Selected Publications (Full list seen Here)

(*: co-corresponding author)

2021

  • S Fang, K Li, JK Shen, S Liu, J LIu, L Yang, CD Hu, J Wan (2021) GESS: A database of Global Evaluation of SARS-CoV-2/hCoV-19 Sequences. Nucleic Acids Research D1, D706.
  • Z Zhou, K Van der Jeught, Y Fang, T Yu, Y Li, Z Ao, S Liu, L Zhang, Y Yang, H Eyvani, M Cox, X Wang, X He, G Ji, B Schneider, F Guo, J Wan, X Zhang, X Lu (2021) Targeted breast cancer immunotherapy with epigenetic modulation of antigen presentation on tumor cells. Nature Biomedical Engineering (Accepted for publication).
  • N Morral, S Liu, AM Conteh, X Chu, Y Wang, XC Dong, Y Liu, AK Linnemann, J Wan (2021) Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms (Accepted for publication).
  • C Xu, Y Fu, S Liu, J Trittipo, X Lu, R Qi, H Du, C Yan, C Zhang, J Wan, MH Kaplan, K Yang (2021) BATF regulates Treg-cell functional specification and fitness of triglyceride metabolism in restraining allergic responses. Journal of Immunology (Accepted for publication).
  • G Song, G Wang, X Luo, Y Cheng, Q Song, J Wan, C Moore, H Song, P Jin, J Qian, H Zhu (2021) An All-to-All Approach to the Identification of Sequence-Specific Readers for Epigenetic DNA Modifications on Cytosine. Nature Communications 12, 795.
  • D Xu, M Yang, M Capitano, B Guo, S Liu, J Wan, H Broxmeyer*, X Huang* (2021) Pharmacological activation of nitric oxide signaling promotes human hematopoietic stem cell homing and engraftment. Leukemia 35, 229. (PMID: 32127640)
  • S Sripathi, MW Hu, M Liu, J Wan, J Cheng, Y Duan, J Mertz, K Wahlin, J Maruotti, C Berlinicke, J Qian, D Zack (2021) Transcriptome Landscape of Epithelial to Mesenchymal Transition of Human Stem Cell-Derived Retinal Pigment Epithelium. Investigative Ophthalmology & Visual Science (Accepted for publication).
  • P Bhat-Nakshatri, H Gao, L Sheng, PC McGuire, X Xuei, J Wan, Y Liu, SK Althouse, A Colter, G Sandusky, AM Storniolo, H Nakshatri (2021) A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells. Cell Reports Medicine (Accepted for publication).
  • MY Zhang, S Fang, H Gao, X Zhang, D Gu, Y Liu, J Wan, J Xie (2021) A critical role of AREG for bleomycin-induced skin fibrosis. Cell & Bioscience (Accepted for publication).

2020

  • E Beketova, S Fang, J Owens, S Liu, X Chen, Q Zhang, A Asberry, X Deng, J Malola, J Huang, C Li, R Pili, B Elzey, T Ratliff, J Wan*, CD Hu* (2020) Protein arginine methyltransferase 5 promotes androgen receptor transcription in a pICln-dependent manner in castration-resistant prostate cancer. Cancer Research 80 (22), 4904. (PMID: 32999000)
  • S Liu, JK Shen, S Fang, K Li, J Liu, L Yang, CD Hu, J Wan (2020) Genetic spectrum and distinct evolution patterns of SARS-CoV-2. Frontiers in Microbiology (Accepted for publication).
  • J Liu, S Liu, H Gao, L Han, X Chu, Y Sheng, W Shou, Y Wang, Y Liu, J Wan*, L Yang* (2020) Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells. Genome Biology 21, 169. (PMID: 32646524)
  • S Dey, S Liu, TD Factora, S Taleb, P Riverahernandez, L Udari, X Zhong, J Wan, J Kota (2020) Global targetome analysis reveals critical role of miR-29a in pancreatic stellate cell mediated regulation of PDAC tumor microenvironment. BMC Cancer (in press).
  • N Lin, J Liu, J Castle, J Wan, A Shendre, Y Liu, C Wang, C He (2020) Genome-wide DNA methylation profiling in human breast tissue by illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray. Epigenetics (in press).
  • R Choudhury, J Beezley, B Davis, J Tomeck, S Gratzl, L Golzarri-Arroyo, J Wan, D Raftery, J Baumes, TM O’Connell (2020) Viime: Visualization and Integration of Metabolomics Experiments. Journal of Open Source Software 5 (54), 2410.
  • Khambu B, Hong H, Liu S, Liu G, Chen X, Dong Z, Wan J, Yin XM (2020) The HMGB1-RAGE axis modulates the growth of autophagy-deficient hepatic tumors. Cell Death & Disease 11 (5), 333. (PMID: 32382012)
  • Xu D, Zhou D, Bum-Erdene K, Bailey BJ, Sishtla K, Liu S, Wan J, Aryal UK, Lee JA, Wells CD, Fishel ML, Corson TW, Pollok KE, Meroueh SO (2020) Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data. ACS Chemical Biology 15 (6), 1424-1444. (PMID: 32243127)
  • JL Owens, E Beketova, S Liu, C Li, J Wan*, CD Hu* (2020) PRMT5 cooperates with pICln to function as a master epigenetic activator of DNA double-strand break repair genes. iScience 23 (1): 100750.
  • J Wen, G Huang, S Liu, J Wan, X Wang, Y Zhu, W Kaliney, C Zhang, L Cheng, X Wen, X Lu (2020) Polymorphonuclear MDSCs are Enriched in the Stroma and Expanded in Metastases of Prostate Cancer. Journal of Pathology: Clinical Research (in print). (PMID: 32149481)
  • Dey S, Kwon JJ, Liu S, Hodge GA, Taleb S, Zimmers TA, Wan J, Kota J (2020) miR-29a is repressed by MYC in pancreatic cancer and its restoration exhibits anti-tumorigenicity via downregulation of LOXL2. Molecular Cancer Research 18 (2), 311-323. (PMID: 31662451)

2019

  • J Xu, Y Liu, Y Li, H Wang, S Stewart, K Van der Jeught, P Agarwal, Y Zhang, S Liu, G Zhao, J Wan, X Lu*, X He* (2019) Precise targeting of POLR2A as a therapeutic strategy for human triple negative breast cancer. Nature Nanotechnology 14 (4): 388.
  • MM Xie, S Fang, Q Chen, H Liu, J Wan*, AL Dent* (2019) Follicular regulatory T cells inhibit the development of granzyme B–expressing follicular helper T cells. JCI insight 4 (16): e128076.
  • AY Hsu, D Wang, S Liu, J Lu, R Syahirah, DA Bennin, A Huttenlocher, DM Umulis, J Wan, Q Deng (2019) Phenotypical microRNA screen reveals a noncanonical role of CDK2 in regulating neutrophil migration. Proceedings of the National Academy of Sciences 116 (37), 18561-18570. (PMID: 31451657)
  • Y Chen, C Yao, Y Teng, R Jiang, X Huang, S Liu, J Wan, H Broxmeyer*, and G Bin* (2019) Phorbol ester induced ex vivo expansion of rigorously-defined phenotypic but not functional human cord blood hematopoietic stem cells: a cautionary tale demonstrating that phenotype does not always recapitulate stem cell function. Leukemia 33 (12): 2962-2966. (PMID: 31350528)
  • J Wan, H Dai, X Zhang, S Liu, Y Ling, A-K Somani, J Xie, J Han (2019) Distinct Transcriptomic Landscapes of Cutaneous Basal Cell Carcinomas and Squamous Cell Carcinomas. Genes & Diseases https://doi.org/10.1016/j.gendis.2019.10.004.
  • HG Kim, M Huang, Y Xin, Y Zhang, X Zhang, G Wang, S Liu, J Wan, AR Ahmadi, Z Sun, S Liangpunsakul, X Xiong, XC Dong (2019) The epigenetic regulator SIRT6 protects the liver from alcohol-induced tissue injury by reducing oxidative stress in mice. Journal of Hepatology 71 (5), 960-969. (PMID: 31295533)
  • C Zibetti, S Liu, J Wan, J Qian, S Blackshaw (2019) Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin. Communications Biology 2 (1), 142.
  • AY Hsu, S Liu, R Syahirah, KA Brasseale, J Wan, Q Deng (2019) Inducible overexpression of zebrafish microRNA-722 suppresses chemotaxis of human neutrophil like cells. Molecular immunology 112, 206-214. (PMID: 31176200)
  • Shinde A, Hardy SD, Kim D, Akhand SS, Jolly MK, Wang WH, Anderson JC, Khodadadi RB, Brown WS, George JT, Liu S, Wan J, Levine H, Willey CD, Krusemark CJ, Geahlen RL, Wendt MK (2019) Spleen tyrosine kinase-mediated autophagy is required for epithelial-mesenchymal plasticity and metastasis in breast cancer. Cancer Research 79 (8), 1831-1843. (PMID: 30733195)
  • Y Jia, D Gu, J Wan, B Yu, X Zhang, E Chiorean, Y Wang, J Xie (2019) The Role of GLI-Sox2 signaling axis for gemcitabine resistance in pancreatic cancer. Oncogene 38 (10), 1764-1777. (PMID: 30382189)
  • A Cerra-Franco, S Liu, M Azar, K Shiue, S Freijie, J Hinton, CR Deig, D Edwards, NCEstabrookIII, SG Ellsworth, K Huang, K Diab, MP Langer, R Zellars, F Kong, J Wan, T Lautenschlaeger (2019) Predictors of Nodal and Metastatic Failure in Early Stage Non–small-cell Lung Cancer After Stereotactic Body Radiation Therapy. Clinical Lung Cancer 20 (3), 186-193. (PMID: 30711394)

2018

  • O Oyinlade, S Wei, K Kammers, S Liu, S Wang, D Ma, Z Huang, J Qian, H Zhu, J Wan*, S Xia* (2018) Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter-enhancer interactions. Epigenetics 13 (7): 751.
  • X Huang, B Guo, S Liu, J Wan, HE Broxmeyer (2018) Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment. Nature communications 9 (1): 2741.
  • Y Liu, H Xu, KV Jeught, Y Li, S Liu, L Zhang, Y Fang, X Zhang, M Radovich, BP Schneider, X He, C Huang, C Zhang, J Wan, G Ji*, X Lu* (2018) Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer. Journal of Clinical Investigation 128 (7): 2951.
  • A Sehdev, O Gbolahan, B Hancock, M Stanley, S Shahda, J Wan, H Wu, M Radovich, B O'Neill (2018) Germline and Somatic DNA Damage Repair Gene Mutations and Overall Survival in Metastatic Pancreatic Adenocarcinoma Patients Treated with FOLFIRINOX. Clinical Cancer Research 24 (24), 6204-6211. (PMID: 30131383)
  • Y Liu, H Xu, KV Jeught, Y Li, S Liu, L Zhang, Y Fang, X Zhang, M Radovich, BP Schneider, X He, C Huang, C Zhang, J Wan, G Ji, X. Lu (2018) Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer. Journal of Clinical Investigation 128 (7), 2951-2965. (PMID: 29649003)
  • EA Newman, DW Kim, J Wan, J Wang, J Qian, S Blackshaw (2018) Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. Developmental Biology 439(2):102-111. (PMID: 29679559)
  • JW Foster, V Shinde, US Soiberman, G Sathe, S Liu, J Wan, J Qian, Y Dauoud, A Pandey, AS Jun, S Chakravarti (2018) Integrated Stress Response and Decreased ECM in Cultured Stromal Cells From Keratoconus Corneas. Investigative Ophthalmology & Visual Science 59 (7), 2977-2986. (PMID: 30029277)
  • M Padua, P Bhat-Nakshartri, M Anjanappa, M Prasad, Y Hao, X Rao, S Liu, J Wan, Y Liu, K McELyea, M Jacobsen, G Sandusky, S Althouse, S Perkins, H Nakshatri (2018) Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis. Breast Cancer Research 20 (1), 35. (PMID: 29720215)
  • Q Cai, Q Fan, K. Nephew, S Liu, J Wan, Y Xu (2018) Changes in mRNA/protein expression and signaling pathways in in vivo passaged mouse ovarian cancer cells. PLoS One 13 (6), e0197404. (PMID: 29927933)
  • O Oyinlade, S Wei, B Lal, J Laterra, H Zhu, CR Goodwin, S Wang, D Ma, J Wan, S Xia (2018) Targeting UDP-α-d-glucose 6-dehydrogenase inhibits glioblastoma growth and migration. Oncogene 37 (20), 2615-2629. (PMID: 29479058)
  • A Cerra-Franco Shiue, R Shapiro, N Estabrook, S Althouse, S Liu, J Wan, Y Zang, N Agrawal, C Zhang, C DesRosiers, G Bartlett, M Ewing, M Langer, G Watson, R Zellars, T Lautenschlaeger (2018) Histology, tumor volume, and radiation dose predict outcomes in non-small cell lung cancer patients after stereotactic ablative radiotherapy. Journal of Thoracic Oncology 13 (10), 1549-1559. (PMID: 29959060)
  • B Kumar, M Prasad, P Bhat-Nakshatri, M Anjanappa, M Kalra, N Marino, AM Storniolo, X Rao, S Liu, J Wan, Y Liu, H Nakshatri (2018) Normal breast-derived epithelial cells with luminal and intrinsic subtype-enriched gene expression document inter-individual differences in their differentiation cascade. Cancer Research 78 (17), 5107-5123. (PMID: 29997232)
  • A Filley, M Henriquez, T Bhowmik, BN Tewari, X Rao, J Wan, M Miller, Y Liu, RT Bentley, M Dey (2018) Immunologic and Gene Expression Profiles of Spontaneous Canine Glioma. Journal of Neuro-Oncology 137 (3), 469. (PMID: 29330750)
  • G Wang, X Luo, J Wang, J Wan, S Xia, H Zhu, J Qian, Y Wang (2018) MeDReaders: a database for transcription factors that bind to methylated DNA. Nucleic Acids Research 46 (D1), D146-D151 (PMID: 29145608).

2017

  • J Wan†, Y Su†, Q Song†, B Tung, O Oyinlade, S Liu, M Ying, G Ming, H Song, J Qian, H Zhu, S Xia (2017) Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. eLife 6: e20068.
  • P Shang, M Valapala, R Grebe, S Hose, S Ghosh, IA Bhutto, JT Handa, GA Lutty, L Lu, J Wan, J Qian, Y Sergeev, R Puertollano, JS Zigler, GT Xu, D Sinha (2017) The amino acid transporter SLC36A4 regulates the amino acid pool in retinal pigmented epithelial cells and mediates the mechanistic target of rapamycin, complex 1 signaling. Aging Cell 16 (2), 349-359. (PMID: 28083894)
  • Z Yang, Y Hou, T Hao, HS Rho, J Wan, Y Luan, X Gao, J Yao, A Pan, Z Xie, J Qian, W Liao, H Zhu, X Zhou (2017) A human proteome array approach to identifying key host proteins targeted by Toxoplasma kinase ROP18. Molecular & Cellular Proteomics 16 (3), 469-484. (PMID: 28087594)
  • Y Zhao, F Wang, S Chen, J Wan, G Wang (2017) Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network. BioMed Research International 2017:8. (PMID: 28656148)
  • Z Li, J Liu, J Li, Y Kong, G Sandusky, X Rao, Y Liu, J Wan, X Liu (2017) Polo-like kinase 1 (Plk1) overexpression enhances ionizing radiation-induced cancer formation in mice. Journal of Biological Chemistry 292 (42), 17461. (PMID: 28900036)
  • S Liu, C Zibetti, J Wan, G Wang, S Blackshaw, J Qian (2017) Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. BMC Bioinformatics 18 (1), 355. (PMID: 28750606)

Selected papers before 2017

  • J Wan, VF Oliver, G Wang, H Zhu, DJ Zack, SL Merbs, J Qian (2015) Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics 16 (1): 49.
  • S Hu†, J Wan† (co-first author), Y Su†, Q Song, Y Zeng, HN Nguyen, J Shin, E Cox, HS Rho, C Woodard, S Xia, S Liu, H Lu, G Ming, H Wade, H Song, J Qian, H Zhu (2013) DNA methylation presents distinct binding sites for human transcription factors. eLife 2: e00726. (Highlighted by the Insight paper “Making the most of methylation” eLife 2013 (2), e01387).
  • J Wan, VF Oliver, H Zhu, D Zack, J Qian, SL Merbs (2013) Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Research 41 (18): 8503.
  • J Wan, T Masuda, L Hackler, K Torres, S Merbs, D Zack, J Qian (2011) Dynamic Usage of Alternative Splicing Exons During Mouse Retina Development. Nucleic Acids Research 39: 7920.
  • J Wan, J Lin, D Zack, J Qian (2009) Relating periodicity of nucleosome organization and gene regulation. Bioinformatics 25: 1782.