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Selected Publications of the CPGR

For the past 5 years with impact factors generally >10

  1. Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z (2020) VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Research 48(D1):D633-D641
  2. Jia P, Dai Y, Hu R, Pei G, Manuel A, Zhao Z (2020) TSEA-DB: A trait-tissue association map for human complex traits and diseases. Nucleic Acids Research 48(D1):D1022-D1030
  3. Mallik S, Zhao Z (2020) Graph- and rule-based learning algorithms: A comprehensive review of their applications for cancer type classification and prognosis using genomic data. Briefings in Bioinformatics. 21(2): 368-394
  4. Hua X, Wang YY, Jia P, Xiong Q, Hu Y, Chang Y, Lai S, Xu Y, Zhao Z, Song J (2020) Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression. BMC Medicine 18:2
  5. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (Zhao Z is a member/co-author) (2020) Pan-cancer analysis of whole genomes. Nature 578(7793): 82-93.
  6. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; (Zhao Z is a member/co-author in) PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium (2020) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578(7793):102-111
  7. 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 (2020) Glucocorticoids enhance the anti-leukemic activity of FLT3 inhibitors in FLT3 mutant acute myeloid leukemia. Blood 136(9):1067-1079
  8. Li A, Mallik S, Luo H, Jia P, DF Lee, Zhao Z (2020) H19, a long non-coding RNA, mediates transcription factors and target genes through interference of microRNAs in pan-cancer. Molecular Therapy – Nucleic Acids. 21:180-191
  9. He Y, Xu P, Wang C, Xia Y, Yu M, Yang Y, Yu K, Cai X, Qu N, Saito K, Wang J, Hyseni I, Robertson M, Piyarathna B, Gao M, Khan S, Liu F, Chen R, Coarfa C, Zhao Z, Tong Q, Sun Z, Xu Y (2020) Estrogen receptor-α expressing neurons in the ventrolateral VMH regulate glucose balance. Nature Communications 11(1):2165
  10. Tang M, Feng X, Pei G, Srivastava M, Wang C, Chen Z, Li S, Zhang H, Zhao Z, Li X, Chen J (2020) FOXK1 participates in DNA damage response by controlling 53BP1 function. Cell Reports 32:108018
  11. Pei G, Hu R, Dai Y, Zhao Z, Jia P (2020) Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network. Oncogene 39:5031-5041
  12. Strunz M, Simon LM, Ansari M, Mattner LF, Angelidis L, Mayr CH, Kathiriya J, Yee M, Ogar P, Sengupta A, Kukhtevich I, Schneider R, Zhao Z, Neumann J, Behr J, Voss C, Stöger T, Lehmann M, Königshoff M, Burgstaller G, O´Reilly M, Chapman HA, Theis FJ, Schiller HB (2020). Alveolar regeneration through a Krt8+ transitional stem cell state that aberrantly persists in human lung fibrosis. Nature Communications, 11:3559. bioRxiv 705244
  13. Savarraj JP, Hergenroeder G, Zhu L, Chang T, Park S, Megjhani M, Vahidy FS, Zhao Z, Kitagawa R, Choi H (2020) Machine learning to predict delayed cerebral ischemia and outcomes in subarachnoid hemorrhage. Neurology 96(4), e553-e562
  14. Simon LM, Yan F, Zhao Z (2020) DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. (Preprint in bioRxiv 2019 doi: https://doi.org/10.1101/864165) GigaScience 9(12):giaa122 (doi: 10.1093/gigascience/giaa122)
  15. Gao Z, Daquinag AC, Fussell C, Zhao Z, Dai Y, Rivera A, Snyder BE, Eckel-Mahan KL, Kolonin MG (2020) Age-associated telomere attrition in adipocyte progenitors predisposes to metabolic disease. Nature Metabolism 2(12):1482-1497 [single cell RNA-seq]
  16. Hu R, Xu H, Jia P, Zhao Z (2021) KinaseMD: kinase mutation and drug response database. Nucleic Acids Research. 49:D552-D561
  17. Dai Y, Hu R, Manuel AM, Liu A, Jia P, Zhao Z (2021) CSEA-DB: An omnibus for human complex trait and cell type associations. Nucleic Acids Research. 49:D862-D870
  18. Pei G, Wang Y, Simon L, Dai Y, Zhao Z , Jia P (2021) Gene expression imputation and cell type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Research 31:146-158
  19. Hong BH, Chapa V, Saini U, Modgil P, Cohn DE, Sood A, Yan Y, Saruppaiyah S, Pei G, Zhao Z, Yoo JY, Kaur B (2021) Oncolytic HSV therapy modulates vesicular trafficking inducing cisplatin sensitivity and antitumor immunity. Clinical Cancer Research 27(2):542-553. PMID: 33087329
  20. Pei G, Hu R, Dai Y, Manuel AM, Zhao Z, Jia P (2021) Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations. Nucleic Acids Research. 49(1):53-66
  21. Xu H, Jia P, Zhao Z (2021) Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Briefings in Bioinformatics. 22(3):bbaa099
  22. Kim P, Li H, Wang S, Zhao Z (2021) Landscape of drug-resistance mutations in kinase regulatory hotspots. Briefings in Bioinformatics 22(3):bbaa108, https://doi.org/10.1093/bib/bbaa108
  23. Jia P, Hu R, Pei G, Dai Y, Wang Y, Zhao Z (2021) Deep generative neural network for accurate drug response imputation. Nature Communications 12:1740
  24. Su F, Daquiang AC, Ahn S, Saha A, Dai Y, Zhao Z, DiGiovanni J, Kolonin MG (2021) Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium. NPJ (Nature) Precision Oncology 2021:26
  25. Xu H, Jia P, Zhao Z (2021) DeepVISP: Deep learning for virus site integration prediction and motif discovery. Advanced Science 2021:2004958
  26. Yuan P, Cheedipudi SM, Louhi L, Fan S, Simon L, Zhao Z, Hong K, Gurha P, Marian A (2021) Single cell RNA-sequencing uncovers paracrine functions of the epicardial-derived cells in arrhythmogenic cardiomyopathy. Circulation 143(22):2169-2187
  27. Pei G, Hu R, Jia P, Zhao Z (2021) DeepFun: A deep learning sequence-based model to decipher noncoding variant effect in a tissue and cell type specific manner. Nucleic Acids Research 49:W131-139
  28. Li B, Pei G, Yao J, Ding Q, Jia P, Zhao Z (2021) Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. Oncogene. 40(28):4686-4694
  29. Simon LM, Wang Y, Zhao Z (2021) Integration of millions of transcriptomes using batch-aware triplet neural networks. Nature Machine Intelligence. 3:705-715
  30. Jia P, Manuel AM, Fernandes BS, Dai Y, Zhao Z (2021) Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. Briefings in Bioinformatics. 22(6):bbab214
  31. Ravirala D, Mistretta B, Gunaratne P, Pei P, Zhao Z, Zhang X (2021) Co-delivery of novel bispecific and trispecific engagers by an amplicon vector augments the therapeutic effect of a HSV-based oncolytic virotherapy. Journal for ImmunoTherapy of Cancer 9(7):e002454
  32. Xu H, Yan F, Hu R, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z (2021) CleftGeneDB: A resource for annotating genes associated with cleft lip and cleft palate. Science Bulletin 66(23): 2340-2342
  33. Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z, Chen, J (2021) Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Research 49(13) 7476-7491
  34. Mendez E, Wei H, Hu R, Stertz L, Fries GR, Wu X, Najera K, Monterey M, Lincoln C, Kim J, Moriel K, Meyer T, Zhao Z, Xu J, Wu J, Selvaraj S, Teixeria A, Walss-Bass C (2021) Angiogenic Gene Networks are Dysregulated in Opioid Use Disorder: Evidence from Multi-Omics and Imaging of Postmortem Human Brain. Molecular Psychiatry 26:7803-7812
  35. Ravirala D, Pei G, Zhao Z, Zhang X (2021) Single cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV replication in tumor tissue. Molecular Therapy, Oncolytics 23:330-341
  36. Ravirala D, Pei G, Zhao Z, Zhang X (2022) Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing. Cancer Immunology, Immunotherapy 71(6):1479-1495. doi: 10.1007/s00262-021-03084-2.
  37. Li H, Xiao Y, Li Q, Yao J, Yuan X, Zhang Y, Yin X, Saito Y, Fan H, Li P, Halpin A, Gibbons DL, Yagita H, Zhao Z, Pang D, Ren G, Yee C, Lee JJ, Yu D (2022) The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1. Cancer Cell 40:36-52
  38. Otani Y, Yoo JY, Lewis CT, Chao S, Swanner J, Shimizu T, Kang JM, Murphy SA, Rivera-Caraballo K, Hong B, Pineda J, Caraballo KR, Palacios BE, Hong B, Glorioso JC, Nakashima H, Lawler SE, Banasavadi-Siddegowda Y, Heiss JD, Yan Y, Pei G, Caligiuri MA, Zhao Z, Chiocca AE, Yu J, Kaur B (2022) NOTCH-induced MDSC recruitment after oHSV virotherapy in CNS cancer models modulates antitumor immunotherapy. Clinical Cancer Research. 28 (7): 1460–1473
  39. Mishra I, Xie WR, Bournat JC, He Y, Wang C, Silva ES, He Y, Liu H, Ku Z, Chen Y, Erokwu BO, Jia P, Zhao Z, An Z, Flask CA, Xu Y, Chopra AR (2022) Protein tyrosine phosphatase receptor δ serves as the orexigenic asprosin receptor. Cell Metabolism 34(4):549-563. https://doi.org/10.1016/j.cmet.2022.02.012
  40. Tu J, Huo Z, Yu Y, Zhu D, Xu A, Huang MF, Hu R, Wang R, Gingold JA, Chen YH, Tsai KL, Forcioli-Conti NR, Huang SXL, Webb TR, Su J, Bazer DA, Jia P, Yustein JT, Wang LL, Hung MC, Zhao Z, Huff CD, Shen J, Zhao R, Lee DF (2022) Hereditary retinoblastoma iPSC model reveals aberrant spliceosome function driving bone malignancies. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 119(16):e2117857119
  41. Feng X, Tang M, Dede M, Su D, Pei G, Jiang D, Wang C, Chen Z, Li M, Nie L, Xiong Y, Li S, Park JM, Zhang H, Huang M, Szymonowicz K, Zhao Z, Hart T, Chen J (2022) Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors. Science Advances. 8(19):eabm6638
  42. Dai Y, Hu R, Liu A, Cho KS, Manuel AM, Li X, Dong X, Jia P, Zhao Z (2022) WebCSEA: web-based Cell-type-specific enrichment analysis of genes. Nucleic Acids Research. 50:W782-790, https://doi.org/10.1093/nar/gkac392
  43. Liu W, Jia J, Dai Y, Chen W, Pei G, Yan Q, Zhao Z (2022) Delineating COVID-19 immunological features using single-cell RNA sequencing. The Innovation (a Cell journal) 3(5):100289
  44. Pei G, Yan F, Simon LM, Dai Y, Jia P, Zhao Z (2023) deCS: A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues. Genomics Proteomics & Bioinformatics 21(2), 370-384
  45. Gu Z, Yao Y, Yang G, Zhu G, Tian Z, Wang R, Wu Q, Wang Y, Wu Y, Chen L, Wang C, Gao J, Kang X, Zhang J, Wang L, Duan S, Zhao Z, Zhang Z, Sun S (2022) Pharmacogenomic landscape of head and neck squamous cell carcinoma informs precision oncology therapy. Science Translational Medicine. 14(661):eabo5987 [elected to be featured cover]
  46. Jia P, Hu R, Yan F, Dai Y, Zhao Z* (2022) scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies. Genome Biology 23:220
  47. Xu H, Zhao Z* (2022) NetBCE: An interpretable deep neural network for accurate prediction of linear B-cell epitopes. Genomics Proteomics & Bioinformatics. 20:1002-1012
  48. Hong B, Sahu U, Mullarkey MP, Hong E, Pei G, Yan Y, Otani Y, Banasavadi-Siddegowda Y, Fan H, Zhao Z, Yu J, Caligiuri MA, Kaur B (2023) PKR induces TGF-β and limits oncolytic immune therapy. Journal for ImmunoTherapy of Cancer 11:e006164
  49. Faraoni EY, Singh K, Chandra V, Roux OL, Dai Y, Sahin I, O’Brien BJ, Strickland LN, Li L, Vucic E, Warner A, Pruski M, Clark T, van Buren G, Thosani NC, Bynon JS, Wray CJ, Bar-Sagi D, Wray C, Bar-Sagi D, Poulsen K, Vornik LA, Savage MI, Sei S, Mohammed A, Zhao Z, Brown BH, Eltzschig HK, McAllister F, Bailey-Lundberg JM (2023) CD73-dependent adenosine signaling through Adora2b drives immunosuppression in ductal pancreatic cancer. Cancer Research 2023 83(7):1111-1127
  50. Xu A, Liu M, Huang M-F, Zhang Y, Hu R, Gingold JA, Liu Y, Zhu D, Chien CS, Wang WC, Liao Z, Yuan F, Hsu CW, Tu J, Yu Y, Rosen T, Xiong F, Jia P, Yang YP, Bazer DA, Chen YW, Li W, Huff CD, Zhu JJ, Aguilo F, Chiou SH, Boles NC, Lai CC, Hung MC, Zhao Z, Nostrand ELV, Zhao R, Lee DF (2023) Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nature Communications 14:1694
  51. Jia P, Hu R, Zhao Z* (2023) Benchmark of embedding-based methods for accurate and transferable prediction of drug response. Briefings in Bioinformatics 24(3): bbad098, Online: 24 March 2023 https://doi.org/10.1093/bib/bbad098
  52. Feofanova EV, Brown MR, Alkis T, Manuel AM, Li X, Tahir U, Li Z, Mendez KM, Kelly RS, Qi Q, Chen H, Larson MG, Lemaitre R, Morrison AC, Grieser C, Wong K, Gersztern RE, Zhao Z, Lasky-Su J, NHLBI Trans-Omics for Precision Medicine (TOPMed), Yu B (2023) Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations. Nature Communications 14:3111
  53. Olcum M, Fan S, Rouhi L, Cheedipudi S, Cathcart B, Jeong HH, Zhao Z, Gurha P, Marian A (2023) Genetic Inactivation of b-Catenin is Salubrious Whereas its Activation is Deleterious in Desmoplakin Cardiomyopathy. Cardiovascular Research 119(17):2712-2728 https://doi.org/10.1093/cvr/cvad137
  54. Xu H, Hu R, Zhao Z* (2023) DegronMD: Leveraging evolutionary and structural features for deciphering protein-targeted degradation, mutations and drug response to degrons. Molecular Biology and Evolution 40(12):msad253
  55. Yan F, Suzuki A, Iwaya C, Yoshioka H, Pei G, Chen X, Yu M, Simon LM, Iwata J, Zhao Z* (2024) Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nature Communications, 15:821
  56. Enduru N, Fernandes BS, Bahrami S, Dai Y, Andreassen OA, Zhao Z* (2024) Genetic overlap between Alzheimer's disease and immune-mediated diseases: An atlas of shared genetic determinants and biological convergence. Molecular Psychiatry 29:2447-2458
  57. Yang D, Sun X, Moniruzzaman R, Wang H, Citu C, Zhao Z, Wistuba II, Wang H, Maitra A, Chen Y (2024) Genetic Deletion of Galectin-3 Inhibits Pancreatic Cancer Progression and Enhances the Efficacy of Immunotherapy. Gastroenterology, 167(2):298-314 (Impact factor 29.4)
  58. Dai Y, Fernandes BS, Zhao Z* (2024) Revisiting the relative contribution of common and rare genetic variants to attention-deficit hyperactivity disorder among diverse populations. Biological Psychiatry 95:822–824
  59. Cathcart B, Cheedipudi SM, Rouhi L, Zhao Z, Gurha P, Marian AJ (2024) 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. Cardiovasc Res 121(10):1582-1593. doi: 10.1093/cvr/cvae063.
  60. Van Drunen R, Dai Y, Wei H, Fekry B, Shivshankar S, Santos RB, Zhao Z, Yoo SH, Justice N, Wu J, Tong Q, Eckel-Mahan K (2024) Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: implications for regulation of systemic biological rhythms. Cell Reports 43(7):114380
  61. Noh MH, Kang JM, Shim JS, Nguyen G, Bueso-Perez AJ, Murphy S, Rivera-Caraballo KA, Otani Y, Kim E, Yoo SH, Yan Y, Banasavadi-Siddegowda Y, Nakashima H, Chiocca EA, Kaur B, Zhao Z, Lee TJ, Yoo JY (2024) Targeting IGF2 to reprogram the tumor microenvironment for enhanced viro-immunotherapy. Neuro-Oncology 26(9):1602-1616
  62. Tripathi A, Bartosh A, Mata J, Jacks C, Madeshiya A, Hussein U, Zhao Z, Pillai A (2025) Microglial type I interferon signaling mediates chronic stress-induced synapse loss and social behavior deficits. Mol Psychiatry 30(2):423-434.
  63. Xu H, Hu R, Dong X, Kuang L, Zhang L, Tu C, Li Z, Zhao Z* (2024) ImmuneApp for HLA-I epitope prediction and immunopeptidome analysis. Nature Communications 15:8926
  64. Yang D, Sun X, Moniruzzaman R, Wang H, Citu C, Zhao Z, Wistuba II, Wang H, Maitra A, Chen Yang (2024) Loss of p53 and SMAD4 induces adenosquamous subtype pancreatic cancer in the absence of oncogenic KRAS mutation. Cell Reports Medicine 5(9):101711.
  65. Yuzhalin A, Lowery F, Saito Y, Yuan X, Yao J, Duan Y, Ding J, Acharya S, Zhang C, Sun Y, Zhang L, Xiao Y, Li P, Lorenzi P, Fan H, Zhao Z, Hung MC, Yu D (2024) Astrocyte-induced Cdk5 expedites breast cancer brain metastasis by suppressing MHC-I expression to evade immune recognition. Nature Cell Biology 26:1773-1789
  66. Saito Y, Xiao Y, Yao J, Li Y, Liu W, Li H, Yuan X, Xia W, Li P, Zhang Q, Badu-Nkansah A, Li Z, Wei Y, Yin X, Zhao J, Sariminia SM, Wu YC, Wang J, Yang J, Jho EH, Chiao PJ, Hwang R, Ying H, Wang H, Zhao Z, Maitra A, Hung MC, DePhinho RA, Yu D (2024) Targeting chemo-induced adaptive signaling circuit confers therapeutic vulnerabilities in pancreatic cancer. Cell Discovery 10(1):109
  67. Zheng M, Lin S, Hu R, Chen K, Wang L, Zhao Z*, Xu H* (2024) MetaDegron: Multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons. Briefings in Bioinformatics 25(6), bbae519
  68. Deng W, Citu C, Liu A, Zhao Z* (2024) Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level. Genome Research 34:1687-1699
  69. Dudeck L, Nussbaumer M, Nickl-Jockschat T, Guest PC, Drbrowolny H, Meyer-Lotz G, Zhao Z, Jacobs R, Shiltz K, Fernandes B, Steiner J (2025) Differences in Blood Leukocyte Subpopulations in Schizophrenia: A Systematic Review and Meta-Analysis. JAMA Psychiatry 82(5):492-504.
  70. Xiao L, Zhang C, Liu W, Ma X, Wang Q, Xian M, Xiong W, Su P, Ye L, Li Y, Zhong L, Qian J, Zhao Z, Yi Q (2025) Adoptively transferred tumor-specific IL-9-producing cytotoxic CD8+ T cells activate host CD4+ T cells to control tumors with antigen loss. Nature Cancer 6:718-735
  71. Ruan W, Li T, Lee J, Bang I, Deng W, Ma X, Li J, Kim B, Yoo SH, Yuan X, Wang YY, Liang Y, Zhou Z, Wang Y, Nair R, Narula J, Zhao Z, Muehlschlegel JD, Tasi KL, Eltzschig HK (2025) The BMAL1/HIF2A heterodimer modulates circadian variations of myocardial injury. Nature 641(8064):1017-1028
  72. Lin S, Tu C, Hu R, Wang H, Dong Z, Luo H, Kuang L, Wang T, Wang L, Zhao Z*, Li Z*, Xu H* (2025) Dr. Kinase: predicting the drug-resistance hotspots of protein kinases. Nucleic Acids Research. 53:W258-265. https://doi.org/10.1093/nar/gkaf366
  73. Tripathi A, Bartosh A, Jose D, Mata J, Hussein U, Laezza F, Zhao Z, Pillai A (2025) Opposing roles of microglial and macrophagic C3ar1 signaling in stress-induced synaptic and behavioral changes. Mol Psychiatry 30(2):423-434
  74. Hsieh KL, Zhang K, Chu Y, Yu L, Li X, Hu N, Kawosa I, Pilie PG, Bhattacharya PK, Zhi D, Jiang X, Zhao Z*, Dai Y* (2025) iGTP: Learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics. Briefings in Bioinformatics. 26(3), bbaf296.
  75. Feng T, Liu Y, Luo Q, Jin Z, Skwarchuk D, Lee R, Nam M, Lorenzi P, Tan L, Pei G, Zhao Z, Zarrin-Khameh N, Paulucci-Holthauzen A, Simon BW, Lee J-S, Kopetz S, Yun J (accepted) Fructose and Glucose from Sugary Drinks Enhance Colorectal Cancer Metastasis via SORD (reference number: NATMETAB-A240812632A). Nature Metabolism 2025 Oct;7(10):2018-2032
  76. Li X, Fernandes BS, Liu A, Chen J, Zhao Z*, Dai Y* (accepted) GRPa-PRS: A risk stratification method to identify genetically-regulated pathways in polygenic diseases. Alzheimer’s & Dementia Journal 2025;21:e70779
  77. Czopik AK, Dabiri A, Tung CH, Vaughn V, Huang X, Wang J, Li H, Moreno N, Piwko NV, Figarella K, Liu H, Zhao Z, Yuan X, Eltzschig HK (2025) miR147 promotes mucosal integrity and healing in intestinal inflammation. JCI Insight 10(20):e190466
  78. Qu G, Enduru N, Liu X, Jiang X, Zhao Z* (2025) BrainGeneBot: Integrating Rank Aggregation with GPT-Informed Polygenic Score Analysis in Alzheimer's Disease. Briefings in Bioinformatics 26(5), bbaf565
  79. Liu A, Citu C, Enduru N, Chen X, Manuel AM, Sinha T, Gorski D, Fernandes BS, Yu M, Schulz PE, S LM, Soto C, Zhao Z* (2025) Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease. Science Advances. 11(51):sciadv.adw4917
  80. Enduru N, Zhao Z* (2026) PRISM-xQTL: Pleiotropic Relationships Integrated with System-level Multiomic xQTL Analysis for Causal Genes and Molecular Mediators in Alzheimer’s Disease. Alzheimer’s & Dementia Journal 22:e71073

Extramural Research Funding of the CPGR

For the past 5 years

National Institute of Health/National Science Foundation

  1. Project Number: U01AG079847 (MPIs: Zhao, Jiang)
    Title: AIM-AI: an Actionable, Integrated and Multiscale genetic map of Alzheimer’s disease via deep learning
    Project/Proposal Start and End Date: (MM/YYYY): 09/15/2023–08/31/2028
    Total Award Amount (including Indirect Costs): $6,436,822
  2. Project Number: R01LM012806-09 (PI: Zhao)
    Title: Predicting Phenotype by Deep Learning Heterogeneous Multi-Omics Data
    Project/Proposal Start and End Date: (MM/YYYY): 08/01/2025–07/31/2029
    Total Award Amount (including Indirect Costs): $1,435,240
  3. Project Number: NSF IIS 2427012 (PI: Zhao)
    Title: Intelligent Biology and Medicine in 2024: Harnessing Artificial Intelligence and Data Science for Education, Collaboration, and Innovation
    Project/Proposal Start and End Date: (MM/YYYY): 12/01/2024–11/30/2025
    Total Award Amount (including Indirect Costs): $19,032
  4. Project Number: R21AG087299 (MPI: Dai, Zhang, Zhao)
    Title: Identify actionable drugs that enhance resilience in Alzheimer's disease individuals
    Project/Proposal Start and End Date: (MM/YYYY): 08/01/2024–04/30/2026
    Total Award Amount (including Indirect Costs): $429,000
  5. Project Number: 2R01LM012806-05 (PI: Zhao)
    Title: Predicting Phenotype by Deep Learning Heterogeneous Multi-Omics Data
    Project/Proposal Start and End Date (MM/YYYY): 06/01/2021–05/31/2026 (NCE)
    Total Award Amount (including Indirect Costs): $1,288,596
  6. Project Number: R01CA276513 (MPI: Sevick, Mohsen, Zhao)
    Title: Personalized, antigen-directed immunotherapy delivered to lymph nodes
    Project/Proposal Start and End Date (MM/YYYY): 07/01/2023-06/30/2027
    Total Award Amount (including Indirect Costs): $2,332,242
  7. Project Number: R01CA276942 (PI: Yoo, Co-I: Zhao)
    Title: Enhanced Viro-Immunotherapy for Breast Cancer Brain Metastasis
    Project/Proposal Start and End Date: 09/22/2023-08/31/2028
    Total Award Amount (including Indirect Costs): $2,476,133
  8. Project Number: R01CA277161 (MPI: Bailey, Thosani; Co-I: Zhao)
    Title: A single-arm phase II study to evaluate the safety and efficacy of combination systematic chemotherapy and multiple rounds of endoscopic ultrasound-guided radiofrequency ablation in pancreatic cancer
    Project/Proposal Start and End Date: (MM/YYYY): 07/01/2023- 06/30/2028
    Total Award Amount (including Indirect Costs): $3,279,093
  9. Project Number: R01DE030122 (PI: Zhao, Iwata)
    Title: Deep learning for decoding genetic regulation and cellular maps in craniofacial development
    Project/Proposal Start and End Date: (MM/YYYY): 04/01/2021-03/31/2026 (NCE)
    Total Award Amount (including Indirect Costs): $1,700,038
  10. Project Number: 5R01DE029818 (PI: Zhao, Iwata)
    Title: Role of cellular metabolism in palate morphogenesis
    Project/Proposal Start and End Date: (MM/YYYY): 07/01/2020–04/30/2026 (NCE)
    Total Award Amount (including Indirect Costs): $1,848,540
  11. Project Number: R01NS127473-01 (PI: Kaur, Co-I: Zhao)
    Title: Next Gen Virotherapy for GBM)
    Project/Proposal Start and End Date: (MM/YYYY): 04/01/2022-03/31/2027
    Total Award Amount (including Indirect Costs): $3,230,326
    Note: Dr. Kaur moved out of UTHealth in 2024.
  12. Project Number: R03AG077191 (PI: Zhao)
    Title: Constructing A Transcriptomic Atlas of Retrotransposon in Alzheimer’s Disease
    Project/Proposal Start and End Date: (MM/YYYY): 06/01/2022-05/31/2025
    Total Award Amount (including Indirect Costs): $312,000
  13. Project Number: 3R01LM012806-07S1 (PI: Zhao)
    Title: Transforming dbGaP genetic and genomic data to FAIR-ready by artificial intelligence and machine learning algorithms
    Project/Proposal Start and End Date: (MM/YYYY): 09/01/2023-05/31/2025
    Total Award Amount (including Indirect Costs): $306,060

Non-Federal Grants

  1. Project Number: RP240610 (PI: Zhao)
    Title: UTHealth Cancer Genomics Core (UTHealth CGC)
    Project/Proposal Start and End Date: (MM/YYYY): 08/31/2024–08/30/2029
    Total Award Amount (including Indirect Costs): $2,000,000
  2. Project Number: RP210045 (PI: Zhao)
    Title: Biomedical Informatics, Genomics and Translational Cancer Research Training Program (BIG-TCR)
    Project/Proposal Start and End Date: (MM/YYYY): 06/01/2021–05/31/2026
    Total Award Amount (including Indirect Costs): $4,068,995

Mentored Grants

  1. Project Number: K01MH121580 (PI: Fries, Zhao: Co-mentor)
    Title: Deciphering the role of neuronal and peripheral DNA methylation in suicide and bipolar disorder
    Project/Proposal Start and End Date: (MM/YYYY): 07/01/2020–06/30/2024
    Total Award Amount (including Indirect Costs): $647,568
  2. Project Number: K99CA256216 (PI: Makhnoon, Zhao: Advisory committee, Faculty Collaborator)
    Title: Multilevel investigation of uncertain and reclassified genomic variants in clinical oncology
    Project/Proposal Start and End Date: (MM/YYYY): 03/01/2021-02/28/2026
    Total Award Amount (including Indirect Costs): $215,738 (K99 phase)
  3. Project Number: 3R01CA276942-01A1S1 (PI: Miller, Zhao: Co-mentor)
    Title: Enhanced Viro-Immunotherapy for Breast Cancer Brain Metastasis
    Project/Proposal Start and End Date: (MM/YYYY): 6/1/2024 - 8/31/2024
    Total Award Amount (including Indirect Costs): NA
  4. Project Number: Pilot project of U54MD007605 (PI: WIdmann, Zhao: Co-mentor)
    Title: Targeting the Host Transcriptome for Therapeutic Intervention of COVID-19
    Project/Proposal Start and End Date: (MM/YYYY): 09/26/2024-05/30/2025
    Total Award Amount (including Indirect Costs): $50,000