughput experimental approaches to generate comprehensive training data, which we then use to construct predictive computational models.

Honors and Awards:

➢ 2018 NSF 1000 Young Scholars Award

➢ 2022 Tsinghua University Outstanding Individual for Graduate Employment

Selected Publications:

• Ming Zhu*, Runda Xu, Junsong Yuan, Jiacheng Wang, Xiaoyu Ren, Tingting Cong, Yaxian You, Anji Ju, Longchen Xu, Huimin Wang, Peiyuan Zheng, Juanjuan Du, Xin Lin, Wei Xie, Yinqing Li*, Xun Lan*, Track-seq reveals the heterogeneity of off-target effects in CRISPR/Cas9-mediated genome editing, Nature Biotechnology, (2024)

• Keyong Sun, Xin Liu and Xun Lan*, A single-cell atlas of chromatin accessibility in mouse organogenesis, Nature Cell Biology, (2024)

• Keyong Sun, Xin Liu, Runda Xu, Chang Liu, Anming Meng* and Xun Lan*, Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq, Nature Cell Biology, (2024)

• Jie Li, Jiahui Chen, Xin Sun, Heli Yang, Keyong Sun, Chang Liu, Yongwang Wang, Mengyue Xu, Xin Ji, Ji Zhang, Xiaojiang Wu, Anqiang Wang, Biao Fan, Xiaolu Zhang, Yue Wu, Peilin Cui*, Junya Peng*, Yupei Zhao*, Wenming Wu*, Honghao Yu*, Zhaode Bu*, Jiafu Ji*, Xun Lan*, Uncovering chromatin accessibility and cancer diagnostic potential via cell-free DNA utilization, Science bulletin, (2024)

• Keyong Sun, Runda Xu, Fuhai Ma, Naixue Yang, Yang Li, Xiaofeng Sun, Peng Jin, Wenzhe Kang, Lemei Jia, Jianping Xiong, Haitao Hu, Yantao Tian*, Xun Lan*, Single cell analysis coupled with TCR sequencing of gastric tumor reveals complex intercellular interaction and an alternative T cell exhaustion trajectory, Nature Communications (2022)

• Xun Lan*, & Jonathan K. Pritchard* Long-term survival of duplicate genes despite absence of subfunctionalized expression. Science (2016)

(2) 其他通讯作者论文：

• Zilan Yu, Mengnan Jiang, Xun Lan*, HeteroTCR: A heterogeneous graph neural network-based method for predicting peptide-TCR interaction, Communications Biology (2024)

• Q Luo, Y Chen, X Lan*, COMSE: Analysis of Single-Cell RNA-seq Data Using Community Detection Based Feature Selection, BMC Biology (Accepted, 2024)

• Mengnan Jiang, Zilan Yu, Xun Lan*, VitTCR: A deep learning method for peptide recognition prediction, iScience (2024)

• J Li, X Sun, H Yang, J Chen, Z Bu, J Ji, X Lan*, Integrated analysis toolkit for dissecting whole genome wide features of cell-free DNA, Clinical and Translational Medicine (2023) 13 (3)

• Lihui Wang, Xun Lan*, Rapid screening of TCR-pMHC interactions by the YAMTAD system, Cell Discovery (2022)

• Qinhuan Luo, Yongzhen Yu, Xun Lan*, SIGNET: Single-cell RNA-seq-based Gene Regulatory Network Prediction using Multiple-Layer Perceptrons Bagging, Briefings in Bioinformatics (2022)

• Fansen Ji, Li Chen, Zhizhuo Chen, Bin Luo#, Yongwang Wang*, X Lan*, TCR repertoire and transcriptional signatures of circulating tumour-associated T cells facilitate effective non-invasive cancer detection, Clinical and Translational Medicine (2022)

• Jie Li, Mengyue Xu, Junya Peng, Jingqiao Wang, Yupei Zhao*, Wenming Wu*, X Lan*, Novel technologies in cfDNA analysis and potential utility in clinic, Chinese Journal of Cancer Research 33 (6), 708 (2021)

• Huanhuan Pang, Yisheng Jiang, Jie Li, Yushen Wang, Meng Nie, Nan Xiao, Shuo Wang, Zhihong Song, Fansen Ji, Yafei Chang, Yu Zheng, Ke Yao, LiAng Yao, Shao Li, Peng Li, Lei Song*, Xun Lan*, Zhiheng Xu*, Zeping Hu*, Aberrant NAD+ metabolism underlies Zika virus–induced microcephaly, Nature Metabolism (2021)

• Jingzhe Lu, Xu Wang, Keyong Sun, Xun Lan*, Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data, Briefings in Bioinformatics (2021), bbab181

• Naixue Yang, Fansen Ji, Liqing Cheng, Jingzhe Lu, Xiaofeng Sun, Xin Lin*, Xun Lan*, Knockout of immunotherapy prognostic marker genes eliminates the effect of the anti-PD-1 treatment. npj Precision Oncology. 5, 37 (2021).

• Longchen Xu, Haohang Zhang, Hengyi Xu, Han Yang, Lei Zhang, Wei Zhang, Fei Gu*, Xun Lan*, The coSIR model predicts effective strategies to limit the spread of SARS-CoV-2 variants with low severity and high transmissibility, Nonlinear dynamics (2021)

• Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan*, Lei Liu*, Feng Li*, Zheng Zhang*, Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis, Virulence (2021)

• Y. Dai, W. Qiang, Y. Gui, X. Tan, T. Pei, K. Lin, S. Cai, L. Sun, G. Ning, J. Wang, H. Guo, Y. Sun, J. Cheng, L. Xie*, X. Lan*, D. Wang*, A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional chinese medicines, Science Bulletin (2021)

• Y Dai, W Qiang, K Lin, Y Gui, X Lan*, D Wang*, An immune-related gene signature for predicting survival and immunotherapy efficacy in hepatocellular carcinoma. Cancer Immunology, Immunotherapy (2020)

• W Zu, H Zhang, X Lan*, X Tan*, Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs. Journal of Genetics and Genomics (2020)

• Y Dai, W Qiang, X Yu, S Cai, K Lin, L Xie, X Lan*, D Wang*, Guizhi Fuling Decoction inhibiting the PI3K and MAPK pathways in breast cancer cells revealed by HTS2 technology and systems pharmacology. Computational and Structural Biotechnology Journal (2020)

• Liu, B.*, Fang, L., Long, R., Lan, X.* and Chou, K.C.* iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinformatics (2015)

(3) 第一及共一作者论文

·Harpak, A. ^#, Lan, X. ^#, Gao, Z., and Pritchard, J. K. (2017) Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates. PNAS 114 (48) 12779-12784.

·Kontur, C. ^#, Kumar, S. ^#, Lan, X. ^#, Pritchard, J. K., and Turkewitz, A. P., (2016) Whole genome sequencing identifies a novel factor required for secretory granule maturation in tetrahymena thermophile. G3: Genes|Genomes|Genetics, vol. 6, no. 8, pp. 2505–2516.

·Chen, Z. ^#, Lan, X. ^#, Thomas-Ahner, J.M., Wu, D., Liu, X., Ye, Z., Wang, L., Sunkel, B., Grenade, C., Chen, J. et al. (2015) Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer. The EMBO Journal, 34, 502-516.

·Banovich, N.E. ^#, Lan, X. ^#, McVicker, G., van de Geijn, B., Degner, J.F., Blischak, J.D., Roux, J., Pritchard, J.K. and Gilad, Y. (2014) Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genetics, 10, e1004663.

·Wang, J.^#, Lan, X.^#, Hsu, P.-Y., Huang, K., Parvin, J., Huang, T.H.-M.H. and Jin, V.X. (2013) Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2 mediated gene regulation. BMC Genomics 14 (1), 70.

·Lan, X., Witt, H., Katsumura, K., Ye, Z., Wang, Q., Bresnick, E.H., Farnham, P.J. and Jin, V.X. (2012) Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Research, 40 (16), 7690-7704

·Lan, X., Farnham, P.J. and Jin, V.X. (2012) Uncovering Transcription Factor Modules Using One-and Three-dimensional Analyses. Journal of Biological Chemistry, 287 (37), 30914-30921.

·Lan, X. and Jin, V.X. (2012) Experimental and computational challenges from array-based to sequence-based ChIP techniques. Current Bioinformatics, Review, 7 (4), 447-453.

·Lan, X., Bonneville, R., Apostolos, J., Wu, W. and Jin, V.X. (2011) W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics, 27, 428-430.

·Lan, X., Adams, C., Landers, M., Dudas, M., Krissinger, D., Marnellos, G., Bonneville, R., Xu, M., Wang, J., Huang, T.H.-M. et al. (2011) High resolution detection and analysis of CpG dinucleotides methylation using MBD-seq technology. PLoS One, 6, e22226.

(4) 其他论文 (列出前六名作者)

·Yu Zheng, Haihui Jiang, Naixue Yang, Shaoping Shen, Daosheng Huang, Lemei Jia, Jing Ling, Longchen Xu, Mingxiao Li, Kefu Yu, Xiaohui Ren, Yong Cui, Xun Lan, Song Lin, Xin Lin, Glioma-derived ANXA1 suppresses the immune response to TLR3 ligands by promoting an anti-inflammatory tumor microenvironment, Cellular & Molecular Immunology (2024)

•J Hao, C Liu, Z Gu, X Yang, X Lan, X Guo，Dysregulation of Wnt/β-catenin signaling contributes to intestinal inflammation through regulation of group 3 innate lymphoid cells，Nature Communications (2024)

·X Liu, X Liu, Y Du, D Zou, C Tian, Y Li, X Lan, CJ David, Q Sun, M Chen, Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression, Cell Reports (2023) 42 (8)

•J Meng, Y Jiang, S Zhao, Y Tao, T Zhang, X Wang, et al. Tumor-derived Jagged1 promotes cancer progression through immune evasion, Cell Reports (2022) 38 (10)

•Y Li, Y He, J Peng, Z Su, Z Li, B Zhang, et al. (2021) Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer. Nature Cancer 2 (1), 49-65

•Y Liu, G Hu, Y Wang, W Ren, X Zhao, F Ji, et al. Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2, PNAS (2021) 118 (12), e2025373118

•C Zhang, H An, J Hu, J Li, W Zhang, X Lan, H Deng, JR Zhang, MetR is a molecular adaptor for pneumococcal carriage in the healthy upper airway, Molecular Microbiology (2021) 116 (2), 438-458

•X Huang, J Wang, J Li, Y Liu, X Liu, Z Li, et al. (2020) Prevalence of phase variable epigenetic invertons among host-associated bacteria. Nucleic acids research 48 (20), 11468-11485

•L Deng, P Yao, L Li, F Ji, S Zhao, C Xu, X Lan, P Jiang (2020) p53-mediated control of aspartate-asparagine homeostasis dictates LKB1 activity and modulates cell survival. Nature communications 11 (1), 1-18

•X Huang, J Wang, J Li, Y Liu, X Liu, Z Li, et al. (2020) Prevalence of phase variable epigenetic invertons among host-associated bacteria. Nucleic acids research 48 (20), 11468-11485

•M Luo, J Bai, B Liu, P Yan, F Zuo, H Sun, et al. (2019) H3K18ac primes mesendodermal differentiation upon nodal signaling. Stem cell reports 13 (4), 642-656

•EC Glassberg, Z Gao, A Harpak, X Lan, JK Pritchard. (2019) Evidence for weak selective constraint on human gene expression. Genetics 211 (2), 757-772

·Yamamoto, R., Wilkinson, A. C., Ooehra, J., Lan, X. et. al. (2018) Large-scale clonal analysis resolves aging of the mouse hematopoietic stem cell compartment. Cell Stem Cell

·Sparvolia, D., Richardsonb, E., Osakadac, H., Lan, X., Iwamotoc, M. et al. (2018) Remodeling the specificity of an endosomal CORVET tether underlies formation of regulated secretory vesicles in the ciliate Tetrahymena thermophile. Current Biology

·W Hankey, Z Chen, MJ Bergman, MO Fernandez, B Hancioglu, X Lan, et al. (2018) Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. Oncotarget 9 (58), 31214

·Chen, Z., Lan, X., Wu, D., Sunkel, B., Ye, Z., Huang, J., ... & Wang, Q. (2015) Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer. Nature Communications, 6.

·Li, N., Zheng, J., Li, H., Deng, J., Hu, M., Wu, H., Li, W., Li, F., Lan, X., Lu, J. et al. (2014) Identification of chimeric TSNAX-DISC1 resulting from intergenic splicing in endometrial carcinoma through high-throughput RNA sequencing. Carcinogenesis, 35, 2687-2697.

·Liu, B., Xu, J., Lan, X., Xu, R., Zhou, J., Wang, X. and Chou, K.C. (2014) iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition. PloS one, 9, e106691.

·Hsu, P.Y., Hsu, H.K., Lan, X., Juan, L., Yan, P.S., Labanowska, J., Heerema, N., Hsiao, T.H., Chiu, Y.C., Chen, Y. et al. (2013) Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell, 24, 197-212.

·Liu, B., Yi, J., Sv, A., Lan, X., Ma, Y., Huang, T.H., Leone, G. and Jin, V.X. (2013) QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions. BMC Genomics, 14 Suppl 8, S3.

·Wang, R., Hsu, H.K., Blattler, A., Wang, Y., Lan, X., Wang, Y., Hsu, P.Y., Leu, Y.W., Huang, T.H., Farnham, P.J. et al. (2013) LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data. PloS one, 8, e67788.

·Ye, Z., Chen, Z., Lan, X., Hara, S., Sunkel, B., Huang, T.H., Elnitski, L., Wang, Q. and Jin, V.X. (2013) Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Research.

·Liu, B., Wang, X., Chen, Q., Dong, Q., Lan, X. (2012) Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection. PloS one, 7 (9), e46633

·Kenney, B.A., Lan, X., Huang, T.H.-M., Farnham, P.J. and Jin, V.X. Using ChIPMotifs for De Novo Motif Discovery of OCT4 and ZNF263 Based on ChIP-Based High-Throughput Experiments. Methods in Molecular Biology, 802, 323-34.

·Liu, R., Lei, J.X., Luo, C., Lan, X., Chi, L., Deng, P., Lei, S., Ghribi, O. and Liu, Q.Y. (2012) Increased EID1 nuclear translocation impairs synaptic plasticity and memory function associated with pathogenesis of Alzheimer's disease. Neurobiology of Disease, 45, 902-912.

·Zuo, T., Liu, T.M., Lan, X., Weng, Y.I., Shen, R., Gu, F., Huang, Y.W., Liyanarachchi, S., Deatherage, D.E., Hsu, P.Y. et al. (2011) Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. Cancer Research, 71, 1752-1762.

·Frietze, S., Lan, X., Jin, V.X. and Farnham, P.J. (2010) Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. Journal of Biological Chemistry, 285, 1393-1403.

·Bapat, S.A., Jin, V., Berry, N., Balch, C., Sharma, N., Kurrey, N., Zhang, S., Fang, F., Lan, X., Li, M. et al. (2010) Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells. Epigenetics, 5, 716-729.

·Zhuang, Y., Lan, X., Wang, ZG., Qi, J., Wang, XB., Zhang, QQ. (2010) Studies on the Induction of Mitogynogenetic Diploids and Their Early Growth of Olive Flounder Paralichthys olivaceus. Periodical of Ocean University of China, 6, 016

·Gan, L., Qiao, S., Lan, X., Chi, L., Luo, C., Lien, L., Yan Liu, Q. and Liu, R. (2008) Neurogenic responses to amyloid-beta plaques in the brain of Alzheimer's disease-like transgenic (pPDGF-APPSw, Ind) mice. Neurobiology of Disease, 29, 71-80.

·Chen, X., Lan, X., Roche, I., Liu, R. and Geiger, J.D. (2008) Caffeine protects against MPTP-induced blood-brain barrier dysfunction in mouse striatum. Journal of Neurochemistry, 107, 1147-1157.

Complete list of publications: https://scholar.google.com/citations?user=hjZ6R54AAAAJ&hl=en