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Cancer Genomics Center

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  • 2018 Publications
    1. Hu R, Dai Y, Jia P, Zhao Z, ANCO-GeneDB: Annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine, and opioid dependence, Database (Oxford). 2018 Jan 1;2018:bay121. doi: 10.1093/database/bay121. PMID: 30403795
    2. Mallik S, Zhao Z, Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm, BMC Syst Biol. 2018 Dec 21;12(Suppl 8):126. doi: 10.1186/s12918-018-0650-2, PMID: 30577846
  • 2019 Publications
    1. Zhang Z, Lee JH, Ruan H, Ye Y, Krakowiak J, et al., Li W#, and Han L, Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer, Nat Commun. 2019 Oct 8;10(1):4562. doi: 10.1038/s41467-019-12543-5. PMID: 31594934
    2. Mallik S, Zhao Z, Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles, Genes (Basel). 2019 Aug 13;10(8):611. doi: 10.3390/genes10080611. PMID: 31412637
    3. Hu R, Pei G, Jia P, Zhao Z, Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. Methods. 2021 May;189:44-53. doi: 10.1016/j.ymeth.2019.10.012. Epub 2019 Oct 28. PMID: 31672653
    4. Jia P, Pei G, Zhao Z, CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures, Bioinformatics. 2019 Dec 15;35(24):5207-5215. doi: 10.1093/bioinformatics/btz441. PMID: 31141125
    5. Pei G, Dai, Y, Zhao Z, deTS: tissue-specific enrichment analysis to decode tissue specificity, Bioinformatics. 2019 Oct 1;35(19):3842-3845. doi: 10.1093/bioinformatics/btz138. PMID: 30824912
    6. Jia P, Zhao Z, Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types, Cell Rep. 2019 Jan 8;26(2):496-506.e3. doi: 10.1016/j.celrep.2018.12.066.
    7. Gallant JN, Sewell A, Almodovar K, Wang Q, Dahlman KB, Abramson RG, Kapp ME, Brown BT, Boyd KL, Gilbert J, Cohen DN, Yarbrough WG, Zhao Z, Lovly CM, Genomic landscape of a metastatic malignant proliferating tricholemmal tumor and its response to PI3K inhibition, NPJ Precis Oncol. 2019 Feb 15;3:5. doi: 10.1038/s41698-019-0077-2. eCollection 2019. PMID: 30793038
  • 2020 Publications
    1. Mallik S, Zhao Z, Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data, Brief Bioinform. 2020 Mar 23;21(2):368-394. doi: 10.1093/bib/bby120. PMID: 30649169
    2. Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterie M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP, Temozolomide-induced RNA interactome uncovers novel lncRNA regulatory loops in glioblastoma. Cancers (Basel). 2020 Sep 10;12(9):2583. doi: 10.3390/cancers12092583. PMID: 32927769
    3. Li A, Mallik S, Luo H, Jia P, DF Lee, Zhao Z, H19, a long non-coding RNA, mediates transcription factors and target genes through interference of microRNAs in pan-cancer. Mol Ther Nucleic Acids. 2020 Sep 4;21:180-191. doi: 10.1016/j.omtn.2020.05.028. Epub 2020 May 27. PMID: 32585626
    4. Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z, VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Res. 2020 Jan 8;48(D1):D633-D641. doi: 10.1093/nar/gkz867. PMID: 31598702
    5. Zhang L, Yao J, Wei Y, Zhou Z, Li P, Qu J, Badu-Nkansah A, Yuan X, Huang Y, Fukumura K, Mao X, Chang W, Saunus J, Lakhani S, Huse JT, Huang M, Yu D, Blocking immunosuppressive neutrophils deters pY696-EZH2-driven brain metastases. Sci Transl Med. 2020 May 27;12(545):eaaz5387. doi: 10.1126/scitranslmed.aaz5387. PMID: 32461334
    6. Gebru MT, Atkinson JM, Young MM, Zhang L, Tang Z, Liu Z, Lu P, Dower CM, Chen L, Annageldiyev C, Sharma A, Kawasawa YI, Zhao Z, Miller BA, Claxton DF, Wang H-G, Glucocorticoids enhance the anti-leukemic activity of FLT3 inhibitors in FLT3 mutant acute myeloid leukemia. Blood. 2020 Aug 27;136(9):1067-1079. doi: 10.1182/blood.2019003124. PMID: 32396937
    7. Xu H, Hu R, Jia P, Zhao Z, 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. PMID: 32091591
    8. Qin G, Mallik S, Mitra R, Li A, Jia P, Zhao Z, MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep. 2020 Jan 21;10(1):852. doi: 10.1038/s41598-020-57834-w. PMID: 31965022
    9. Jia P, Dai Y, Hu R, Pei G, Manuel A, Zhao Z, TSEA-DB: A trait-tissue association map for human complex traits and diseases, Nucleic Acids Res. 2020 Jan 8;48(D1):D1022-D1030. doi: 10.1093/nar/gkz957. PMID: 31680168
    10. Pei G, Hu R, Dai Y, Zhao Z, Jia P, Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network. Oncogene. 2020 Jul;39(27):5031-5041. doi: 10.1038/s41388-020-1343-z. Epub 2020 Jun 11. PMID: 32528130
    11. Mallik S, Qin G, Jia P, Zhao Z, Molecular signatures identified by integrating gene expression and methylation in nonseminoma and seminoma of testicular germ cell tumors, Epigenetics. Jan-Feb 2021;16(2):162-176. doi: 10.1080/15592294.2020.1790108. Epub 2020 Jul 13. PMID: 32615059
    12. Mallik S, Seth S, Bhardra T, Zhao Z, A linear regression and deep learning approach for detecting reliable genetic alterations in cancer using DNA methylation and gene expression data. Genes (Basel). 2020 Aug 12;11(8):931. doi: 10.3390/genes11080931. PMID: 32806782
    13. An Xu, Mo-Fan Huang, Dandan Zhu, Julian A. Gingold, Danielle A. Bazer, Betty Chang, Donghui Wang, Chien-Chen Lai, Ihor R. Lemischka, Ruiying Zhao and Dung-Fang Lee, LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes. Front Genet. 2021 Jan 15;11:611823. doi: 10.3389/fgene.2020.611823. eCollection 2020. PMID: 33519915
    14. Bangxing Hong, Valerie Chapa, Uksha Saini, Puneet Modgil, David E. Cohn, Guangan He, Zahid H. Siddik, Anil K. Sood, Yuanqing Yan, Karuppaiyah Selvendiran, Guangsheng Pei,Zhongming Zhao, Ji Young Yoo, and Balveen Kaur, Oncolytic HSV therapy modulates vesicular trafficking inducing cisplatin sensitivity and anti-tumor immunity. Clin Cancer Res. 2021 Jan 15;27(2):542-553. doi: 10.1158/1078-0432.CCR-20-2210. Epub 2020 Oct 21. PMID: 33087329
    15. Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik and Zhongming Zhao, In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):499. doi: 10.1186/s12859-020-03849-z. PMID: 33371879
    16. Lukas M. Simon , Fangfang Yan and Zhongming Zhao, DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. Gigascience. 2020 Dec 10;9(12):giaa122. doi: 10.1093/gigascience/giaa122. PMID: 33301553
    17. Saurav Mallik & Zhongming Zhao, Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise. Sci Rep. 2020 Dec 17;10(1):22164. doi: 10.1038/s41598-020-78463-3. PMID: 33335112
    18. Yulin Dai, Timothy D. O’Brien, Guangsheng Pei, Zhongming Zhao, and Peilin Jia, Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders. BMC Med Genomics. 2020 Dec 28;13(Suppl 11):192. doi: 10.1186/s12920-020-00832-8. PMID: 33371872
    19. Zhanguo Gao, Alexes C. Daquinag, Cale Fussell, Zhongming Zhao, Yulin Dai, Angielyn Rivera, Brad E. Snyder, Kristin L. Eckel-Mahan and Mikhail G. Kolonin, Age-associated telomere attrition in adipocyte progenitors predisposes to metabolic disease. Nat Metab. 2020 Dec;2(12):1482-1497. doi: 10.1038/s42255-020-00320-4. Epub 2020 Dec 14. PMID: 33324010
    20. Ruifeng Hu, Haodong Xu, Peilin Jia and Zhongming Zhao, KinaseMD: kinase mutations and drug response database. Nucleic Acids Res. 2021 Jan 8;49(D1):D552-D561. doi: 10.1093/nar/gkaa945. PMID: 33137204
    21. Teng Liu, Peilin Jia, Bingliang Fang and Zhongming Zhao, Differential expression of viral transcripts from single-cell RNA sequencing of moderate and severe COVID-19 patients and its implications for case severity. Front Microbiol. 2020 Oct 16;11:603509. doi: 10.3389/fmicb.2020.603509. eCollection 2020. PMID: 33178176
    22. Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim, Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation. Res Sq. 2020 Dec 11;rs.3.rs-114758. doi: 10.21203/rs.3.rs-114758/v1. Preprint. PMID: 33330858
    23. Aimin Li, Saurav Mallik, Haidan Luo, Peilin Jia, Dung-Fang Lee, and Zhongming Zhao. H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. Mol Ther Nucleic Acids. 2020 Sep 4;21:180-191. doi: 10.1016/j.omtn.2020.05.028. Epub 2020 May 27. PMID: 32585626
    24. Sabrina Fritah, Arnaud Muller, Wei Jiang, Ramkrishna Mitra, Mohamad Sarmini, Monika Dieterle, Anna Golebiewska , Tao Ye, Eric Van Dyck, Christel Herold-Mende,Zhongming Zhao, Francisco Azuaje and Simone P. Niclou, Temozolomide-induced rna interactome uncovers novel lncrna regulatory loops in glioblastoma. Cancers (Basel). 2020 Sep 10;12(9):2583. doi: 10.3390/cancers12092583. PMID: 32927769
    25. Hong BH, Chapa V, Saini U, Modgil P, Cohn DE, Sood A, Yan Y, Saruppaiyah S, Pei G, Zhao Z, Yoo JY, Kaur B, Oncolytic HSV therapy modulates vesicular trafficking inducing cisplatin sensitivity and anti-tumor immunity. Clin Cancer Res. 2021 Jan 15;27(2):542-553. doi: 10.1158/1078-0432.CCR-20-2210. Epub 2020 Oct 21. PMID: 33087329
    26. Tang M, Feng X, Pei G, Srivastava M, Wang C, Chen Z, Li S, Zhang H, Zhao Z, Li X, Chen J, FOXK1 participates in DNA damage response by controlling 53BP1 function. Cell Rep. 2020 Aug 11;32(6):108018. doi: 10.1016/j.celrep.2020.108018.
  • 2021 Publications
    1. Hu R, Pei G, Jia P, Zhao Z, Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. Methods. 2021 May;189:44-53. doi: 10.1016/j.ymeth.2019.10.012. Epub 2019 Oct 28. PMID: 31672653
    2. Kim P, Li H, Wang S, Zhao Z, Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform. 2021 May 20;22(3):bbaa108. doi: 10.1093/bib/bbaa108. PMID: 32510566
    3. Hu H, Jia P, Zhao Z, Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Brief Bioinform. 2021 May 20;22(3):bbaa099. doi: 10.1093/bib/bbaa099. PMID: 32578842
    4. Nathaniel K. Berg, Jiwen Li, Boyun Kim, Tingting Mills, Guangsheng Pei, Zhongming Zhao, Xiangyun Li1, Xu Zhang, Wei Ruan, Holger K. Eltzschig, Xiaoyi Yuan, Hypoxia-inducible factor-dependent induction of myeloid-derived netrin-1 attenuates natural killer cell infiltration during endotoxin-induced lung injury. FASEB J. 2021 Apr;35(4):e21334. doi: 10.1096/fj.202002407R. PMID: 33715200
    5. Margaret Yeh, Yin?Ying Wang, Ji Young Yoo, Christina Oh, Yoshihiro Otani, Jin Muk Kang, Eun S. Park, Eunhee Kim, Sangwoon Chung, Young?Jun Jeon, George A. Calin, Balveen Kaur, Zhongming Zhao & Tae Jin Lee, MicroRNA-138 suppresses glioblastoma proliferation through downregulation of CD44. Sci Rep. 2021 Apr 28;11(1):9219. doi: 10.1038/s41598-021-88615-8. PMID: 33911148
    6. Danesh H. Sopariwala, Neah Likhite, Gungsheng Pei, Fnu Haroon, Lisa Lin, Vikas Yadav, Zhongming Zhao, Vihang A. Narkar, Estrogen-related receptor ? is involved in angiogenesis and skeletal muscle revascularization in hindlimb ischemia. FASEB J. 2021 May;35(5):e21480. doi: 10.1096/fj.202001794RR. PMID: 33788962
    7. Fei Su, Alexes C. Daquinag, Songyeon Ahn, Achinto Saha, Yulin Dai, Zhongming Zhao, John DiGiovanni and Mikhail G. Kolonin, Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium. NPJ Precis Oncol. 2021 Mar 22;5(1):26. doi: 10.1038/s41698-021-00160-9. PMID: 33753872
    8. Ping Yuan, Sirisha M. Cheedipudi, Leila Rouhi, Siyang Fan, Lukas Simon, Zhongming Zhao, Kui Hong , Priyatansh Gurha , Ali J. Marian, Single Cell RNA-Sequencing Uncovers Paracrine Functions of the Epicardial-Derived Cells in Arrhythmogenic Cardiomyopathy. Circulation. 2021 Jun;143(22):2169-2187. doi: 10.1161/CIRCULATIONAHA.120.052928. Epub 2021 Mar 17. PMID: 33726497
    9. Yinjie Zhang, Baibing Yang, Joy M. Davis, Madeline M. Drake, Mamoun Younes,Qiang Shen, Zhongming Zhao , Yanna Cao , and Tien C. Ko, Distinct Murine Pancreatic Transcriptomic Signatures during Chronic Pancreatitis Recovery. Mediators Inflamm. 2021 May 15;2021:5595464. doi: 10.1155/2021/5595464. eCollection 2021. PMID: 34104113
    10. Tang, Deyou; Li, Yucheng; Tan, Daqiang; Fu, Juan; Tang, Yelei; Lin, Jiabin; Zhao, Rong; Du, Hongli; Zhao, Zhongming; KCOSS: an ultra-fast k-mer counter for assembled genome analysis. Bioinformatics. 2022 Jan 27;38(4):933-940. doi: 10.1093/bioinformatics/btab797. PMID: 34849595 (2021)
    11. Bhadra, Tapas; Mallik, Saurav; Sohel, Amir; Zhao, Zhongming; Unsupervised Feature Selection Using an Integrated Strategy of Hierarchical Clustering with Singular Value Decomposition: An Integrative Biomarker Discovery Method with Application to Acute Myeloid Leukemia. IEEE/ACM Transactions on Computational Biology and Bioinformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2022 May-Jun;19(3):1354-1364. doi: 10.1109/TCBB.2021.3110989. Epub 2022 Jun 3. PMID: 34495838 (2021)
    12. Ravirala, Divya; Pei, Guangsheng; Zhao, Zhongming; Zhang, Xiaoliu; Single-cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV infection in tumor tissue. Molecular Therapy-Oncolytics. 2021 Oct 20:23:330-341. doi: 10.1016/j.omto.2021.10.006. eCollection 2021 Dec 17. PMID: 34786476 (2021)
    13. Fan, Huihui; Jia, Peilin; Zhao, Zhongming; Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis. Cancers. 2021 Nov 30;13(23):6024. doi: 10.3390/cancers13236024. PMID: 34885134 (2021)
    14. Hsieh, Kanglin; Wang, Yinyin; Chen, Luyao; Zhao, Zhongming; Savitz, Sean; Jiang, Xiaoqian; Tang, Jing; Kim, Yejin; Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence. Scientific reports. 2021 Nov 30;11(1):23179. doi: 10.1038/s41598-021-02353-5.PMID: 34848761 (2021)
    15. Sopariwala, Danesh H; Likhite, Neah; Pei, Gungsheng; Haroon, Fnu; Lin, Lisa; Yadav, Vikas; Zhao, Zhongming; Narkar, Vihang A; Estrogen?related receptor ? is involved in angiogenesis and skeletal muscle revascularization in hindlimb ischemia. The FASEB Journal. 2021 Apr;35(4):e21334. doi: 10.1096/fj.202002407R. 33788962 (2021)
    16. Berg, Nathaniel K; Li, Jiwen; Kim, Boyun; Mills, Tingting; Pei, Guangsheng; Zhao, Zhongming; Li, Xiangyun; Zhang, Xu; Ruan, Wei; Eltzschig, Holger K; Hypoxia?inducible factor?dependent induction of myeloid?derived netrin?1 attenuates natural killer cell infiltration during endotoxin?induced lung injury. The FASEB Journal. 2021 Apr;35(4):e21334. doi: 10.1096/fj.202002407R. PMID: 33715200 (2021)
    17. Yuan, Ping; Cheedipudi, Sirisha M; Rouhi, Leila; Fan, Siyang; Simon, Lukas; Zhao, Zhongming; Hong, Kui; Gurha, Priyatansh; Marian, Ali J; Single-cell RNA sequencing uncovers paracrine functions of the epicardial-derived cells in arrhythmogenic cardiomyopathy. Circulation. 2021 Jun;143(22):2169-2187. doi: 10.1161/CIRCULATIONAHA.120.052928. Epub 2021 Mar 17. PMID: 33726497 (2021)
    18. Ravirala, Divya; Pei, Guangsheng; Zhao, Zhongming; Zhang, Xiaoliu; Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing. Cancer Immunology, Immunotherapy. 2022 Jun;71(6):1479-1495. doi: 10.1007/s00262-021-03084-2. Epub 2021 Oct 30. PMID: 34716463 (2021)
    19. Li, Hongzhong; Xiao, Yi; Li, Qin; Yao, Jun; Yuan, Xiangliang; Zhang, Yuan; Yin, Xuedong; Saito, Yohei; Fan, Huihui; Li, Ping; The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1. Cancer cell. 2022 Jan 10;40(1):36-52.e9. doi: 10.1016/j.ccell.2021.11.002. Epub 2021 Nov 24. PMID: 34822775 (2021)
    20. Lukas M. Simon, Yin-Ying Wang and Zhongming Zhao, Integration of millions of transcriptomes using batch-aware triplet neural networks. Nature Machine Intelligence volume 3, pages705–715 (2021)
    21. Andi Liu, Yulin Dai, Emily F. Mendez,Ruifeng Hu,Gabriel R. Fries,Katherine E. Najera, Shan Jiang, Thomas D. Meyer, Laura Stertz, Peilin Jia, Consuelo Walss-Bass, Zhongming Zhao, Genome-wide correlation of DNA methylation and gene expression in postmortem brain tissues of opioid use disorder patients. Int J Neuropsychopharmacol. 2021 Nov 12;24(11):879-891. doi: 10.1093/ijnp/pyab043. PMID: 34214162
    22. Astrid M. Manuel, Yulin Dai, Leorah A. Freeman, Peilin Jia, Zhongming Zhao, An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. Mol Cell Neurosci. 2021 Sep;115:103656. doi: 10.1016/j.mcn.2021.103656. Epub 2021 Jul 17. PMID: 34284104
    23. Haodong Xu, Peilin Jia and Zhongming Zhao, Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Brief Bioinform. 2021 May 20;22(3):bbaa099. doi: 10.1093/bib/bbaa099. PMID: 32578842
    24. Pora Kim, Hanyang Li, Junmei Wang and Zhongming Zhao, Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform. 2021 May 20;22(3):bbaa108. doi: 10.1093/bib/bbaa108. PMID: 32510566
    25. Haodong Xu, Peilin Jia, and Zhongming Zhao, DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery. Adv Sci (Weinh). 2021 Mar 8;8(9):2004958. doi: 10.1002/advs.202004958. eCollection 2021 May. PMID: 33977077
    26. Yulin Dai, Junke Wang, Hyun?Hwan Jeong, Wenhao Chen, Peilin Jia, Zhongming Zhao, Hum Genet. 2021 Sep;140(9):1313-1328. doi: 10.1007/s00439-021-02305-z. Epub 2021 Jun 21. PMID: 34155559
    27. Bingrui Li, Guangsheng Pei, Jun Yao, Qingqing Ding, Peilin Jia and Zhongming Zhao, Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. Oncogene. 2021 Jul;40(28):4686-4694. doi: 10.1038/s41388-021-01870-x. Epub 2021 Jun 17. PMID: 34140640
    28. Peilin Jia, Astrid M. Manuel, Brisa S. Fernandes, Yulin Dai and Zhongming Zhao, Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. Brief Bioinform. 2021 Nov 5;22(6):bbab214. doi: 10.1093/bib/bbab214. PMID: 34086851
    29. Ruifeng Hu, Guangsheng Pei, Peilin Jia, Zhongming Zhao, Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. Methods. 2021 May;189:44-53. doi: 10.1016/j.ymeth.2019.10.012. Epub 2019 Oct 28. PMID: 31672653
    30. Guangsheng Pei, Ruifeng Hu , Peilin Jia , and Zhongming Zhao, DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue-and cell type-specific manner. Nucleic Acids Res. 2021 Jul 2;49(W1):W131-W139. doi: 10.1093/nar/gkab429. PMID: 34048560
    31. Peilin Jia, Ruifeng Hu, Guangsheng Pei, Yulin Dai , Yin-Ying Wang & Zhongming Zhao, Deep generative neural network for accurate drug response imputation. Nat Commun. 2021 Mar 19;12(1):1740. doi: 10.1038/s41467-021-21997-5. PMID: 33741950
    32. Hyun-Hwan Jeong, Johnathan Jia, Yulin Dai, Lukas M. Simon and Zhongming Zhao, Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches. Genes (Basel). 2021 Apr 24;12(5):635. doi: 10.3390/genes12050635. PMID: 33923155
    33. Guangsheng Pei, Yin-Ying Wang, Lukas M. Simon, Yulin Dai, Zhongming Zhao, and Peilin Jia, Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Res. 2021 Jan;31(1):146-158. doi: 10.1101/gr.265769.120. Epub 2020 Dec 3. PMID: 33272935
    34. Guangsheng Pei, Ruifeng Hu, Yulin Dai, Astrid Marilyn Manuel, Zhongming Zhao and Peilin Jia, Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations. Nucleic Acids Res. 2021 Jan 11;49(1):53-66. doi: 10.1093/nar/gkaa1137. PMID: 33300042
    35. Yulin Dai, Ruifeng Hu, Astrid Marilyn Manuel, Andi Liu, Peilin Jia , and Zhongming Zhao, CSEA-DB: an omnibus for human complex trait and cell type associations. Nucleic Acids Res. 2021 Jan 8;49(D1):D862-D870. doi: 10.1093/nar/gkaa1064. PMID: 33211888
    36. Ruoyu Wang, Joo-Hyung Lee, Feng Xiong, Jieun Kim, Lana Al Hasani, Xiaoyi Yuan, Pooja Shivshankar, Joanna Krakowiak, Chuangye Qi, Yanyu Wang, Holger K. Eltzschig, Wenbo Li, SARS-CoV-2 Restructures the Host Chromatin Architecture. bioRxiv. 2021 Jul 21;2021.07.20.453146. doi: 10.1101/2021.07.20.453146. Preprint PMID: 34312624
    37. Ji-Young Yoo, Margaret Yeh, Yin-Ying Wang, Christina Oh, Zhong-Ming Zhao, Balveen Kaur and Tae-Jin Lee, MicroRNA-138 Increases Chemo-Sensitivity of Glioblastoma through Downregulation of Survivin. Biomedicines. 2021 Jul 6;9(7):780. doi: 10.3390/biomedicines9070780. PMID: 34356844
    38. Feng Xiong, Ruoyu Wang, Joo-Hyung Lee, Shenglan Li, Shin-Fu Chen, Zian Liao, Lana Al Hasani, Phuoc T. Nguyen, Xiaoyu Zhu, Joanna Krakowiak, Dung-Fang Lee, Leng Han, Kuang-Lei Tsai, Ying Liu and Wenbo Li, RNA m6A Modification Orchestrates a LINE-1/Host Interaction That Facilitates Retrotransposition and Contributes to Long Gene Vulnerability. Cell Res. 2021 Aug;31(8):861-885. doi: 10.1038/s41422-021-00515-8. Epub 2021 Jun 9. PMID: 34108665
    39. Fangfang Yan, Zhongming Zhao, and Lukas M. Simon, EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. Patterns (N Y). 2021 Jul 20;2(8):100311. doi: 10.1016/j.patter.2021.100311. eCollection 2021 Aug 13. PMID: 34430929
    40. Joo-Hyung Lee, Ruoyu Wang, Feng Xiong, Joanna Krakowiak, Zian Liao, Phuoc T. Nguyen, Elena V. Moroz-Omori, Jiaofang Shao, Xiaoyu Zhu, Michael J. Bolt, Haoyi Wu, Pankaj K. Singh, Mingjun Bi,Caleb J. Shi, Naadir Jamal, Guojie Li, Ragini Mistry, Sung Yun Jung, Kuang-Lei Tsai, Josephine C. Ferreon, Fabio Stossi, Amedeo Caflisch, Zhijie Liu, Michael A. Mancini, and Wenbo Li, Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell. 2021 Aug 19;81(16):3368-3385.e9. doi: 10.1016/j.molcel.2021.07.024. Epub 2021 Aug 9. PMID: 34375583
    41. Emma Rodriguez, Guangsheng Pei, Sang T. Kim, Alexis German and Prema Robinson, Substance P Antagonism as a Novel Therapeutic Option to Enhance Efficacy of Cisplatin in Triple Negative Breast Cancer and Protect PC12 Cells against Cisplatin-Induced Oxidative Stress and Apoptosis. Cancers (Basel). 2021 Jul 31;13(15):3871. doi: 10.3390/cancers13153871. PMID: 34359773
    42. Mengfan Tang, Guangsheng Pei, Dan Su, Chao Wang, Xu Feng, Mrinal Srivastava, Zhen Chen, Zhongming Zhao, and Junjie Chen, Genome-wide CRISPR Screens Reveal Cyclin C as Synthetic Survival Target of BRCA2. Nucleic Acids Res. 2021 Jul 21;49(13):7476-7491. doi: 10.1093/nar/gkab540. PMID: 34197614
  • 2022 Publications
    1. Qiang Wang, Zhijuan Lin, Zhuo Wang, Lingqun Ye, Miao Xian, Liuling Xiao, Pan Su, Enguang Bi, Yung-hsing Huang, Jianfei Qian, Lintao Liu, Xingzhe Ma, Maojie Yang, Wei Xiong, Youli Zu, Sai Ravi Pingali, Bing Xu, and Qing Yi, RAR? activation sensitizes human myeloma cells to carfilzomibtreatment through OAS-RNase L innate immune pathway. Blood. 2022 Jan 6;139(1):59-72. doi: 10.1182/blood.2020009856. PMID: 34411225
    2. Yan, Fangfang; Zhao, Zhongming; Simon, Lukas M; EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data. bioRxiv. 2021 Jul 20;2(8):100311. doi: 10.1016/j.patter.2021.100311. eCollection 2021 Aug 13. PMID: 34430929 (2022)
    3. Liu, Wendao; Jia, Johnathan; Dai, Yulin; Chen, Wenhao; Pei, Guangsheng; Yan, Qiheng; Zhao, Zhongming; Delineating COVID-19 immunological features using single-cell RNA sequencing. The Innovation. 2022 Sep 13;3(5):100289. doi: 10.1016/j.xinn.2022.100289. Epub 2022 Jul 21. PMID: 35879967 (2022)
    4. Liu, Wendao; Ye, Xiaohua; An, Zhiqiang; Zhao, Zhongming; The challenges and opportunities of scRNA-seq in COVID-19 research and clinical translation. Virology Journal. 2022 Dec 15;19(1):217. doi: 10.1186/s12985-022-01923-x. PMID: 36522785 (2022)
    5. Jia, Peilin; Hu, Ruifeng; Yan, Fangfang; Dai, Yulin; Zhao, Zhongming; scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies. Genome biology. 2022 Oct 17;23(1):220. doi: 10.1186/s13059-022-02785-w. PMID: 36253801 (2022)
    6. Zheng, Mingjie; Li, Rich G; Song, Jia; Zhao, Xiaolei; Tang, Li; Erhardt, Shannon; Chen, Wen; Nguyen, Bao H; Li, Xiao; Li, Min; Hippo-Yap signaling maintains sinoatrial node homeostasis. Circulation. 2022 Nov 29;146(22):1694-1711. doi: 10.1161/CIRCULATIONAHA.121.058777. Epub 2022 Nov 1. PMID: 36317529 (2022)
    7. Yu, Yang; Zhao, Yanling; Choi, Jongmin; Shi, Zhongcheng; Guo, Linjie; Elizarraras, John; Gu, Andy; Cheng, Feng; Pei, Yanxin; Lu, Dai; ERK Inhibitor Ulixertinib Inhibits High-Risk Neuroblastoma Growth In Vitro and In Vivo. Cancers. 2022 Nov 10;14(22):5534. doi: 10.3390/cancers14225534. PMID: 36428626 (2022)
    8. Zhao, Xiaolei; Tang, Li; Le, Tram P; Nguyen, Bao H; Chen, Wen; Zheng, Mingjie; Yamaguchi, Hiroyuki; Dawson, Brian; You, Shuangjie; Martinez-Traverso, Idaliz M; Yap and Taz promote osteogenesis and prevent chondrogenesis in neural crest cells in vitro and in vivo. Science signaling. Yap and Taz promote osteogenesis and prevent chondrogenesis in neural crest cells in vitro and in vivo PMID: 36282910 (2022)
    9. Ghose, Partho; Alavi, Muhaddid; Tabassum, Mehnaz; Uddin, Ashraf; Biswas, Milon; Mahbub, Kawsher; Gaur, Loveleen; Mallik, Saurav; Zhao, Zhongming; Detecting COVID-19 infection status from chest X-ray and CT scan via single transfer learning-driven approach. Frontiers in genetics. 2022 Sep 21:13:980338. doi: 10.3389/fgene.2022.980338. eCollection 2022. PMID: 36212141 (2022)
    10. Zhu, Xiaoyu; Qi, Chuangye; Wang, Ruoyu; Lee, Joo-Hyung; Shao, Jiaofang; Bei, Lanxin; Xiong, Feng; Nguyen, Phuoc T; Li, Guojie; Krakowiak, Joanna; Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Cell reports. 2022 Nov 1;41(5):111576. doi: 10.1016/j.celrep.2022.111576. PMID: 36323253 (2022)
    11. Fernandes, Brisa S; Dai, Yulin; Jia, Peilin; Zhao, Zhongming; Charting the proteome landscape in major psychiatric disorders: from biomarkers to biological pathways towards drug discovery. European Neuropsychopharmacology. 2022 Aug:61:43-59. doi: 10.1016/j.euroneuro.2022.06.001. Epub 2022 Jun 25. PMID: 35763977 (2022)
    12. Mallik, Saurav; Qin, Guimin; Jia, Peilin; Zhao, Zhongming; Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours. Epigenetics. 2021 Jan-Feb;16(2):162-176. doi: 10.1080/15592294.2020.1790108. Epub 2020 Jul 13. PMID: 32615059 (2022)
    13. Xu, Haodong; Zhao, Zhongming; NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-Cell Epitopes. bioRxiv. 2022 Oct;20(5):1002-1012. doi: 10.1016/j.gpb.2022.11.009. Epub 2022 Dec 13. PMID: 36526218 (2022)
    14. Divya Ravirala, Guangsheng Pei, Zhongming Zhao, Xiaoliu Zhang; Immunotherapy Comperhensive characterization of tumor immune landscape following oncolytic virotheraoy by single-cell RNA sequencing. Cancer Immunol Immunother. 2022 Jun;71(6):1479-1495. doi: 10.1007/s00262-021-03084-2. Epub 2021 Oct 30. PMID: 34716463 (2022)
    15. Liu, Wendao; Jia, Johnathan; Dai, Yulin; Chen, Wenhao; Pei, Guangsheng; Yan, Qiheng; Zhao, Zhongming; Delineating COVID-19 immunological features using single-cell RNA sequencing. The Innovation. 2022 Sep 13;3(5):100289. doi: 10.1016/j.xinn.2022.100289. Epub 2022 Jul 21. PMID: 35879967 (2022)
    16. Seth, Soumita; Mallik, Saurav; Bhadra, Tapas; Zhao, Zhongming; Dimensionality Reduction and Louvain Agglomerative Hierarchical Clustering for Cluster-Specified Frequent Biomarker Discovery in Single-Cell Sequencing Data. Frontiers in genetics. 2022 Feb 7:13:828479. doi: 10.3389/fgene.2022.828479. eCollection 2022. PMID: 35198011 (2022)
    17. Munquad, Sana; Si, Tapas; Mallik, Saurav; Das, A; Zhao, Zhongming; A Deep Learning–Based Framework for Supporting Clinical Diagnosis of Glioblastoma Subtypes. Frontiers in genetics. 2022 Mar 28:13:855420. doi: 10.3389/fgene.2022.855420. eCollection 2022. PMID: 35419027 (2022)
    18. Pothiawala, Azim; Sahbazoglu, Berke E; Ang, Bryan K; Matthias, Nadine; Pei, Guangsheng; Yan, Qing; Davis, Brian R; Huard, Johnny; Zhao, Zhongming; Nakayama, Naoki; GDF5+ chondroprogenitors derived from human pluripotent stem cells preferentially form permanent chondrocytes. Development. 2022 Jun 1;149(11):dev196220. doi: 10.1242/dev.196220. Epub 2022 Jun 6.PMID: 35451016 (2022)
    19. Li, Gang; Li, Xin; Yang, Li; Wang, Shuyue; Dai, Yulin; Fekry, Baharan; Veillon, Lucas; Tan, Lin; Berdeaux, Rebecca; Eckel-Mahan, Kristin; Adipose tissue–specific ablation of Ces1d causes metabolic dysregulation in mice. Life science alliance. 2022 Apr 22;5(8):e202101209. doi: 10.26508/lsa.202101209. Print 2022 Aug. PMID: 35459739 (2022)
    20. Sharma, Pallabi; Balabantaray, B; Bora, Kangkana; Mallik, Saurav; Kasugai, Kunio; Zhao, Zhongming; An Ensemble-Based Deep Convolutional Neural Network for Computer-Aided Polyps Identification From Colonoscopy. Frontiers in Genetics. 2022 Apr 26:13:844391. doi: 10.3389/fgene.2022.844391. eCollection 2022. PMID: 35559018 (2022)
    21. Wang, Qiang; Lin, Zhijuan; Wang, Zhuo; Ye, Lingqun; Xian, Miao; Xiao, Liuling; Su, Pan; Bi, Enguang; Huang, Yung-hsing; Qian, Jianfei; RAR? activation sensitizes human myeloma cells to carfilzomib treatment through the OAS-RNase L innate immune pathway. Blood. 2022 Jan 6;139(1):59-72. doi: 10.1182/blood.2020009856. PMID: 34411225 (2022)
    22. Choi, Kyoung-Jae; Quan, My Diem; Qi, Chuangye; Lee, Joo-Hyung; Tsoi, Phoebe S; Zahabiyon, Mahla; Bajic, Aleksandar; Hu, Liya; Prasad, BV; Liao, Shih-Chu Jeff; NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. Nature cell biology. 2022 May;24(5):737-747. doi: 10.1038/s41556-022-00896-x. Epub 2022 Apr 28. PMID: 35484250 (2022)
    23. Li, Hongzhong; Xiao, Yi; Li, Qin; Yao, Jun; Yuan, Xiangliang; Zhang, Yuan; Yin, Xuedong; Saito, Yohei; Fan, Huihui; Li, Ping; The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1. Cancer cell. 2022 Jan 10;40(1):36-52.e9. doi: 10.1016/j.ccell.2021.11.002. Epub 2021 Nov 24. PMID: 34822775 (2022)
    24. Yuan, Qichen; Gao, Xue; Multiplex base-and prime-editing with drive-and-process CRISPR arrays. Nature communications. 2022 May 19;13(1):2771. doi: 10.1038/s41467-022-30514-1. PMID: 35589728 (2022)
    25. Bedi, Yudhishtar S; Roach, Alexis N; Thomas, Kara N; Mehta, Nicole A; Golding, Michael C; Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome. Epigenetics & chromatin. 2022 Jan 6;15(1):2. doi: 10.1186/s13072-021-00433-4. PMID: 34991687 (2022)
    26. Olcum, Melis; Cheedipudi, Sirisha M; Rouhi, Leila; Fan, Siyang; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; The WNT/?-catenin pathway regulates expression of the genes involved in cell cycle progression and mitochondrial oxidative phosphorylation in the postmitotic cardiac myocytes. The journal of cardiovascular aging. 2022;2(2):15. doi: 10.20517/jca.2021.35. Epub 2022 Jan 28. PMID: 35224561 (2022)
    27. Skibber, Max A; Olson, Scott D; Prabhakara, Karthik S; Gill, Brijesh S; Cox Jr, Charles S; Enhancing Mesenchymal Stromal Cell Potency: Inflammatory Licensing via Mechanotransduction. Frontiers in Immunology. 2022 Jul 6:13:874698. doi: 10.3389/fimmu.2022.874698. eCollection 2022. PMID: 35874742 (2022)
    28. Bhadra, Tapas; Mallik, Saurav; Hasan, Neaj; Zhao, Zhongming; Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. BMC bioinformatics. 2022 Apr 28;23(Suppl 3):153. doi: 10.1186/s12859-022-04678-y. PMID: 35484501 (2022)
    29. Pei, Guangsheng; Yan, Fangfang; Simon, Lukas M; Dai, Yulin; Jia, Peilin; Zhao, Zhongming; deCS: a tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues. Genomics, Proteomics & Bioinformatics. 2023 Apr;21(2):370-384. doi: 10.1016/j.gpb.2022.04.001. PMID: 35470070
    30. Liu, Andi; Manuel, Astrid M; Dai, Yulin; Zhao, Zhongming; Prioritization of risk genes in multiple sclerosis by a refined Bayesian framework followed by tissue-specificity and cell type feature assessment. BMC genomics. 2022 May 11;23(Suppl 4):362. doi: 10.1186/s12864-022-08580-y. PMID: 35545758 (2022)
    31. Yan, Fangfang; Simon, Lukas M; Suzuki, Akiko; Iwaya, Chihiro; Jia, Peilin; Iwata, Junichi; Zhao, Zhongming; Spatiotemporal MicroRNA-Gene Expression Network Related to Orofacial Clefts. Journal of Dental Research. 2022 Oct;101(11):1398-1407. doi: 10.1177/00220345221105816. Epub 2022 Jun 30. PMID: 35774010 (2022)
    32. Liu, Andi; Manuel, Astrid M; Dai, Yulin; Fernandes, Brisa S; Enduru, Nitesh; Jia, Peilin; Zhao, Zhongming; Identifying candidate genes and drug targets for Alzheimer’s disease by an integrative network approach using genetic and brain region-specific proteomic data. Human Molecular Genetics. 2022 Sep 29;31(19):3341-3354. doi: 10.1093/hmg/ddac124. PMID: 35640139 (2022)
    33. Otani, Yoshihiro; Yoo, Ji Young; Lewis, Cole T; Chao, Samantha; Swanner, Jessica; Shimizu, Toshihiko; Kang, Jin Muk; Murphy, Sara A; Rivera-Caraballo, Kimberly; Hong, Bangxing; NOTCH-induced MDSC recruitment after oHSV virotherapy in CNS cancer models modulates antitumor immunotherapy. Clinical Cancer Research. 2022 Apr 1;28(7):1460-1473. doi: 10.1158/1078-0432.CCR-21-2347. PMID: 35022322 (2022)
    34. Dai, Yulin; Yu, Hui; Yan, Qiheng; Li, Bingrui; Liu, Andi; Liu, Wendao; Jiang, Xiaoqian; Kim, Yejin; Guo, Yan; Zhao, Zhongming; Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments. Genes. 2022 Jul 6;13(7):1210. doi: 10.3390/genes13071210. PMID: 35885993 (2022)
    35. Dai, Yulin; Hu, Ruifeng; Liu, Andi; Cho, Kyung Serk; Manuel, Astrid Marilyn; Li, Xiaoyang; Dong, Xianjun; Jia, Peilin; Zhao, Zhongming; WebCSEA: web-based cell-type-specific enrichment analysis of genes. Nucleic Acids Research. 2022 Jul 5;50(W1):W782-W790. doi: 10.1093/nar/gkac392. PMID: 35610053 (2022)
    36. Rouhi, Leila; Fan, Siyang; Cheedipudi, Sirisha M; Olcum, Melis; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; Effects of tamoxifen inducible MerCreMer on gene expression in cardiac myocytes in mice. The journal of cardiovascular aging. 2022:2:8. doi: 10.20517/jca.2021.30. Epub 2022 Jan 5. PMID: 35079750 (2022)
    37. Dai, Yulin; Jia, Peilin; Zhao, Zhongming; Gottlieb, Assaf; A Method for Bridging Population-Specific Genotypes to Detect Gene Modules Associated with Alzheimer’s Disease. Cells. 2022 Jul 16;11(14):2219. doi: 10.3390/cells11142219. PMID: 35883662 (2022)
    38. Fekry, Baharan; Ribas?Latre, Aleix; Drunen, Rachel Van; Santos, Rafael Bravo; Shivshankar, Samay; Dai, Yulin; Zhao, Zhongming; Yoo, Seung?hee; Chen, Zheng; Sun, Kai; Hepatic circadian and differentiation factors control liver susceptibility for fatty liver disease and tumorigenesis. The FASEB Journal. 2022 Sep;36(9):e22482. doi: 10.1096/fj.202101398R. PMID: 35947136 (2022)
    39. Feng, Xu; Tang, Mengfan; Dede, Merve; Su, Dan; Pei, Guangsheng; Jiang, Dadi; Wang, Chao; Chen, Zhen; Li, Mi; Nie, Litong; Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors. Science advances. 2022 May 13;8(19):eabm6638. doi: 10.1126/sciadv.abm6638. Epub 2022 May 13. PMID: 35559673 (2022)
    40. Fernandes, Brisa S; Dai, Yulin; Jia, Peilin; Zhao, Zhongming; Charting the proteome landscape in major psychiatric disorders: From biomarkers to biological pathways towards drug discovery. European Neuropsychopharmacology. 2022 Aug:61:43-59. doi: 10.1016/j.euroneuro.2022.06.001. Epub 2022 Jun 25. PMID: 35763977 (2022)
    41. Tu, Jian; Huo, Zijun; Yu, Yao; Zhu, Dandan; Xu, An; Huang, Mo-Fan; Hu, Ruifeng; Wang, Ruoyu; Gingold, Julian A; Chen, Yi-Hung; Hereditary retinoblastoma iPSC model reveals aberrant spliceosome function driving bone malignancies. Proceedings of the National Academy of Sciences. 2022 Apr 19;119(16):e2117857119. doi: 10.1073/pnas.2117857119. Epub 2022 Apr 11. PMID: 35412907 (2022)
  • 2023 Publications
    1. Gao, Zhanguo; Yu, Yongmei; Dai, Yulin; Zhao, Zhongming; Eckel-Mahan, Kristin; Kolonin, Mikhail G; Gene expression in mice with endothelium-specific telomerase knockout. Frontiers in Cell and Developmental Biology. Dec 7:11:1295072. doi: 10.3389/fcell.2023.1295072. eCollection. PMID: 38161328 (2023) Li, Xiaoyang; Fernandes, Brisa S; Liu, Andi; Chen, Jingchun; Chen, Xiangning; Zhao, Zhongming; Dai, Yulin; GRPa-PRS: A risk stratification method to identify genetically-regulated pathways in polygenic diseases. medRxiv. [Preprint]. 2024 Jul 5:2023.06.19.23291621. doi: 10.1101/2023.06.19.23291621.. eCollection PMID: 37425929 (2023)
    2. Kiyama, Takae; Altay, Halit Y; Badea, Tudor C; Mao, Chai-An; Pou4f1-Tbr1 transcriptional cascade controls the formation of Jam2-expressing retinal ganglion cells. Frontiers in ophthalmology. 2023:3:1175568. doi: 10.3389/fopht.2023.1175568. Epub 2023 May 18. PMID: 38469155 (2023)
    3. Olcum, Melis; Fan, Siyang; Rouhi, Leila; Cheedipudi, Sirisha; Cathcart, Benjamin; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; Genetic inactivation of β-catenin is salubrious, whereas its activation is deleterious in desmoplakin cardiomyopathy. Cardiovascular Research. 2023 Dec 30;119(17):2712-2728. doi: 10.1093/cvr/cvad137. PMID: 37625794(2023)
    4. Lin, Sue-Hwa; yu, guoyu; Prostate cancer-induced endothelial-to-osteoblast transition generates an immunosuppressive bone tumor microenvironment. bioRxiv. [Preprint]. 2023 Dec 2:2023.11.30.569496. doi: 10.1101/2023.11.30.569496. PMID: 38076845 (2023)
    5. da Silva, Meiricris Tomaz; Joshi, Aniket S; Castillo, Micah B; Koike, Tatiana E; Roy, Anirban; Gunaratne, Preethi H; Kumar, Ashok; Fn14 promotes myoblast fusion during regenerative myogenesis. Life Science Alliance. 2023 Oct 9;6(12):e202302312.doi: 10.26508/lsa.202302312. Print 2023 Dec. PMID: 37813488 (2023)
    6. Saikia, Sudarshan; Si, Tapas; Deb, Darpan; Bora, Kangkana; Mallik, Saurav; Maulik, Ujjwal; Zhao, Zhongming; Lesion detection in women breast’s dynamic contrast-enhanced magnetic resonance imaging using deep learning. Scientific Reports. 2023 Dec 18;13(1):22555. doi: 10.1038/s41598-023-48553-z. PMID: 38110462 (2023)
    7. Derbel, Houssemeddine; Zhao, Zhongming; Liu, Qian; Accurate prediction of functional effect of single amino acid variants with deep learning. Computational and Structural Biotechnology Journal. 2023 Nov 10:21:5776-5784. doi: 10.1016/j.csbj.2023.11.017. eCollection 2023. PMID: 38074467 (2023)
    8. Uzan, Melis Olcum; Fan, Siyang; Rouhi, Leila; Cheedipudi, Sirisha; Cathcart, Benjamin; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; Genetic Inactivation of Beta-Catenin Attenuates and Its Activation Aggravates Desmoplakin Cardiomyopathy. bioRxiv. 2023 Aug 25:cvad137. doi: 10.1093/cvr/cvad137. Online ahead of print. PMID: 37625794 (2023)
    9. Yu, Yang; Cao, Wen-Ming; Cheng, Feng; Shi, Zhongcheng; Han, Lili; Yi, Jin-Ling; da Silva, Edaise M; Dopeso, Higinio; Chen, Hui; Yang, Jianhua; FOXK2 amplification and overexpression promotes breast cancer development and chemoresistance. bioRxiv. 2023 May 30:2023.05.28.542643. doi: 10.1101/2023.05.28.542643. Preprint PMID: 37398114 (2023)
    10. Xu, Haodong; Jia, Johnathan; Jeong, Hyun-Hwan; Zhao, Zhongming; Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome. Patterns. 2023 Feb 10;4(2):100674. doi: 10.1016/j.patter.2022.100674. PMID: 36873907 (2023)
    11. Parchem, Jacqueline G; Fan, Huihui; Mann, Lovepreet K; Chen, Qiuying; Won, Jong H; Gross, Steven S; Zhao, Zhongming; Taegtmeyer, Heinrich; Papanna, Ramesha; Fetal metabolic adaptations to cardiovascular stress in twin-twin transfusion syndrome. Iscience. 2023 Jul 20;26(8):107424. doi: 10.1016/j.isci.2023.107424. eCollection 2023 Aug 18. PMID: 37575192 (2023)
    12. Fan, Huihui; Li, Jinze; Manuel, Astrid M; Zhao, Zhongming; Enzalutamide-induced signatures revealed by epigenetic plasticity using single-cell multi-omics sequencing in prostate cancer. Molecular Therapy-Nucleic Acids. 2023 Feb 18:31:648-661. doi: 10.1016/j.omtn.2023.02.022. eCollection 2023 Mar 14. PMID: 36910711 (2023)
    13. Choe, Joshua H; Kawase, Tatsuya; Xu, An; Guzman, Asja; Obradovic, Aleksandar Z; Low-Calle, Ana Maria; Alaghebandan, Bita; Raghavan, Ananya; Long, Kaitlin; Hwang, Paul M; Li–Fraumeni syndrome–associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death. Cancer Discovery. 2023 May 4;13(5):1250-1273. doi: 10.1158/215-8290.CD-22-0882. PMID: 37067901 (2023)
    14. Li, Xiaoyang; Fernandes, Brisa S; Liu, Andi; Lu, Yimei; Chen, Jingchun; Zhao, Zhongming; Dai, Yulin; Genetically-regulated pathway-polygenic risk score (GRPa-PRS): A risk stratification method to identify genetically regulated pathways in polygenic diseases. medRxiv. 2023 Jun 27:2023.06.19.23291621. doi: 10.1101/2023.06.19.23291621. Preprint PMID: 37425929 (2023)
    15. Sahu, Upasana; Mullarkey, Matthew P; Pei, Guangsheng; Zhao, Zhongming; Hong, Bangxing; Kaur, Balveen; oHSV-P10 reduces glioma stem cell enrichment after oncolytic HSV therapy. Molecular Therapy-Oncolytics. 2023 Apr 3:29:30-41. doi: 10.1016/j.omto.2023.03.003. eCollection 2023 Jun 15. PMID: 37114074 (2023)
    16. Xu, An; Liu, Mo; Huang, Mo-Fan; Zhang, Yang; Hu, Ruifeng; Gingold, Julian A; Liu, Ying; Zhu, Dandan; Chien, Chian-Shiu; Wang, Wei-Chen; Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nature communications. 2023 Mar 27;14(1):1694. doi: 10.1038/s41467-023-37398-9. PMID: 36973285 (2023)
    17. Mallik, Saurav; Seth, Soumita; Si, Amalendu; Bhadra, Tapas; Zhao, Zhongming; Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data. Frontiers in Bioinformatics. 2023 Jul 27:3:1182176. doi: 10.3389/fbinf.2023.1182176. eCollection 2023. PMID: 37576714 (2023)
    18. Hong, Bangxing; Sahu, Upasana; Mullarkey, Matthew P; Hong, Evan; Pei, Guangsheng; Yan, Yuanqing; Otani, Yoshihiro; Banasavadi-Siddegowda, Yeshavanth; Fan, Huihui; Zhao, Zhongming; PKR induces TGF-? and limits oncolytic immune therapy. Journal for immunotherapy of cancer. 2023 Feb;11(2):e006164. doi: 10.1136/jitc-2022-006164. PMID: 36796878 (2023)
    19. Manuel, Astrid M; Dai, Yulin; Jia, Peilin; Freeman, Leorah A; Zhao, Zhongming; A gene regulatory network approach harmonizes genetic and epigenetic signals and reveals repurposable drug candidates for multiple sclerosis. Human Molecular Genetics. 2023 Mar 6;32(6):998-1009. doi: 10.1093/hmg/ddac265. PMID: 36282535 (2023)
    20. Olcum, Melis; Rouhi, Leila; Fan, Siyang; Gonzales, Maya M; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; PANoptosis is a prominent feature of desmoplakin cardiomyopathy. The journal of cardiovascular aging. 2023 Feb;3(1):3. doi: 10.20517/jca.2022.34. Epub 2023 Jan 1. PMID: 36818425 (2023)
    21. Pati, Soumen Kumar; Gupta, Manan Kumar; Banerjee, Ayan; Mallik, Saurav; Zhao, Zhongming; PPIGCF: A Protein–Protein Interaction-Based Gene Correlation Filter for Optimal Gene Selection. Genes. 2023 May 10;14(5):1063. doi: 10.3390/genes14051063. PMID: 37239423 (2023)
    22. Fan, Huihui; Wang, Feng; Zeng, Andy; Murison, Alex; Tomczak, Katarzyna; Hao, Dapeng; Jelloul, Fatima Zahra; Wang, Bofei; Barrodia, Praveen; Liang, Shaoheng; Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Communications Biology. 2023 Jul 21;6(1): 765.doi: 10.1038/s42003-023-05120-6. PMID: 37479893 (2023)
    23. Sopariwala, Danesh H; Rios, Andrea S; Pei, Guangsheng; Roy, Anirban; da Silva, Meiricris Tomaz; Nguyen, Hao Thi Thu; Saley, Addison; Van Drunen, Rachel; Kralli, Anastasia; Mahan, Kristin; Innately expressed estrogen-related receptors in the skeletal muscle are indispensable for exercise fitness. FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 2023 Feb;37(2):e22727.doi: 10.1096/fj.202201518R. PMID: 36583689 (2023)
    24. Makhnoon, Sukh; Levin, Brooke; Ensinger, Megan; Mattie, Kristin; Volk, Robert J; Zhao, Zhongming; Mendoza, Tito; Shete, Sanjay; Samiian, Laila; Grana, Generosa; A multicenter study of clinical impact of variant of uncertain significance reclassification in breast, ovarian and colorectal cancer susceptibility genes. Cancer medicine. 2023 Feb;12(3):2875-2884. doi: 10.1002/cam4.5202. Epub 2022 Nov 24. PMID: 36426404 (2023)
    25. Inam, Mehmet Enes; Fernandes, Brisa S; Salagre, Estela; Grande, Iria; Vieta, Eduard; Quevedo, João; Zhao, Zhongming; The kynurenine pathway in major depressive disorder, bipolar disorder, and schizophrenia: a systematic review and meta-analysis of cerebrospinal fluid studies. Brazilian Journal of Psychiatry. 2023 May 1. doi: 10.47626/1516-4446-2022-2973. Online ahead of print. PMID: 37127280 (2023)
    26. Sahoo, Karam Kumar; Ghosh, Raghunath; Mallik, Saurav; Roy, Arup; Singh, Pawan Kumar; Zhao, Zhongming; Wrapper-based deep feature optimization for activity recognition in the wearable sensor networks of healthcare systems. Scientific Reports. 2023 Jan 18;13(1):965. doi: 10.1038/s41598-022-27192-w. PMID: 36653370 (2023)
    27. Fernandes, Brisa S; Inam, Mehmet Enes; Enduru, Nitesh; Quevedo, Joao; Zhao, Zhongming; The kynurenine pathway in Alzheimer’s disease: a meta-analysis of central and peripheral levels. Brazilian Journal of Psychiatry. 2023 May-Jun;45(3):286-297. doi: 10.47626/1516-4446-2022-2962. Epub 2022 Feb 8. PMID: 36754068 (2023)
    28. Faraoni, Erika Y; Singh, Kanchan; Chandra, Vidhi; Le Roux, Olivereen; Dai, Yulin; Sahin, Ismet; O'Brien, Baylee J; Strickland, Lincoln N; Li, Le; Vucic, Emily; CD73-dependent adenosine signaling through Adora2b drives immunosuppression in ductal pancreatic cancer. Cancer Research. 2023 Apr 4;83(7):1111-1127. doi: 10.1158/0008-5472.CAN-22-2553. PMID: 36720042 (2023)
    29. Kaushik, Aman Chandra; Zhao, Zhongming; Machine learning-driven exploration of drug therapies for triple-negative breast cancer treatment. Frontiers in Molecular Biosciences. 2023 Aug 4:10:1215204. doi: 10.3389/fmolb.2023.1215204. eCollection 2023. PMID: 37602329 (2023)
    30. Mallik, Saurav; Sarkar, Anasua; Nath, Sagnik; Maulik, Ujjwal; Das, Supantha; Pati, Soumen Kumar; Ghosh, Soumadip; Zhao, Zhongming; 3PNMF-MKL: A non-negative matrix factorization-based multiple kernel learning method for multi-modal data integration and its application to gene signature detection. Frontiers in Genetics. 2023 Feb 14:14:1095330. doi: 10.3389/fgene.2023.1095330. eCollection 2023. PMID: 36865387 (2023)
    31. Olcum, Melis; Fan, Siyang; Rouhi, Leila; Cheedipudi, Sirisha; Cathcart, Benjamin; Jeong, Hyun-Hwan; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; Genetic inactivation of ?-catenin is salubrious whereas its activation is deleterious in desmoplakin cardiomyopathy. Cardiovascular Research. 2023 Aug 25:cvad137. doi: 10.1093/cvr/cvad137. Online ahead of print. PMID: 37625794 (2023)
    32. Dai, Yulin; Hsu, Yu-Chun; Fernandes, Brisa S; Zhang, Kai; Li, Xiaoyang; Enduru, Nitesh; Liu, Andi; Manuel, Astrid M; Jiang, Xiaoqian; Zhao, Zhongming; Disentangling accelerated cognitive decline from the normal aging process and unraveling its genetic components: A neuroimaging-based deep learning approach. 2023 Sep 8:rs.3.rs-3328861. doi: 10.21203/rs.3.rs-3328861/v1. Preprint PMID: 37720047 (2023)
    33. Das, Himanish Shekhar; Das, Akalpita; Neog, Anupal; Mallik, Saurav; Bora, Kangkana; Zhao, Zhongming; Breast cancer detection: Shallow convolutional neural network against deep convolutional neural networks based approach. Frontiers in Genetics. 2023 Jan 4:13:1097207. doi: 10.3389/fgene.2022.1097207. eCollection 2022. PMID: 36685963 (2023)
    34. Huang, Min; Yao, Fuwen; Nie, Litong; Wang, Chao; Su, Dan; Zhang, Huimin; Li, Siting; Tang, Mengfan; Feng, Xu; Yu, Bin; FACS-based genome-wide CRISPR screens define key regulators of DNA damage signaling pathways. Molecular cell. 2023 Aug 3;83(15):2810-2828.e6. doi: 10.1016/j.molcel.2023.07.004. PMID: 37541219 (2023)
    35. Liu, Andi; Fernandes, Brisa S; Citu, Citu; Zhao, Zhongming; Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: An integrative study of single-nucleus transcriptomes and genetic association. 2023 Sep 12:rs.3.rs-3335643. doi: 10.21203/rs.3.rs-3335643/v1 PMID: 37790454 (2023)
    36. Kang, Jiajinlong; Dai, Yulin; Li, Jinze; Fan, Huihui; Zhao, Zhongming; Investigating cellular heterogeneity at the single-cell level by the flexible and mobile extrachromosomal circular DNA. Computational and Structural Biotechnology Journal. 2023 Jan 24:21:115-1121. doi: 10.1016/j.csbj.2023.01.025. eCollection 2023. PMID: 36789262 (2023)
    37. Wang, Mingqiang; Deng, Wankun; Samuels, David C; Zhao, Zhongming; Simon, Lukas M; MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data. Genes. 2023 Jun 4;14(6):1222. doi: 10.3390/genes14061222. PMID: 37372402 (2023)
    38. Wang, Ruoyu; Lee, Joo-Hyung; Kim, Jieun; Xiong, Feng; Hasani, Lana Al; Shi, Yuqiang; Simpson, Erin N; Zhu, Xiaoyu; Chen, Yi-Ting; Shivshankar, Pooja; SARS-CoV-2 restructures host chromatin architecture. Nature microbiology. 2023 Apr;8(4):679-694. doi: 10.1038/s41564-023-01344-8. Epub 2023 Mar 23. PMID: 36959507 (2023)
  • 2024 Publications
    1. Yang, Daowei; Sun, Xinlei; Moniruzzaman, Rohan; Wang, Hua; Citu, Citu; Zhao, Zhongming; Wistuba, Ignacio I; Wang, Huamin; Maitra, Anirban; Chen, Yang; Genetic Deletion of Galectin-3 Inhibits Pancreatic Cancer Progression and Enhances the Efficacy of Immunotherapy. Gastroenterology. 2024 Jul;167(2):298-314. doi: 10.1053/j.gastro.2024.03.007. Epub 2024 Mar 11. PMID: 38467382 (2024)
    2. Noh, Min Hye; Kang, Jin Muk; Miller, Alexandra A; Nguyen, Grace; Huang, Minxin; Shim, Ji Seon; Bueso-Perez, Alberto J; Murphy, Sara A; Rivera-Caraballo, Kimberly A; Otani, Yoshihiro; Targeting IGF2-IGF1R Signaling to Reprogram the Tumor Microenvironment for Enhanced Viro-Immunotherapy. Neuro-oncology. 2024 Sep 5;26(9):1602-1616. doi: 10.1093/neuonc/noae105. PMID: 38853689 (2024)
    3. Nath, Anindita; Mwesigwa, Savannah; Dai, Yulin; Jiang, Xiaoqian; Zhao, Zhongming; GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console. Bioinformatics. 2024 Oct 1;40(10):btae500. doi: 10.1093/bioinformatics/btae500. PMID: 39115390 (2024)
    4. Liu, Wendao; Li, Wenbo; Zhao, Zhongming; Single-cell transcriptomics reveals pre-existing COVID-19 vulnerability factors in lung cancer patients. Molecular Cancer Research. 2024 Mar 1;22(3):240-253. doi: 10.1158/1541-7786.MCR-23-0692. PMID: 38063850 (2024)
    5. Tindall, Rachel R; Yang, Yuntao; Hernandez, Isabella; Qin, Amy; Li, Jiajing; Zhang, Yinjie; Gomez, Thomas H; Younes, Mamoun; Shen, Qiang; Bailey-Lundberg, Jennifer M; Aging-and alcohol-associated spatial transcriptomic signature in mouse acute pancreatitis reveals heterogeneity of inflammation and potential pathogenic factors. Journal of Molecular Medicine. 2024 Aug;102(8):1051-1061.doi: 10.1007/s00109-024-02460-6. Epub 2024 Jun 28. PMID: 38940937
    6. Findley, Tina O; Palei, Ana Carolina; Cho, Kyung Serk; Zhao, Zhongming; Shi, Caleb; Mahajan, Gouri; Corno, Antonio Francesco; Salazar, Jorge; McCullough, Louise; Sex differences in metabolic adaptation in infants with cyanotic congenital heart disease. Pediatric Research. 2024 Oct;96(5):1201-1209. doi: 10.1038/s41390-024-03291-4. Epub 2024 Jun 5. PMID: 38839995 (2024)
    7. Gao, Zhanguo; Santos, Rafael Bravo; Rupert, Joseph; Van Drunen, Rachel; Yu, Yongmei; Eckel?Mahan, Kristin; Kolonin, Mikhail G; Endothelial?specific telomerase inactivation causes telomere?independent cell senescence and multi?organ dysfunction characteristic of aging. Aging Cell. 2024 Jun;23(6):e14138. doi: 10.1111/acel.14138. Epub 2024 Mar 12. PMID: 38475941 (2024)
    8. Enduru, Nitesh; Fernandes, Brisa S; Zhao, Zhongming; Dissecting the shared genetic architecture between Alzheimer’s disease and frailty: a cross-trait meta-analyses of genome-wide association studies. Frontiers in Genetics. 2024 Apr 19:15:1376050. doi: 10.3389/fgene.2024.1376050. eCollection 2024. PMID: 38706793
    9. Manuel, Astrid M; Gottlieb, Assaf; Freeman, Leorah; Zhao, Zhongming; Montelukast as a repurposable additive drug for standard-efficacy multiple sclerosis treatment: Emulating clinical trials with retrospective administrative health claims data. Multiple Sclerosis Journal. 2024 May;30(6):696-706. doi: 10.1177/13524585241240398. Epub 2024 Apr 25. PMID: 38660773 (2024)
    10. Enduru, Nitesh; Fernandes, Brisa S; Bahrami, Shahram; Dai, Yulin; Andreassen, Ole A; Zhao, Zhongming; Genetic overlap between Alzheimer’s disease and immune-mediated diseases: an atlas of shared genetic determinants and biological convergence. Molecular Psychiatry. 2024 Aug;29(8):2447-2458. doi: 10.1038/s41380-024-02510-y. Epub 2024 Mar 18. PMID: 38499654 (2024)
    11. Dai, Yulin; Itai, Toshiyuki; Pei, Guangsheng; Yan, Fangfang; Chu, Yan; Jiang, Xiaoqian; Weinberg, Seth M; Mukhopadhyay, Nandita; Marazita, Mary L; Simon, Lukas M; DeepFace: Deep learning-based framework to contextualize orofacial cleft-related variants during human embryonic craniofacial development. Human Genetics and Genomics Advances. 2024 Jul 18;5(3):100312. doi: 10.1016/j.xhgg.2024.100312. Epub 2024 May 24. PMID: 38796699 (2024)
    12. Sanders, Keith L; Manuel, Astrid M; Liu, Andi; Leng, Boyan; Chen, Xiangning; Zhao, Zhongming; Unveiling Gene Interactions in Alzheimer’s Disease by Integrating Genetic and Epigenetic Data with a Network-Based Approach. Epigenomes. 2024 Apr 1;8(2):14. PMID: 38651367 doi: 10.3390/epigenomes8020014. (2024)
    13. Strickland, Lincoln N; Liu, Wendao; Hussein, Usama; Mardik, Nicolette; Chen, Xian; Mills, Tingting; Vornik, Lana A; Savage, Michelle I; Sei, Shizuko; Clifford, John; Preventive Treatment with a CD73 Small Molecule Inhibitor Enhances Immune Surveillance in K-Ras Mutant Pancreatic Intraepithelial Neoplasia. Cancer Prevention Research. 2024 Oct 1;17(10):457-470. doi: 10.1158/1940-6207.CAPR-24-0200. PMID: 39099209 (2024)
    14. Zhao, Zhongming; Liu, Andi; Citu, Citu; Enduru, Nitesh; Chen, Xian; Manuel, Astrid; Sinha, Tirthankar; Gorski, Damian; Fernandes, Brisa; Yu, Meifang; Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease. Research Square. [Preprint]. 2024 Aug 1:rs.3.rs-4622123. doi: 10.21203/rs.3.rs-4622123/v1. PMID: 39149497 (2024)
    15. Yu, Guoyu; Corn, Paul G; Mak, Celia Sze Ling; Liang, Xin; Zhang, Miao; Troncoso, Patricia; Song, Jian H; Lin, Song-Chang; Song, Xingzhi; Liu, Jingjing; Prostate cancer–induced endothelial-cell-to-osteoblast transition drives immunosuppression in the bone–tumor microenvironment through Wnt pathway–induced M2 macrophage polarization. 2024 Aug 13;121(33):e2402903121. doi: 10.1073/pnas.2402903121. Epub 2024 Aug 5. PMID: 39102549 (2024)
    16. Yin, Ling; Hu, Xiaoding; Pei, Guangsheng; Tang, Mengfan; Zhou, You; Zhang, Huimin; Huang, Min; Li, Siting; Zhang, Jie; Citu, Citu; Genome-wide CRISPR screen reveals the synthetic lethality between BCL2L1 inhibition and radiotherapy. Life science alliance. 2024 Feb 5;7(4):e202302353. doi: 10.26508/lsa.202302353. Print 2024 Apr. PMID: 38316463 (2024)
    17. Yulin Dai 1, Toshiyuki Itai 1, Guangsheng Pei 1, Fangfang Yan 1, Yan Chu 2, Xiaoqian Jiang 2, Seth M Weinberg 3, Nandita Mukhopadhyay 4, Mary L Marazita 5, Lukas M Simon 6, Peilin Jia 1, Zhongming Zhao 7, DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. Human Genetics and Genomics Advances. 2024 Jul 18;5(3):100312. doi: 10.1016/j.xhgg.2024.100312. Epub 2024 May 24. PMID: 38796699 (2024)
    18. Tomaszowski, Karl-Heinz; Chen, Yue; Roy, Sunetra; Harris, Momo; Zhang, Jianhua; Tsai, Chi-Lin; Schlacher, Katharina; Diet induced mitochondrial DNA replication instability in Rad51c mutant mice drives sex-bias in anemia of inflammation. bioRxiv. [Preprint]. 2024 Sep 21:2024.09.21.613572. doi: 10.1101/2024.09.21.613572. PMID: 39345482 (2024)
    19. Shuang, Li; Deng, Xiangyu; Deepak, Pathak; Basavaraj, Rashmi; Sun, Lina; Cheng, Yating; Li, Jian-Rong; Burke, Marissa; Britz, Gavin; Cheng, Chao; Deficiency of m6A RNA methylation promotes ZBP1-mediated cell death. bioRxiv. [Preprint]. 2024 Jun 30:2024.06.29.601251. doi: 10.1101/2024.06.29.601251. PMID: 38979320 (2024)
    20. Yu, Yang; Cao, Wen-Ming; Cheng, Feng; Shi, Zhongcheng; Han, Lili; Yi, Jinling; da Silva, Edaise M; Dopeso, Higinio; Chen, Hui; Yang, Jianhua; FOXK2 amplification promotes breast cancer development and chemoresistance. Cancer Letters. 2024 Aug 10:597:217074. doi: 10.1016/j.canlet.2024.217074. Epub 2024 Jun 18. PMID: 38901667 (2024)
    21. Liu, Andi; Fernandes, Brisa S; Citu, Citu; Zhao, Zhongming; Unraveling the intercellular communication disruption and key pathways in Alzheimer’s disease: an integrative study of single-nucleus transcriptomes and genetic association. Alzheimer's Research & Therapy. 2024 Jan 2;16(1):3. doi: 10.1186/s13195-023-01372-w. PMID: 38167548 (2024)
    22. Yang, Daowei; Sun, Xinlei; Moniruzzaman, Rohan; Wang, Hua; Citu, Citu; Zhao, Zhongming; Wistuba, Ignacio I; Wang, Huamin; Maitra, Anirban; Chen, Yang; Loss of p53 and SMAD4 induces adenosquamous subtype pancreatic cancer in the absence of an oncogenic KRAS mutation. Cell Reports Medicine. 2024 Sep 17;5(9):101711. doi: 10.1016/j.xcrm.2024.101711. Epub 2024 Sep 3. PMID: 39232498 (2024)
    23. Liu, Wendao; Zhao, Zhongming; Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model. bioRxiv. [Preprint]. 2024 Aug 19:2024.08.15.608093. doi: 10.1101/2024.08.15.608093. PMID: 39229048 (2024)
    24. Cathcart, Benjamin; Cheedipudi, Sirisha M; Rouhi, Leila; Zhao, Zhongming; Gurha, Priyatansh; Marian, Ali J; DNA double-stranded breaks, a hallmark of aging, defined at the nucleotide resolution, are increased and associated with transcription in the cardiac myocytes in LMNA-cardiomyopathy. Cardiovascular Research. 2024 Apr 5:cvae063. doi: 10.1093/cvr/cvae063. Online ahead of print. PMID: 38577741 (2024)
    25. Yuzhalin, Arseniy E; Lowery, Frank J; Saito, Yohei; Yuan, Xiangliang; Yao, Jun; Duan, Yimin; Ding, Jingzhen; Acharya, Sunil; Zhang, Chenyu; Fajardo, Abigail; Astrocyte-induced Cdk5 expedites breast cancer brain metastasis by suppressing MHC-I expression to evade immune recognition. Nature Cell Biology. 2024 Oct;26(10):1773-1789. doi: 10.1038/s41556-024-01509-5. Epub 2024 Sep 20. PMID: 39304713 (2024)
    26. Zeineddine, Hussein A; Hong, Sung-Ha; Peesh, Pedram; Dienel, Ari; Torres, Kiara; Thankamani Pandit, Peeyush; Matsumura, Kanako; Huang, Shuning; Li, Wen; Chauhan, Anjali; Neutrophils and neutrophil extracellular traps cause vascular occlusion and delayed cerebral ischemia after subarachnoid hemorrhage in mice. Arteriosclerosis, Thrombosis, and Vascular Biology. 2024 Mar;44(3):635-652. doi: 10.1161/ATVBAHA.123.320224. Epub 2024 Feb 1. PMID: 38299355
  • 2025 Publications
    1. Saito, Yohei; Xiao, Yi; Yao, Jun; Li, Yunhai; Liu, Wendao; Yuzhalin, Arseniy E; Shyu, Yueh-Ming; Li, Hongzhong; Yuan, Xiangliang; Li, Ping; Targeting a chemo-induced adaptive signaling circuit confers therapeutic vulnerabilities in pancreatic cancer. Cell Discov. 2024 Oct 29;10(1):109. doi: 10.1038/s41421-024-00720-w. PMID: 39468013 (2025)
    2. Ting, Shun-Ming; Zhao, Xiurong; Sun, Guanghua; Ricote, Mercedes; Aronowski, Jaroslaw; Retinoid-X-Receptor as a Mediator of Post-Stroke Recovery by Reversing Age-Associated Phenotypes of Microglia/Hematogenous Macrophages. J Neurosci. 2025 Sep 10;45(37):e0248252025. doi: 10.1523/JNEUROSCI.0248-25.2025. PMID: 40803891 (2025)
    3. Mwesigwa, Savannah; Dai, Yulin; Enduru, Nitesh; Zhao, Zhongming; Enhancing the utility of polygenic scores in Alzheimer’s disease through systematic curation and annotation. Front Genet. 2025 Feb 4:16:1507395. doi: 10.3389/fgene.2025.1507395. eCollection 2025. PMID: 39967687 (2025)
    4. GC, Bibek; Wu, Chenggang; The CarSR two-component system directly controls radD expression as a global regulator that senses bacterial coaggregation in Fusobacterium nucleatum. bioRxiv [Preprint]. 2024 Dec 14:2024.12.13.628403. doi: 10.1101/2024.12.13.628403. PMID: 39713435 (2025)
    5. Enduru, Nitesh; Manuel, Astrid M; Zhao, Zhongming; Genetic, Transcriptomic, and Epigenomic Insights into Sjögren's Disease: An Integrative Network Investigation and Immune Diseases Comparison. Int J Mol Sci. 2025 May 13;26(10):4637. doi: 10.3390/ijms26104637. PMID: 40429780 (2025)
    6. Rupert, Joseph; Daquinag, Alexes; Yu, Yongmei; Dai, Yulin; Zhao, Zhongming; Kolonin, Mikhail G; Depletion of adipose stroma-like cancer-associated fibroblasts potentiates pancreatic cancer immunotherapy. Cancer Res Commun. 2025 Jan 1;5(1):5-12. doi: 10.1158/2767-9764.CRC-24-0298. PMID: 39620946 (2025)
    7. Citu, Citu; Chang, Le; Manuel, Astrid M; Enduru, Nitesh; Zhao, Zhongming; Identification and catalog of viral transcriptional regulators in human diseases. iScience. 2025 Feb 21;28(3):112081. doi: 10.1016/j.isci.2025.112081. eCollection 2025 Mar 21. PMID: 40124487 (2025)
    8. Kinnear, Evan; Derbel, Houssemeddine; Zhao, Zhongming; Liu, Qian; Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach. Comput Struct Biotechnol J. 2025 Feb 14:27:631-638. doi: 10.1016/j.csbj.2025.02.007. eCollection 2025. PMID: 40041569 (2025)
    9. Tripathi, Ashutosh; Bartosh, Alona; Jose, Dania; Mata, Jocelyn; Hussein, Usama; Laezza, Fernanda; Zhao, Zhongming; Pillai, Anilkumar; Opposing roles of microglial and macrophagic C3ar1 signaling in stress-induced synaptic and behavioral changes. Mol Psychiatry. 2025 Jul 10. doi: 10.1038/s41380-025-03097-8. Online ahead of print. PMID: 40640554 (2025)
    10. Roy, Ethan R; Wang, Qiang; Huang, Kexin; Li, Sanming; Fan, Yuanyuan; Escobar, Estrella; Atkins, Constance L; Huang, Shuning; Herrera, Juan J; Li, Wenbo; Non-mutated human tau stimulates Alzheimer’s disease-relevant neurodegeneration in a microglia-dependent manner. Sci Rep. 2025 Jul 29;15(1):27664. doi: 10.1038/s41598-025-12869-9. PMID: 40730612 (2025)
    11. Nguyen, Grace H; Noh, MinHye; Kang, Jin Muk; Miller, Alexandra A; Huang, Minxin; Kim, Jiyeon; Lee, Jeong-Yeon; Chung, Sangwoon; Wang, Hongyu; Calin, George A; Simultaneous Targeting of Tumor Cells and Tumor-Associated Macrophages To Reprogram Glioblastoma Using Trypsinized Extracellular Vesicles Carrying Tumor Suppressive MicroRNA. Nano Lett. 2025 May 21;25(20):8414-8422. doi: 10.1021/acs.nanolett.5c01897. Epub 2025 May 13. PMID: 40357748 (2025)
    12. Ganie, Shahid Mohammad; Dutta Pramanik, Pijush Kanti; Zhao, Zhongming; Enhanced and Interpretable Prediction of Multiple Cancer Types Using a Stacking Ensemble Approach with SHAP Analysis. Bioengineering (Basel). 2025 Apr 29;12(5):472. doi: 10.3390/bioengineering12050472. PMID: 40428091 (2025)
    13. Hsieh, Kang-Lin; Zhang, Kai; Chu, Yan; Yu, Lishan; Li, Xiaoyang; Hu, Nuo; Kawosa, Isha; Pilié, Patrick G; Bhattacharya, Pratip K; Zhi, Degui; iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics. medRxiv [Preprint]. 2024 Nov 25:2024.03.29.24305092. doi: 10.1101/2024.03.29.24305092. PMID: 39649598 (2025)
    14. Shafeeque, Chathathayil M; Harmanci, Arif O; Thomas, Sithara; Dienel, Ari C; McBride, Devin W; Peeyush, Kumar T; Blackburn, Spiros L; Gene expression changes in human cerebral arteries following hemoglobin exposure: implications for vascular responses in SAH. Front Physiol. 2025 Apr 3:16:1529113. doi: 10.3389/fphys.2025.1529113. eCollection 2025. PMID: 40247928 (2025)
    15. Zamorano, Miriam; Udtha, Sanjna; Collier, Aidan M; Underwood, Erica; El Sayed, Razan; Agarwal, Ankit; Hatchell, Devin S; Tan, Chunfeng; Nietert, Paul J; Olson, Scott D; Transcriptomic and histological characteristics of innate immune activation in brain parenchyma in a rat model of neonatal intraventricular hemorrhage. Fluids Barriers CNS. 2025 Jul 3;22(1):68. doi: 10.1186/s12987-025-00678-1. PMID: 40611255 (2025)
    16. Tripathi, Ashutosh; Bartosh, Alona; Mata, Jocelyn; Jacks, Chale; Madeshiya, Amit Kumar; Hussein, Usama; Hong, L Elliot; Zhao, Zhongming; Pillai, Anilkumar; Microglial type I interferon signaling mediates chronic stress-induced synapse loss and social behavior deficits. Mol Psychiatry. 2025 Feb;30(2):423-434. doi: 10.1038/s41380-024-02675-6. Epub 2024 Aug 2. PMID: 39095477 (2025)
    17. Tang, Mengfan; Li, Siting; Zhu, Ziqiang; Wang, Chao; Ding, Shuai; Zhang, Huimin; Huang, Min; Keast, Sarah; Chen, Zhen; Yin, Ling; USP37 counteracts HLTF to protect damaged replication forks and promote survival of BRCA1-deficient cells and PARP inhibitor resistance. Nucleic Acids Res. 2025 Jun 20;53(12):gkaf544. doi: 10.1093/nar/gkaf544. PMID: 40548939 (2025)
    18. Nagata, Mizuki; Gadhvi, Gaurav T; Komori, Taishi; Arai, Yuki; Manabe, Hiroaki; Chu, Angel Ka Yan; Kaur, Ramandeep; Ali, Meer; Yang, Yuntao; Tsutsumi-Arai, Chiaki; Wnt-directed CXCL12-expressing apical papilla progenitor cells drive tooth root formation. Nat Commun. 2025 Jul 1;16(1):5510. doi: 10.1038/s41467-025-61048-x. PMID: 40595672 (2025)
    19. Mwesigwa, Savannah; Dai, Yulin; Enduru, Nitesh; Zhao, Zhongming; Enhancing the utility of polygenic scores in Alzheimer's disease through systematic curation and annotation. Front Genet. 2025 Feb 4:16:1507395. doi: 10.3389/fgene.2025.1507395. eCollection 2025. PMID: 39967687 (2025)
    20. Wankun Deng; Citu Citu; Andi Liu; Zhongming Zhao; Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level. Genome research. 2024 Oct 29;34(10):1687-1699. doi: 10.1101/gr.279363.124. PMID: 39424325 (2024)
    21. Van Drunen, Rachel; Dai, Yulin; Wei, Haichao; Fekry, Baharan; Noori, Sina; Shivshankar, Samay; Bravo, Rafael; Zhao, Zhongming; Yoo, Seung-hee; Justice, Nicholas; Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: Implications for regulation of systemic biological rhythms. Cell Rep. 2024 Jul 23;43(7):114380. doi: 10.1016/j.celrep.2024.114380. Epub 2024 Jun 26. PMID: 38935503 (2024)
    22. Strickland, Lincoln N; Liu, Wendao; Hussein, Usama; Mardik, Nicolette; Chen, Xian; Mills, Tingting; Vornik, Lana A; Savage, Michelle I; Sei, Shizuko; Clifford, John; Preventive Treatment with a CD73 Small Molecule Inhibitor Enhances Immune Surveillance in K-Ras Mutant Pancreatic Intraepithelial Neoplasia. Cancer Prev Res (Phila). 2024 Oct 1;17(10):457-470. doi: 10.1158/1940-6207.CAPR-24-0200. PMID: 39099209 (2024)
    23. Sadanandan, Jayanarayanan; Thomas, Sithara; Mathew, Iny Elizabeth; Huang, Zhen; Blackburn, Spiros L; Tandon, Nitin; Lokhande, Hrishikesh; McCrea, Pierre D; Bresnick, Emery H; Dash, Pramod K; Key epigenetic and signaling factors in the formation and maintenance of the blood-brain barrier. Elife. 2024 Dec 13:12:RP86978. doi: 10.7554/eLife.86978. PMID: 39670988 (2024)
    24. Noh, Min Hye; Kang, Jin Muk; Miller, Alexandra A; Nguyen, Grace; Huang, Minxin; Shim, Ji Seon; Bueso-Perez, Alberto J; Murphy, Sara A; Rivera-Caraballo, Kimberly A; Otani, Yoshihiro; Targeting IGF2 to reprogram the tumor microenvironment for enhanced viro-immunotherapy. Neuro Oncol. 2024 Sep 5;26(9):1602-1616. doi: 10.1093/neuonc/noae105. PMID: 38853689 (2024)
    25. Maneix, Laure; Iakova, Polina; Lee, Charles G; Moree, Shannon E; Lu, Xuan; Datar, Gandhar K; Hill, Cedric T; Spooner, Eric; King, Jordon CK; Sykes, David B; Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. 2024 Apr;26(4):593-603. doi: 10.1038/s41556-024-01387-x. Epub 2024 Mar 29. PMID: 38553595 (2024)
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