Selected Publications (Full list seen Here)

(§: co-corresponding author, *: co-first author)

    2024

    1. Ramdas B, Dayal N, Pandey R, Larocque E, Kumar S, Liu S, Kanellopoulou C, Chu ERF, Mohallem R, Virani S, Chopra G, Aryal UK, Lapidus R, Wan J, Emadi A, Haneline L, Holtsberg F, Aman MJ, Sintim H, Kapur R (2024) Alkynyl nicotinamides with antileukemic activity for treating poor prognosis AML. JCI 134(12): e169245. (PMID: 38950330)
    2. Heller DT, Kolson DR, Brandebura AN, Amick EM, Wan J, Ramadan J, Holcomb PS, Liu S, Deerinck TJ, Ellisman MH, Qian Q, Mathers PH, Spirou GA (2024) Astrocyte Ensheathment of Calyx-Forming Axons of the Auditory Brainstem Precedes Accelerated Expression of Myelin Genes and Myelination. Journal of Comparative Neurology 532(2):e25552 (featured on the Cover). (PMID: 37916792).
    3. Zhang Y, Hu J, Zhang X, Liang M, Wang X, Gan D, Li J, Lu X, Wan J, Feng S, Lu X (2024) Protein Signature Differentiating Neutrophils and Myeloid-Derived Suppressor Cells Determined Using a Human Isogenic Cell Line Model and Protein Profiling. Cells 13(10):795. (PMID:38786019).
    4. Noble P, Pozhitkov A, Singh K, Woods E, Liu C, Levin M, Javan G, Wan J, Abouhashem A, Mathew-Steiner S, Sen C (2024) Unraveling the Enigma of Organismal Death: Insights, Implications, and Frontiers. Physiology (Bethesda) 39(5). (PMID:38624244)
    5. Kittaka M, Mizuno N, Morino H, Yoshimoto T, Zhu T, Liu S, Wang Z, Mayahara K, Iio K, Kondo K, Kondo T, Hayashi T, Coghlan S, Teno Y, Doan AAP, Levitan M, Choi RB, Matsuda S, Ouhara K, Wan J, Cassidy AM, Pelletier S, Nampoothiri S, Urtizbera AJ, Robling AG, Ono M, Kawakami H, Reichenberger EJ, Ueki Y (2024) Loss-of-function OGFRL1 variants identified in autosomal recessive cherubism families. JBMR Plus 8(6):ziae050. (PMID:38699440)
    6. Mijit M, Kpenu E, Chowdhury NN, Gampala S, Wireman R, Liu S, Babb O, Georgiadis MM, Wan J, Fishel ML, Kelley MR (2024) In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer. Redox Biology 69:102977 (PMID:38056311).

    2023

    1. Gu X*, Li K*, Zhang M, Chen Y, Zhou J, Yao C, Zang Y, He J§, Wan J§, Guo B§ (2023) Aspartyl-tRNA synthetase 2 orchestrates iron-sulfur metabolism in hematopoietic stem cells via fine-tuning alternative RNA splicing. Cell Reports 42(10):113264. (PMID: 37838946)
    2. Han L, Huang D, Wu S, Liu S, Wang C, Sheng Y, Lu X, Broxmeyer HE, Wan J, Yang L (2023) Lipid droplet-associated long non-coding RNA LIPTER preserves cardiac lipid metabolism. Nature Cell Biology 25, 1033–1046. (PMID: 37264180)
    3. Mijit M*, Liu S*, Sishtla K, Hartman GD, Wan J§, Corson TW§, Kelley MR§ (2023) Identification of novel pathways regulated by APE1/Ref-1 in human retinal endothelial cells. International Journal of Molecular Science 24(2):1101. (PMID: 36674619)
    4. Zhu Y, Zhao Y, Wen J, Liu S, Huang T, Hatial I, Peng X, Janabi HA, Huang G, Mittlesteadt J, Cheng M, Bhardwaj A, Ashfeld BL, Kao KR, Maeda DY, Dai X, Wiest O, Blagg BSJ, Lu X, Cheng L, Wan J, Lu X (2023) Targeting the chromatin effector Pygo2 promotes cytotoxic T cell responses and overcomes immunotherapy resistance in prostate cancer. Science Immunology 8(81):eade4656. (PMID: 36897957)
    5. Noonan ML, Ni P, Solis E, Marambio YG, Agoro R, Chu X, Wang Y, Gao H, Xuei X, Clinkenbeard EL, Jiang G, Liu S, Stegen S, Carmeliet G, Thompson WR, Liu Y, Wan J, White KE (2023) Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23. Bone Research 11(1):7. (PMID: 36650133)
    6. Zhou Z, Van der Jeught K, Li Y, Sharma S, Yu T, Moulana I, Liu S, Wan J, Territo PR, Opyrchal M, Zhang X, Wan G, Lu X (2023) A T cell-engaging tumor organoid platform for pancreatic cancer immunotherapy. Advanced Science 2023:e230058. (PMID: 37271874)
    7. Jiang J, Srivastava S, Liu S, Seim G, Claude R, Zhong M, Cao S, Davé U, Kapur R, Mosley AL, Zhang C, Wan J, Fan J, Zhang J (2023) Asparagine starvation suppresses histone demethylation through iron depletion. iScience 26(4):106425. (PMID: 37034982)
    8. Zhao T, Liu S, Hanna NH, Jalal S, Ding X, Wan J, Yan C§, Du H§ (2023) LAL deficiency induced myeloid-derived suppressor cells as targets and biomarkers for lung cancer. Journal of Immunotherapy of Cancer 11(3):e006272. (PMID: 36914206)
    9. Dausinas Ni P, Hartman M, Slack J, Basile C, Liu S, Wan J, O'Leary HA (2023) Novel differential calcium regulation of hematopoietic stem and progenitor cells under physiological low oxygen conditions. Journal of Cellular Physiology 238(7):1492-1506. (PMID: 37051890)
    10. Zhao YQ, Jin HR, Kim D, Jung SH, Liu S, Wan J, Lo H-Y, Fu XQ, Wang Q, Hao C, Bellail AC (2023) SUMO1 degrader induces ER stress and ROS accumulation through deSUMOylation of TCF4 and inhibition of its transcription of StarD7 in colon cancer. Molecular Carcinogenesis (in press). (PMID: 37191369)
    11. Agoro R, Nookaew I, Noonan ML, Marambio YG, Liu S, Chang W, Gao H, Horan D, Thompson WR, Xuei X, Liu Y, Zhang C, Robling AG, Bonewald LF, Wan J, White KE (2023) Single Cell Cortical Bone Transcriptomics Defines Novel Osteolineage Gene Sets Altered in Chronic Kidney Disease. Frontiers in Endocrinology 14:1063083. (PMID: 36777346)
    12. Pal D, Ghatak S, Singh K, Abouhashem AS, Kumar M, Masry ME, Mohanty SK, Palakurti R, Rustagi Y, Tabasum S, Khona DK, Khanna S, Kacar S, Srivastava R, Bhasme P, Verma SS, Hernandez E, Sharma A, Reese D, Verma P, Ghosh N, Gorain M, Wan J, Liu S, Liu Y, Castro NH, Gnyawali SC, Lawrence W, Moore J, Perez DG, Roy S, Yoder MC, Sen CK (2023) Identification of a physiological vasculogenic fibroblast state to achieve tissue repair. Nature Communications 14(1):1129. (PMID: 36854749)
    13. Pasupuleti SK, Chao K, Ramdas B, Kanumuri R, Palam LR, Liu S, Wan J, Annesley C, Loh ML, Stieglitz E, Burke MJ, Kapur R (2023) Potential clinical use of Azacitidine and MEK inhibitor combination therapy in PTPN11-mutated Juvenile myelomonocytic leukemia. Molecular Therapy (in press) (PMID: 36739480)
    14. Chen H, Bai Y, Kobayashi M, Xiao S, Cai W, Barajas S, Chen S, Miao J, Meke FN, Vemula S, Ropa J, Croop J, Boswell HS, Wan J, Jia Y, Liu H, Li L, Altman JK, Eklund EA, Ji P, Tong W, Band H, Huang D, Platanias LC, Zhang ZY, Liu Y (2023) PRL2 phosphatase enhances oncogenic FLT3 signaling via dephosphorylation of the E3 ubiquitin ligase CBL at tyrosine 371. Blood 141(3):244. (PMID: 36206490)

    2022

    1. S Fang, S Liu, D Yang, L Yang, C-D Hu, J Wan (2022) Decoding Regulatory Associations of G-quadruplex with Epigenetic and Transcriptomic Functional Components. Frontiers in Genetics 13:957023.
    2. K Li, AKY Wang, S Liu, S Fang, AZ Lu, J Shen, L Yang, C-D Hu, K Yang, J Wan (2022) Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2. Frontiers in Medicine 9: 813964.
    3. AM Asberry*, S Liu*, HS Nam, X Deng, J Wan§, CD Hu§ (2022) Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation. Computational and Structural Biotechnology Journal 20:5873-5885
    4. J Owens, E Beketova, S Liu, Q Shen, JS Pawar, AM Asberry, J Yang, X Deng, BD Elzey, TL Ratliff, L Cheng, CR Choo, DE Citrin, TJ Polascik, B Wang, J Huang, C Li, J Wan§, CD Hu§ (2022) Targeting protein arginine methyltransferase 5 (PRMT5) suppresses radiation-induced neuroendocrine differentiation and sensitizes prostate cancer cells to radiation. Molecular Cancer Therapeutics 21 (3), 448.
    5. Q Liu, J Wan§, G Wang§ (2022) A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. Briefings in Bioinformatics 23 (1), bbab416.
    6. C Shao*, J Wan*, FC Lam*, H Tang, AR Marley, Y Song, C Miller, M Brown, J Han, G Adeboyeje (2022) A comprehensive literature review and meta-analysis of the prevalence of pan-cancer BRCA mutations, homologous recombination repair gene mutations, and homologous recombination deficiencies. Environmental and Molecular Mutagenesis 63(6):308-316
    7. PW Zhang, SH Zhang, WF Li, CJ Keuthan, S Li, F Takaesu, CA Berlinicke, J Wan, J Sun, DJ Zack (2022) Fatality assessment and variant risk monitoring for COVID-19 using three new hospital occupancy related metrics. eBioMedicine (Part of THE LANCET Discovery Science) 83:104225.
    8. AM Asberry, X Cai, X Deng, U Santiago, S Liu, HS Sims, W Liang, X Xu, J Wan, W Jiang, CJ Camacho, M Dai, CD Hu (2022) Discovery and Biological Characterization of PRMT5:MEP50 Protein-Protein Interaction Inhibitors. Journal of Medicinal Chemistry 65(20):13793-13812.
    9. J Du, Q Wand, S Yang, S Chen, Y Fu, S Spath, P Domeier, D Hagin, S Anover-Sombke, M Haouili, S Liu, J Wan, L Han, J Liu, L Yang, N Sangani, Y Li, X Lu, SC Janga, MH Kaplan, TR Torgerson, SF Ziegler, B Zhou (2022) FOXP3 exon 2 controls Treg stability and autoimmunity. Science Immunology 7 (72), eabo5407.
    10. K Singh, Y Rustagi, AS Abouhashem, S Tabasum, P Verma, E Hernandez, D Pal, DK Khona, SK Mohanty, M Kumar, R Srivastava, PR Guda, SS Verma, S Mahajan, JA Killian, LA Walker, S Ghatak, SS Mathew-Steiner, K Wanczyk, S Liu, J Wan, P Yan, R Bundschuh, S Khanna, GM Gordillo, MP Murphy, S Roy, CK Sen (2022) Genome-wide DNA hypermethylation opposes healing in chronic wound patients by impairing epithelial-to-mesenchymal transition. Journal of Clinical Investigation 132(17):e157279.
    11. T Zhao, S Liu, X Ding, EM Johnson, NH Hanna, K Singh, CK Sen, J Wan, H Du§, C Yan§ (2022) Lysosomal acid lipase, CSF1R and PD-L1 determine functions of CD11c+ myeloid-derived suppressor cells. JCI Insight 7(17):e156623.
    12. Y Rustagi, AS Abouhashem, P Verma, SS Verma, E Hernandez, S Liu, M Kumar, PR Guda, R Srivastava, SK Mohanty, S Kacar, S Mahajan, KE Wanczyk, S Khanna, MP Murphy, GM Gordillo, S Roy, J Wan, CK Sen, K Singh (2022) Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy. Diabetes 71 (5),1149.
    13. J Liu, Y Zhang, L Han, S Guo, S Wu, EH Doud, C Wang, H Chen, M Rubart-von der Lohe, J Wan, L Yang (2022) Genome-wide Analyses Revealed the Detrimental Impacts of SARS-CoV-2 Viral Gene Orf9c on Human Pluripotent Stem Cell-derived Cardiomyocytes. Stem Cell Reports 17 (3), 522.
    14. X Zhong, A Narasimhan, LM Silverman, AR Young, S Shahda, S Liu, J Wan, Y Liu, LG Koniaris, TA Zimmers (2022) Sex specificity of pancreatic cancer cachexia phenotypes, mechanisms, and treatment in mice and humans – role of Activin. J Cachexia Sarcopenia Muscle 13(4):2146-2161.
    15. Y Rustagi, AS Abouhashem, P Verma, SS Verma, E Hernandez, S Liu, M Kumar, PR Guda, R Srivastava, SK Mohanty, S Kacar, S Mahajan, KE Wanczyk, S Khanna, MP Murphy, GM Gordillo, S Roy, J Wan, CK Sen, K Singh (2022) Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy. Diabetes 71(5), 1149.
    16. Z Shi, J Lopez, W Kalliney, B Sutton, J Simpson, K Maggert, S Liu, J Wan, MS Stack (2022) Development and evaluation of ActSeq: a targeted next-generation sequencing panel for clinical oncology use. PLoS One 17(4): e0266914.
    17. AY Hsu, T Wang, R Syahirah, S Liu, K Li, W Zhang, J Wang, Z Cao, S Tian, S Matosevic, C Staiger, J Wan, Q Deng (2022) RORA regulates neutrophil migration and activation in zebrafish. Frontiers in Immunology 13:756034.
    18. J Xu, Y Liu, S Liu, W Ou, A White, S Stewart, KHR Tkaczuk, LM Ellis, J Wan, X Lu§, X He§ (2022) Metformin bicarbonate-mediated efficient RNAi for precise targeting of TP53 deficiency in colon and rectal cancers. Nano Today 43, 101406
    19. GM Cunningham, F Shen, X Wu, EL Cantor, L Gardner, S Philips, G Jiang, CL Bales, Z Tan, Y Liu, J Wan, JC Fehrenbacher, BP Schneider (2022) The impact of SBF2 on taxane-induced peripheral neuropathy. PLoS Genetics 18 (1), e1009968.

    2021

    1. Y Chen, S Fang, Q Ding, R Jiang, J He, Q Wang, Y Jin, X Huang, S Liu, ML Capitano, T Trinh, Y Teng, Q Meng§, J Wan§, HE Broxmeyer§, B Guo§ (2021) ADGRG1 enriches for functional human hematopoietic stem cells following ex vivo expansion-induced mitochondrial oxidative stress. Journal of Clinical Investigation 131 (20), e148329.
    2. 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 49(D1):D706-D714.
    3. S Fang, S Liu, J Shen, AZ Lu, AKY Wang, Y Zhang, K Li, J Liu, L Yang, CD Hu, J Wan (2021) Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association. Journal of Medical Virology  (selected as cover image) 93 (12), 6525-6534.
      jmv-cover-image
    4. 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) An organoid-based screen for epigenetic inhibitors that stimulate antigen presentation and potentiate T-cell-mediated cytotoxicity. Nature Biomedical Engineering 5 (11), 1320.
    5. 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 1864 (3), 194691.
    6. SR Sripathi, MW Hu, RC Turaga, J Mertz, MM Liu, J Wan, J Maruotti, KJ Wahlin, CA Berlinicke, J Qian, DJ Zack (2021) Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT. Molecular & Cellular Proteomics 20, 100131.
    7. W Zhao, L Jiang, T Fang, F Fang, Y Liu, Y Zhao, Y You, H Zhou, X Su, J Wang, S Liu, Y Chen, J Wan, X Huang (2021) β-Lapachone selectively kills hepatocellular carcinoma cells by targeting NQO1 to induce extensive DNA damage and PARP1 hyperactivation. Frontiers in Oncology 11, 747282.
    8. 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 206 (9), 2088.
    9. 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 (1), 795.
    10. 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 (1), 229. (PMID: 32127640)
    11. J Wan, H Dai, X Zhang, S Liu, Y Ling, A-K Somani, J Xie§, J Han§ (2021) Distinct Transcriptomic Landscapes of Cutaneous Basal Cell Carcinomas and Squamous Cell Carcinomas. Genes & Diseases 8 (2), 181.
    12. NP Rayana, CK Sugali, J Dai, M Peng, S Liu, Y Zhang, J Wan, W Mao (2021) Using CRISPR interference as a therapeutic approach to treat TGFβ2-induced ocular hypertension and glaucoma. Investigative Ophthalmology & Visual Science 62 (12), 7.
    13. J Liu, S Liu, L Han, Y Sheng, Y Zhang, I Kim, J Wan, L Yang (2021) LncRNA HBL1 is Required for Genome-Wide PRC2 Occupancy and Function in Cardiogenesis from Human Pluripotent Stem Cells. Development 148 (13).
    14. C Zhu, M Huang, HG Kim, K Chowdhury, J Gao, S Liu, J Wan, L Wei, XC Dong (2021) SIRT6 controls hepatic lipogenesis by suppressing LXR, ChREBP, and SREBP1. Biochimica et Biophysica Acta - Molecular Basis of Disease 1867 (12), 166249
    15. 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 62 (4), 1.
    16. 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 2 (3), 100219.
    17. N Lin, J Liu, J Castle, J Wan, A Shendre, Y Liu, C Wang, C He (2021) Genome-wide DNA methylation profiling in human breast tissue by illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray. Epigenetics 16 (7), 754-769.
    18. 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 11 (1), 40.

    2020

    1. 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)
    2. 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 11, 593548.
    3. 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)
    4. 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 20 (1), 651.
    5. 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.
    6. 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)
    7. 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)
    8. 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.
    9. 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)
    10. S Dey, JJ Kwon, S Liu, GA Hodge, S Taleb, TA Zimmers, J Wan, J Kota (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

    1. 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.
    2. 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.
    3. 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)
    4. 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)
    5. 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)
    6. 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.
    7. 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)
    8. 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)
    9. 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)
    10. 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

    1. 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.
    2. 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.
    3. 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.
    4. 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)
    5. 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)
    6. 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)
    7. 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)
    8. 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)
    9. 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)
    10. 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)
    11. 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)
    12. 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)
    13. 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)
    14. 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

    1. 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.
    2. 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)
    3. 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)
    4. 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)
    5. 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)
    6. 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 in Bioinformatics before 2017

    1. 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.
    2. T Masuda*, K Wahlin*, J Wan* (co-first author), J Hu, J Maruotti, X Yang, J Iacovelli, N Wolkow, R Kist, JL Dunaief, J Qian, DJ Zack, N Esumi (2014) Transcription Factor SOX9 Plays a Key Role in the Regulation of Visual Cycle Gene Expression in the Retinal Pigment Epithelium. Journal of Biological Chemistry 289 (18): 12908.
    3. 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).
    4. 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.
    5. 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 (18): 7920.
    6. L Hackler*, J Wan* (co-first author), A Swaroop, J Qian, DJ Zack (2010) MicroRNA profile of the developing mouse retina. Investigative Ophthalmology & Visual Science 51 (4): 1823.
    7. J Wan, J Lin, D Zack, J Qian (2009) Relating periodicity of nucleosome organization and gene regulation. Bioinformatics 25: 1782.