Cancer Genomics Center

Oncogenomics

Publications

  1. 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)
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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.
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. Xu H, Hu R, Jia P, Zhao Z, 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. PMID: 32091591
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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.
  66. 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
  67. 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
  68. 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