Skip Navigation and Go To Content

Outcomes

  • Funding Outcomes
    Funded Projects/Grant Awards Supported
      Funding Source Grant ID Total Amount Received
    (Entire grant period)    		 Total Project Period of Investment/Award
    2018
      NIH 1R01HL142003 $933,667.00 5/1/2018 4/30/2020
      Jintel Inc   $8333.33 5/17/2018 5/16/2019
      NIH R01CA232892 $473,286.00 7/1/2018 6/30/2023
      CPRIT RP180734 $4,429,126.00 8/31/2018 8/30/2023
    Total Amount : $5,844,412.33
    2019
      NIH R03 DE027393 $308,000.00 9/15/2018 8/31/2020
      NIH R03 DE028103 $308,000.00 9/15/2018 8/31/2020
      NIH 1R01CA230746-01A1 $1,777,388.00 3/1/2019 2/29/2024
      NIH 1R01AR072368-01A1 $1,917,918.00 3/4/2019 2/29/2024
      NSF IIS 1902617 $17,950.00 4/1/2019 3/31/2020
      NIH 1R01LM012974-01A1 $1,402,073.00 7/1/2019 6/30/2023
      NIH 1R21NS108091-01A1 $425,583.00 7/1/2019 6/30/2021
      NIH 1UL1TR003167-01 $28,135,332.00 7/24/2019 6/30/2021
    Total Amount : $34,292,244.00
    2020
      NIH R21EB029575 $617,750.00 3/1/2020 12/31/2022
      NIH 1R01AG066749-01 $3,752,852.00 4/1/2020 3/31/2025
      NIH 3R01AG066749-01S1 $389,580.00 4/1/2020 3/31/2021
      NIH KL2 TR003168 $330,800.00 7/1/2020 6/30/2022
      NIH K01AI148593-01 $481,000.00 7/1/2020 6/30/2024
    Total Amount : $5,571,982.00
    2021
      NIH NIH 1R56AI150272-01A1 $801,194.00 9/1/2020 8/31/2021
      ANRF Arthritis Nat’l Res. Fdn $100,000.00 9/1/2020 8/31/2021
      CPRIT RP210045 $3,998,553.00 6/1/2021 5/31/2026
    Total Amount : $4,899,747.00
    2022
      CPRIT RP220244 $1,397,258.00 4/1/2022 3/31/2026
      NIH 1R21NS123685-01A1 $429,000 4/1/2022 3/31/2024
      Roderick D. MacDonald Baylor St. Luke’s Award 66727-1 $50,000 5/2022 4/2023
      DOD W81XWH-22-1-0162 $1,169,825 5/1/2022 4/30/2025
      NIH K08AR081402-01 $820,800 8/10/2022 7/31/2027
    Total Amount : $3,866,883.00
    2023
      NIH 1U24MH130988-01 $4,868,345 9/1/2022 6/30/2027
      NIH 5R21DE031440 $454,028 9/19/2022 9/18/2024
      NIH 1R01AR081280-01A1 $1,124,325 5/1/2023 4/30/2028
    Total Amount : $6,446,698.00
    2024
      NIH 1K23AR083506 $812,700 2/12/2024 1/31/2029
      NIH 1UM1TR004906-01 $55,500,000 7/24/2024 6/30/2029
  • Publications
    1. Roberts, K., Demner-Fushman, D., Voorhees, E. M., Hersh, W. R., Bedrick, S., Lazar, A. J. & Pant, S. Overview of the TREC 2017 Precision  Medicine Track. Text Retr Conf 26 (2017).
    2. Brusco, L. L., Wathoo, C., Mills Shaw, K. R., Holla, V. R., Bailey, A. M., Johnson, A. M., Khotskaya, Y. B., Litzenburger, B. C., Sanchez, N. S., Zeng, J., Bernstam, E. V., Eng, C., Kee, B. K., Amaria, R. N., Routbort, M. J., Mills, G. B., Mendelsohn, J. & Meric-Bernstam, F. Physician interpretation of genomic test results and treatment selection. Cancer 124, 966-972, doi:10.1002/cncr.31112 (2018).
    3. Chen, G., Tsoi, A., Xu, H. & Zheng, W. J. Predict effective drug combination by deep belief network and ontology fingerprints. J Biomed Inform 85, 149-154, doi:10.1016/j.jbi.2018.07.024 (2018).
    4. Jiang, W., Guo, Z., Lages, N., Zheng, W. J., Feliers, D., Zhang, F. & Wang, D. A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms. Sci Rep 8, 5742, doi:10.1038/s41598-018-24039-1 (2018).
    5. Liu, Z., Nyitray, A. G., Hwang, L. Y., Swartz, M. D., Abrahamsen, M., Lazcano-Ponce, E., Villa, L. L. & Giuliano, A. R. Acquisition, Persistence, and Clearance of Human Papillomavirus Infection Among Male Virgins Residing in Brazil, Mexico, and the United States. J Infect Dis 217, 767-776, doi:10.1093/infdis/jix588 (2018).
    6. Mallik, S. & Zhao, Z. Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm. BMC Syst Biol 12, 126, doi:10.1186/s12918-018-0650-2 (2018).
    7. Nguyen, C., Lairson, D. R., Swartz, M. D. & Du, X. L. Risks of Major Long-Term Side Effects Associated with Androgen-Deprivation Therapy in Men with Prostate Cancer. Pharmacotherapy 38, 999-1009, doi:10.1002/phar.2168 (2018).
    8. Rasmy, L., Wu, Y., Wang, N., Geng, X., Zheng, W. J., Wang, F., Wu, H., Xu, H. & Zhi, D. A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J Biomed Inform 84, 11-16, doi:10.1016/j.jbi.2018.06.011 (2018).
    9. Shah, M. S., DeSantis, T., Yamal, J. M., Weir, T., Ryan, E. P., Cope, J. L. & Hollister, E. B. Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. PLoS One 13, e0207002, doi:10.1371/journal.pone.0207002 (2018).
    10. Zhu, L. & Zheng, W. J. Informatics, Data Science, and Artificial Intelligence. JAMA 320, 1103-1104, doi:10.1001/jama.2018.8211 (2018).
    11. Advani, S. M., Advani, P. S., Brown, D. W., DeSantis, S. M., Korphaisarn, K., VonVille, H. M., Bressler, J., Lopez, D. S., Davis, J. S., Daniel, C. R., Sarshekeh, A. M., Braithwaite, D., Swartz, M. D. & Kopetz, S. Global differences in the prevalence of the CpG island methylator phenotype of colorectal cancer. BMC Cancer 19, 964, doi:10.1186/s12885-019-6144-9 (2019).
    12. Chang, J. T., Volk, D. E., Gorenstein, D. G., Steffen, D. & Bernstam, E. V. Bioinformatics service center projects go beyond service. J Biomed Inform 94, 103192, doi:10.1016/j.jbi.2019.103192 (2019).
    13. Chen, G., Jia, Y., Zhu, L., Li, P., Zhang, L., Tao, C. & Jim Zheng, W. Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. BMC Med Inform Decis Mak 19, 20, doi:10.1186/s12911-019-0738-7 (2019).
    14. Chen, G., Ramirez, J. C., Deng, N., Qiu, X., Wu, C., Zheng, W. J. & Wu, H. Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. Database (Oxford) 2019, doi:10.1093/database/bay145 (2019).
    15. Datta, S., Bernstam, E. V. & Roberts, K. A frame semantic overview of NLP-based information extraction for cancer-related EHR notes. J Biomed Inform 100, 103301, doi:10.1016/j.jbi.2019.103301 (2019).
    16. Echeverria, G. V., Ge, Z., Seth, S., Zhang, X., Jeter-Jones, S., Zhou, X., Cai, S., Tu, Y., McCoy, A., Peoples, M., Sun, Y., Qiu, H., Chang, Q., Bristow, C., Carugo, A., Shao, J., Ma, X., Harris, A., Mundi, P., Lau, R., Ramamoorthy, V., Wu, Y., Alvarez, M. J., Califano, A., Moulder, S. L., Symmans, W. F., Marszalek, J. R., Heffernan, T. P., Chang, J. T. & Piwnica-Worms, H. Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Sci Transl Med 11, doi:10.1126/scitranslmed.aav0936 (2019).
    17. Huang, V. J. & Lai, D. Interim Analysis of Clinical Trials: Simulation Studies of Conditional Power under Fractional Brownian Motion (https://www.worldscientific.com/doi/abs/10.1142/S0218348X19501330). Fractals 27, 1950133, doi:https://doi.org/10.1142/S0218348X19501330 (2019).
    18. Jia, P., Pei, G. & Zhao, Z. CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. Bioinformatics 35, 5207-5215, doi:10.1093/bioinformatics/btz441 (2019).
    19. Jia, P. & Zhao, Z. Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types. Cell Rep 26, 496-506 e493, doi:10.1016/j.celrep.2018.12.066 (2019).
    20. Mai, T. T., Tran, D. Q., Roos, S., Rhoads, J. M. & Liu, Y. Human Breast Milk Promotes the Secretion of Potentially Beneficial Metabolites by Probiotic Lactobacillus reuteri DSM 17938. Nutrients 11, doi:10.3390/nu11071548 (2019).
    21. Mallik, S. & Zhao, Z. Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles. Genes (Basel) 10, doi:10.3390/genes10080611 (2019).
    22. Mungi, C., Lai, D. & Du, X. L. Spatial Analysis of Industrial Benzene Emissions and Cancer Incidence Rates in Texas. Int J Environ Res Public Health 16, doi:10.3390/ijerph16152627 (2019).
    23. Nguyen, C., Lairson, D. R., Swartz, M. D. & Du, X. L. Cost-Effectiveness of Adding Androgen Deprivation Therapy to Radiation Therapy for Men with Advanced Prostate Cancer from a U.S. Payer's Perspective. J Manag Care Spec Pharm 25, 225-234, doi:10.18553/jmcp.2019.25.2.225 (2019).
    24. Nguyen, C., Lairson, D. R., Swartz, M. D. & Du, X. L. Racial, Socioeconomic, and Geographic Disparities in the Receipt, Timing to Initiation, and Duration of Adjuvant Androgen Deprivation Therapy in Men with Prostate Cancer. J Racial Ethn Health Disparities 6, 133-142, doi:10.1007/s40615-018-0508-8 (2019).
    25. Pei, G., Sun, H., Dai, Y., Liu, X., Zhao, Z. & Jia, P. Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. BMC Genomics 20, 79, doi:10.1186/s12864-018-5373-7 (2019).
    26. Pena, D., Barman, A., Suescun, J., Jiang, X., Schiess, M. C., Giancardo, L. & Alzheimer's Disease Neuroimaging, I. Quantifying Neurodegenerative Progression With DeepSymNet, an End-to-End Data-Driven Approach. Front Neurosci 13, 1053, doi:10.3389/fnins.2019.01053 (2019).
    27. Roberts, K., Demner-Fushman, D., Voorhees, E. M., Hersh, W. R., Bedrick, S., Lazar, A. J., Pant, S. & Meric-Bernstam, F. in Twenty-Eighth Text Retrieval Conference (TREC 2019).
    28. Si, Y. & Roberts, K. Deep Patient Representation of Clinical Notes via Multi-Task Learning for Mortality Prediction. AMIA Jt Summits Transl Sci Proc 2019, 779-788 (2019).
    29. Si, Y., Wang, J., Xu, H. & Roberts, K. Enhancing clinical concept extraction with contextual embeddings. J Am Med Inform Assoc 26, 1297-1304, doi:10.1093/jamia/ocz096 (2019).
    30. Sonawane, K., Nyitray, A. G., Nemutlu, G. S., Swartz, M. D., Chhatwal, J. & Deshmukh, A. A. Prevalence of Human Papillomavirus Infection by Number of Vaccine Doses Among US Women. JAMA Netw Open 2, e1918571, doi:10.1001/jamanetworkopen.2019.18571 (2019).
    31. Sun, H., Kim, P., Jia, P., Park, A. K., Liang, H. & Zhao, Z. Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. Brief Bioinform 20, 1502-1512, doi:10.1093/bib/bby020 (2019).
    32. Wei, Q. & Lai, D. Test for Homogeneity of Odds Ratios Using U-Statistics (https://www.scirp.org/journal/paperinformation.aspx?paperid=93080). Open Journal of Statistics 9, 347-360, doi:doi: 10.4236/ojs.2019.93024 (2019).
    33. Xiang, Y., Xu, J., Si, Y., Li, Z., Rasmy, L., Zhou, Y., Tiryaki, F., Li, F., Zhang, Y., Wu, Y., Jiang, X., Zheng, W. J., Zhi, D., Tao, C. & Xu, H. Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Med Inform Decis Mak 19, 58, doi:10.1186/s12911-019-0766-3 (2019).
    34. Yu, J. & Lai, D. Sequential monitoring of covariate adaptive randomized clinical trials with sample size re-estimation. Contemp Clin Trials 87, 105874, doi:10.1016/j.cct.2019.105874 (2019).
    35. Zeng, J., Shufean, M. A., Khotskaya, Y., Yang, D., Kahle, M., Johnson, A., Holla, V., Sanchez, N., Mills Shaw, K. R., Bernstam, E. V. & Meric-Bernstam, F. OCTANE: Oncology Clinical Trial Annotation Engine. JCO Clin Cancer Inform 3, 1-11, doi:10.1200/CCI.18.00145 (2019).
    36. Baek, M., Chang, J. T. & Echeverria, G. V. Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside. J Mammary Gland Biol Neoplasia 25, 289-304, doi:10.1007/s10911-020-09470-3 (2020).
    37. Barnholtz-Sloan, J. S., Rollison, D. E., Basu, A., Borowsky, A. D., Bui, A., DiGiovanna, J., Garcia-Closas, M., Genkinger, J. M., Gerke, T., Induni, M., Lacey, J. V., Jr., Mirel, L., Permuth, J. B., Saltz, J., Shenkman, E. A., Ulrich, C. M., Zheng, W. J., Nadaf, S. & Kibbe, W. A. Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes. JCO Clin Cancer Inform 4, 108-116, doi:10.1200/CCI.19.00166 (2020).
    38. Dai, Y., O'Brien, T. D., Pei, G., Zhao, Z. & Jia, P. Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders. BMC Med Genomics 13, 192, doi:10.1186/s12920-020-00832-8 (2020).
    39. Dong, X., Li, J., Soysal, E., Bian, J., DuVall, S. L., Hanchrow, E., Liu, H., Lynch, K. E., Matheny, M., Natarajan, K., Ohno-Machado, L., Pakhomov, S., Reeves, R. M., Sitapati, A. M., Abhyankar, S., Cullen, T., Deckard, J., Jiang, X., Murphy, R. & Xu, H. COVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes. J Am Med Inform Assoc 27, 1437-1442, doi:10.1093/jamia/ocaa145 (2020).
    40. Ferguson, B., Bokka, N. R., Maddipati, K. R., Ayilavarapu, S., Weltman, R., Zhu, L., Chen, W., Zheng, W. J., Angelov, N., Van Dyke, T. E. & Lee, C. T. Distinct Profiles of Specialized Pro-resolving Lipid Mediators and Corresponding Receptor Gene Expression in Periodontal Inflammation. Front Immunol 11, 1307, doi:10.3389/fimmu.2020.01307 (2020).
    41. Goodrum, H., Roberts, K. & Bernstam, E. V. Automatic classification of scanned electronic health record documents. International Journal of Medical Informatics 144, 104302 (2020).
    42. Griffiths, J. I., Wallet, P., Pflieger, L. T., Stenehjem, D., Liu, X., Cosgrove, P. A., Leggett, N. A., McQuerry, J. A., Shrestha, G., Rossetti, M., Sunga, G., Moos, P. J., Adler, F. R., Chang, J. T., Sharma, S. & Bild, A. H. Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy. Proc Natl Acad Sci U S A 117, 16072-16082, doi:10.1073/pnas.1918937117 (2020).
    43. Hwang, H., Follen, M., Guillaud, M., Scheurer, M., MacAulay, C., MacAulay, C., Staerkel, G. A., van Niekerk, D. & Yamal, J. M. Cervical cytology reproducibility and associated clinical and demographic factors. Diagn Cytopathol 48, 35-42, doi:10.1002/dc.24325 (2020).
    44. Kim, P., Li, H., Wang, J. & Zhao, Z. Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform, doi:10.1093/bib/bbaa108 (2020).
    45. Kim, S., Park, H. J., Cui, X. & Zhi, D. Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer. Sci Rep 10, 3920, doi:10.1038/s41598-020-60845-2 (2020).
    46. Kim, Yejin, Shuyu Zheng, Jing Tang, Wenjin Jim Zheng, Zhao Li, and Xiaoqian Jiang. Anticancer drug synergy prediction in understudied tissues using transfer learning. Journal of the American Medical Informatics Association 28, no. 1 (2021): 42-51.
    47. Kiser, K. J., Ahmed, S., Stieb, S., Mohamed, A. S. R., Elhalawani, H., Park, P. Y. S., Doyle, N. S., Wang, B. J., Barman, A., Li, Z., Zheng, W. J., Fuller, C. D. & Giancardo, L. PleThora: Pleural effusion and thoracic cavity segmentations in diseased lungs for benchmarking chest CT processing pipelines. Med Phys 47, 5941-5952, doi:10.1002/mp.14424 (2020).
    48. Li, A., Mallik, S., Luo, H., Jia, P., Lee, D. F. & 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 21, 180-191, doi:10.1016/j.omtn.2020.05.028 (2020).
    49. Liu, X., Gosline, S. J., Pflieger, L. T., Wallet, P., Iyer, A., Guinney, J., Bild, A. H. & Chang, J. T. Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier. bioRxiv (2020).
    50. Mallik, S., Seth, S., Bhadra, 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) 11, doi:10.3390/genes11080931 (2020).
    51. Mallik, S. & Zhao, Z. Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise. Scientific reports 10, 1-14 (2020).
    52. Mandal, M., Sahoo, S. K., Patra, P., Mallik, S. & Zhao, Z. In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. BMC Bioinformatics 21, 499, doi:10.1186/s12859-020-03849-z (2020).
    53. Maroufy, V., Shah, P., Asghari, A., Deng, N., Le, R. N. U., Ramirez, J. C., Yaseen, A., Zheng, W. J., Umetani, M. & Wu, H. Gene expression dynamic analysis reveals co-activation of Sonic Hedgehog and epidermal growth factor followed by dynamic silencing. Oncotarget 11, 1358-1372, doi:10.18632/oncotarget.27547 (2020).
    54. Matmati, N., Hassan, B. H., Ren, J., Shamssedine, A. A., Jeong, E., Shariff, B., Snider, J., Rodkaer, S. V., Chen, G., Mohanty, B. K., Zheng, W. J., Obeid, L. M., Rossel-Larsen, M., Faergeman, N. J. & Hannun, Y. A. Yeast Sphingolipid Phospholipase Gene ISC1 Regulates the Spindle Checkpoint by a CDC55-Dependent Mechanism. Mol Cell Biol 40, doi:10.1128/MCB.00340-19 (2020).
    55. Morris, V. E., Hashmi, S. S., Zhu, L., Maili, L., Urbina, C., Blackwell, S., Greives, M. R., Buchanan, E. P., Mulliken, J. B., Blanton, S. H., Zheng, W. J., Hecht, J. T. & Letra, A. Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate. Hum Genet 139, 1261-1272, doi:10.1007/s00439-020-02169-9 (2020).
    56. Patra, B. G., Kar, R., Roberts, K. & Wu, H. Mental Health Severity Detection from Psychological Forum Data using Domain-Specific Unlabelled Data. AMIA Jt Summits Transl Sci Proc 2020, 487-496 (2020).
    57. Patra, B. G., Maroufy, V., Soltanalizadeh, B., Deng, N., Zheng, W. J., Roberts, K. & Wu, H. A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets. J Biomed Inform 104, 103399, doi:10.1016/j.jbi.2020.103399 (2020).
    58. Patra, B. G., Soltanalizadeh, B., Deng, N., Wu, L., Maroufy, V., Wu, C., Zheng, W. J., Roberts, K., Wu, H. & Yaseen, A. An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries. Database (Oxford) 2020, doi:10.1093/database/baaa074 (2020).
    59. Powell, R. T., Redwood, A., Liu, X., Guo, L., Cai, S., Zhou, X., Tu, Y., Zhang, X., Qi, Y. & Jiang, Y. Pharmacologic profiling of patient-derived xenograft models of primary treatment-naïve triple-negative breast cancer. Scientific reports 10, 1-11 (2020).
    60. Qin, G., Mallik, S., Mitra, R., Li, A., Jia, P., Eischen, C. M. & Zhao, Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep 10, 852, doi:10.1038/s41598-020-57834-w (2020).
    61. Rasmy, L., Tiryaki, F., Zhou, Y., Xiang, Y., Tao, C., Xu, H. & Zhi, D. Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J Am Med Inform Assoc 27, 1593-1599, doi:10.1093/jamia/ocaa180 (2020).
    62. Roberts, K., Demner-Fushman, D., Voorhees, E. M., Bedrick, S. & Hersh, W. R. Overview of the TREC 2020 Precision Medicine Track. Proceedings of the Text Retrieval Conference (2020).
    63. Si, Y., Du, J., Li, Z., Jiang, X., Miller, T., Wang, F., Jim Zheng, W. & Roberts, K. Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review. J Biomed Inform, 103671, doi:10.1016/j.jbi.2020.103671 (2020).
    64. Skaug, B., Khanna, D., Swindell, W. R., Hinchcliff, M. E., Frech, T. M., Steen, V. D., Hant, F. N., Gordon, J. K., Shah, A. A., Zhu, L., Zheng, W. J., Browning, J. L., Barron, A. M. S., Wu, M., Visvanathan, S., Baum, P., Franks, J. M., Whitfield, M. L., Shanmugam, V. K., Domsic, R. T., Castelino, F. V., Bernstein, E. J., Wareing, N., Lyons, M. A., Ying, J., Charles, J., Mayes, M. D. & Assassi, S. Global skin gene expression analysis of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive inflammatory profile. Ann Rheum Dis 79, 379-386, doi:10.1136/annrheumdis-2019-215894 (2020).
    65. Soltanalizadeh, B., Gonzalez Rodriguez, E., Maroufy, V., Zheng, W. J. & Wu, H. Modelling of hypoxia gene expression for three different cancer cell lines. Int J Comput Biol Drug Des 13, 124-143, doi:10.1504/ijcbdd.2020.10026794 (2020).
    66. 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 48, D633-D641, doi:10.1093/nar/gkz867 (2020).
    67. Wang, Y. & Lai, D. Empirical Size and Power of a Hybrid Statistic for Matched and Unmatched Designs in Interim Analysis of Clinical Trials: A Simulation Study.  (2020).
    68. Williams, G., Maroufy, V., Rasmy, L., Brown, D., Yu, D., Zhu, H., Talebi, Y., Wang, X., Thomas, E., Zhu, G., Yaseen, A., Miao, H., Leon Novelo, L., Zhi, D., DeSantis, S. M., Zhu, H., Yamal, J. M., Aguilar, D. & Wu, H. Vasopressor treatment and mortality following nontraumatic subarachnoid hemorrhage: a nationwide electronic health record analysis. Neurosurg Focus 48, E4, doi:10.3171/2020.2.FOCUS191002 (2020).
    69. Xiang, Y., Ji, H., Zhou, Y., Li, F., Du, J., Rasmy, L., Wu, S., Zheng, W. J., Xu, H., Zhi, D., Zhang, Y. & Tao, C. Asthma Exacerbation Prediction and Risk Factor Analysis Based on a Time-Sensitive, Attentive Neural Network: Retrospective Cohort Study. J Med Internet Res 22, e16981, doi:10.2196/16981 (2020).
    70. Xu, H., Jia, P. & Zhao, Z. Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Brief Bioinform, doi:10.1093/bib/bbaa099 (2020).
    71. Ye, J. & Lai, D. Estimations of treatment effects based on covariate adjusted nonparametric methods (https://www.tandfonline.com/doi/full/10.1080/25742558.2020.1750878). Cogent Mathematics & Statistics 7, 1750878, doi:https://doi.org/10.1080/25742558.2020.1750878 (2020).
    72. Yuan, Z., Ye, X., Zhu, L., Zhang, N., An, Z. & Zheng, W. J. Virome assembly and annotation in brain tissue based on next-generation sequencing. Cancer Med 9, 6776-6790, doi:10.1002/cam4.3325 (2020).
    73. Zheng, F., Shi, J., Yang, Y., Zheng, W. J. & Cui, L. A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. J Am Med Inform Assoc 27, 1568-1575, doi:10.1093/jamia/ocaa123 (2020).
    74. Aggarwal, P., Goepfert, R. P., Garden, A. S., Garg, N., Zaveri, J. S., Du, X. L., Swartz, M. D., Lai, S. Y., Fuller, C. D. & Ferrarotto, R. Risk and Clinical Risk Factors Associated With Late Lower Cranial Neuropathy in Long-term Oropharyngeal Squamous Cell Carcinoma Survivors. JAMA Otolaryngology–Head & Neck Surgery 147, 469-478 (2021).
    75. Bora, K., Bhuyan, M., Kasugai, K., Mallik, S. & Zhao, Z. Computational learning of features for automated colonic polyp classification. Scientific Reports 11, 1-16 (2021).
    76. Carr, H. S., Chang, J. T. & Frost, J. A. The PDZ domain protein SYNJ2BP regulates GRK-dependent Sst2A phosphorylation and downstream MAPK signaling. Endocrinology 162, bqaa229 (2021).
    77. Chi, F., Liu, J., Brady, S. W., Cosgrove, P. A., Nath, A., McQuerry, J. A., Majumdar, S., Moos, P. J., Chang, J. T. & Kahn, M. Aone-two punch'therapy strategy to target chemoresistance in estrogen receptor positive breast cancer. Translational oncology 14, 100946 (2021).
    78. Dai, Y., Hu, R., Manuel, A. M., Liu, A., Jia, P. & Zhao, Z. CSEA-DB: an omnibus for human complex trait and cell type associations. Nucleic Acids Research 49, D862-D870 (2021).
    79. Greene, T. J., DeSantis, S. M., Brown, D. W., Wilkinson, A. V. & Swartz, M. D. A machine learning compatible method for ordinal propensity score stratification and matching. Stat Med 40, 1383-1399, doi:10.1002/sim.8846 (2021).
    80. ; Hu, R., Xu, H., Jia, P. & Zhao, Z. KinaseMD: kinase mutations and drug response database. Nucleic Acids Research 49, D552-D561 (2021).
    81. Jeong, H.-H., Jia, J., Dai, Y., Simon, L. M. & Zhao, Z. Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches. Genes 12, 635 (2021).
    82. Jia, P., Hu, R., Pei, G., Dai, Y., Wang, Y.-Y. & Zhao, Z. Deep generative neural network for accurate drug response imputation. Nature communications 12, 1-16 (2021).
    83. Kiser, K. J., Barman, A., Stieb, S., Fuller, C. D. & Giancardo, L. Novel autosegmentation spatial similarity metrics capture the time required to correct segmentations better than traditional metrics in a thoracic cavity segmentation workflow. Journal of Digital Imaging, 1-13 (2021).
    84. Li, B., Pei, G., Yao, J., Ding, Q., Jia, P. & Zhao, Z. Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. Oncogene, 1-9 (2021).
    85. Li, Z., Li, R., Kiser, K. J., Giancardo, L. & Zheng, W. J. in ACM-BCB 2021.
    86. Liu, A., Dai, Y., Mendez, E. F., Hu, R., Fries, G. R., Najera, K. E., Jiang, S., Meyer, T. D., Stertz, L. & Jia, P. Genome-wide correlation of DNA methylation and gene expression in postmortem brain tissues of opioid use disorder patients. International Journal of Neuropsychopharmacology (2021).
    87. Mallik, S., Qin, G., Jia, P. & Zhao, Z. Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours. Epigenetics 16, 162-176, doi:10.1080/15592294.2020.1790108 (2021).
    88. McGrail, D., Pilié, P., Rashid, N., Voorwerk, L., Slagter, M., Kok, M., Jonasch, E., Khasraw, M., Heimberger, A. & Lim, B. High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types. Annals of Oncology 32, 661-672 (2021).
    89. Minegishi, Ryu, Osamu Gotoh, Norio Tanaka, Reo Maruyama, Jeffrey T. Chang, and Seiichi Mori. A method of sample-wise region-set enrichment analysis for DNA methylomics. Epigenomics 13, no. 14 (2021): 1081-1093.
    90. Pei, G., Hu, R., Jia, P. & Zhao, Z. DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue-and cell type-specific manner. Nucleic Acids Research (2021).
    91. Rasmy, L., Xiang, Y., Xie, Z., Tao, C. & Zhi, D. Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. NPJ digital medicine 4, 1-13 (2021).
    92. Xu, H., Jia, P. & Zhao, Z. DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery. Advanced Science 8, 2004958 (2021).
    93. Ye, J. & Lai, D. Covariate Adjusted Nonparametric Methods under Propensity Analysis. Journal of Modern Applied Statistical Methods In Press (2021).
    94. Yeh, M., Wang, Y.-Y., Yoo, J. Y., Oh, C., Otani, Y., Kang, J. M., Park, E. S., Kim, E., Chung, S. & Jeon, Y.-J. MicroRNA-138 suppresses glioblastoma proliferation through downregulation of CD44. Scientific reports 11, 1-11 (2021).
    95. Yuan, Z., Fan, X., Zhu, J. J., Fu, T. M., Wu, J., Xu, H., Zhang, N., An, Z. & Zheng, W. J. Presence of complete murine viral genome sequences in patient-derived xenografts. Nat Commun 12, 2031, doi:10.1038/s41467-021-22200-5 (2021).
    96. Yuan, Zihao, Yuntao Yang, Ningyan Zhang, Claudio Soto, Xiaoqian Jiang, Zhiqiang An, and Wenjin Jim Zheng. Human endogenous retroviruses in glioblastoma multiforme. Microorganisms 9, no. 4 (2021): 764.
    97. Zuo, X., Li, J., Zhao, B., Zhou, Y., Dong, X., Duke, J., Natarajan, K., Hripcsak, G., Shah, N., Banda, J. M., Reeves, R., Miller, T. & Xu, H. Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study. AMIA Annu Symp Proc 2020, 1441-1450 (2021).
    98. David J. H. Shih, Mei-Kuang Chen, Jun Yin, Daniel J. McGrail, Hui Dai, Rongbin Wei, Jing Zhang, Wenjin J. Zheng, Kim-Anh Do, Liuqing Yang, Mien-Chie Hung, Shiaw-Yih Lin: Transcriptomic characterization identifies induced vulnerability in PARPi-resistant breast cancer, American Journal of Cancer Research, accepted, 2022
    99. Shih, David JH, Ruoxing Li, Peter Müller, W. Jim Zheng, Kim-Anh Do, Shiaw-Yih Lin, and Scott L. Carter. CNGPLD: case–control copy-number analysis using Gaussian process latent difference. Bioinformatics 38, no. 8 (2022): 2096-2101.
    100. Asghari, Arvand, Katherine Wall, Michael Gill, Natascha Del Vecchio, Farnaz Allahbakhsh, Jacky Wu, Nan Deng et al. A novel group of genes that cause endocrine resistance in breast cancer identified by dynamic gene expression analysis. Oncotarget 13 (2022): 600.
    101. Clinton Yam, Er-Yen Yen, Jeffrey T. Chang, Roland L. Bassett, Jr., Gheath Alatrash, Haven Garber, Lei Huo, Fei Yang, Anne V. Philips, Qing-Qing Ding, Bora Lim, Naoto T. Ueno, Kasthuri Kannan, Xiangjie Sun, Baohua Sun, Edwin Roger Parra Cuentas, William Fraser Symmans, Jason B. White, Elizabeth Ravenberg, Sahil Seth, Jennifer L. Guerriero, Gaiane M. Rauch, Senthil Damodaran, Jennifer K. Litton, Jennifer A. Wargo, Gabriel N. Hortobagyi, Andrew Futreal, Ignacio I. Wistuba, Ryan Sun, Stacy L. Moulder, and Elizabeth A. Mittendorf. Immune Phenotype and Response to Neoadjuvant Therapy in Triple-Negative Breast Cancer. Clin Cancer Res. 2021.
    102. Singh, Swarnima, Nigel Lee, Diego A. Pedroza, Igor Bado, Licheng Zhang, Sergio Aguirre, Clark Hamor et al. Chemotherapy coupled to macrophage inhibition leads to enhanced T and B cell infiltration and durable triple negative breast cancer regression. bioRxiv (2021): 2021-02.
    103. Prijic, Sara, and Jeffrey T. Chang. ABCA1 expression is upregulated in an EMT in breast cancer cell lines via MYC-mediated de-repression of its proximal Ebox element. Biomedicines 10, no. 3 (2022): 581.
    104. Yam, Clinton, Nour Abuhadra, Ryan Sun, Beatriz E. Adrada, Qing-Qing Ding, Jason B. White, Elizabeth E. Ravenberg et al. Molecular Characterization and Prospective Evaluation of Pathologic Response and Outcomes with Neoadjuvant Therapy in Metaplastic Triple-Negative Breast Cancer. Clinical Cancer Research 28, no. 13 (2022): 2878-2889.
    105. Liu, Xuan, Zhongqi Ge, Fei Yang, Alejandro Contreras, Sanghoon Lee, Jason B. White, Yiling Lu et al. Identification of biomarkers of response to preoperative talazoparib monotherapy in treatment naïve g BRCA+ breast cancers. npj Breast Cancer 8, no. 1 (2022): 64.
    106. Shikun Wang^, Zhao Li^, Lan Lan, Jieyi Zhao, W. Jim Zheng*, Liang Li*: GPU accelerated estimation of a shared random effect joint model for dynamic prediction, Computational Statistics & Data Analysis, Volume 174, 2022, 107528, ISSN 0167-9473, https://doi.org/10.1016/ j.csda.2022.107528. (^. Equal contribution, * Corresponding authors)
    107. Kumar, Tapsi, Evie Hobbs, Fei Yang, Jeffrey T. Chang, Alejandro Contreras, Edwin Roger Parra Cuentas, Haven Garber et al. Tumor immune microenvironment changes by multiplex .
    108. Anupam K. Chakravarty, Daniel J. Mcgrail, Thomas M. Lozanoski, Brandon S. Dunn, David J.H. Shih, Kara M. Cirillo, Sueda Cetinkaya, W. Jim Zheng, Gordon B. Mills, S. Stephen Yi, Daniel F. Jarosz and Nidhi Sahni: Biomolecular condensation: A new phase in cancer research, Cancer Discovery, 2022 Jul 19:OF1-OF13. doi: 10.1158/2159-8290.CD-21-1605. Epub ahead of print. PMID: 35852417.
    109. Teresa T. Nguyen, Dong Ho Shin, Sagar Sohoni, Yisel Rivera-Molina, Hong Jiang, Xuejun Fan, Sanjay K. Singh, Joy Gumin, Frederick F. Lang, Marta M. Alonso, Lisha Zhu, W. Jim Zheng, Lijie Zhai, Erik Ladomersky, Kristen L. Lauing, Derek A. Wainwright, Candelaria Gomez-Manzano, Juan Fueyo: Reshaping the tumor microenvironment with oncolytic viruses, positive regulation of the immune synapse, and blockade of the immunosuppressive oncometabolic circuitry, Journal for ImmunoTherapy of Cancer, 10(7):e004935 2022, PMID: 35902132, PMCID: PMC9341188.
    110. Tripathi, Shikha, Teresa Arroyo-Gallego, and Luca Giancardo. Keystroke-dynamics for Parkinson's disease signs detection in an at-home uncontrolled population: a new benchmark and method. IEEE Transactions on Biomedical Engineering 70, no. 1 (2022): 182-192.
    111. Pena, Danilo, Jessika Suescun, Mya Schiess, Timothy M. Ellmore, Luca Giancardo, and Alzheimer’s Disease Neuroimaging Initiative. Toward a Multimodal Computer-Aided Diagnostic Tool for Alzheimer’s Disease Conversion. Frontiers in neuroscience (2022): 1644.
    112. Sujit, Sheeba J., Eliana Bonfante, Azin Aein, Ivan Coronado, Roy Riascos-Castaneda, and Luca Giancardo. Deep learning enabled brain shunt valve identification using mobile phones. Computer methods and programs in biomedicine 210 (2021): 106356.
    113. Li, Zhao, Rongbin Li, Kendall J. Kiser, Luca Giancardo, and W. Jim Zheng. Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks. In Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 1-8. 2021.
    114. Holcomb, Jennifer, Luis C. Oliveira, Linda Highfield, Kevin O. Hwang, Luca Giancardo, and Elmer Victor Bernstam. Predicting health-related social needs in Medicaid and Medicare populations using machine learning. Scientific Reports 12, no. 1 (2022): 1-10.
    115. Fan, Shuyang, Mehmet Enes Inam, Danilo Peña, Peng Roc Chen, and Luca Giancardo. X-ray based automatic detection of brain coil compaction using unsupervised learning. In 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), pp. 625-629. IEEE, 2021.
    116. Estrada, Uma Maria Lal-Trehan, Grant Meeks, Sergio Salazar-Marioni, Fabien Scalzo, Mudassir Farooqui, Juan Vivanco-Suarez, Santiago Ortega Gutierrez, Sunil A. Sheth, and Luca Giancardo. Quantification of infarct core signal using CT imaging in acute ischemic stroke. NeuroImage: Clinical 34 (2022): 102998.
    117. Fan, Huihui, Peilin Jia, and Zhongming Zhao. Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis. Cancers 13, no. 23 (2021): 6024.
    118. Bhadra, Tapas, Saurav Mallik, Amir Sohel, and Zhongming Zhao. 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 19, no. 3 (2021): 1354-1364.
    119. Fernandes, Brisa S., Yulin Dai, Peilin Jia, and Zhongming Zhao. Charting the proteome landscape in major psychiatric disorders: From biomarkers to biological pathways towards drug discovery. European Neuropsychopharmacology 61 (2022): 43-59.
    120. Bhadra, Tapas, Saurav Mallik, Neaj Hasan, and Zhongming Zhao. Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. BMC bioinformatics 23, no. 3 (2022): 1-19.
    121. Deng, Nan, Canglin Wu, Ashraf Yaseen, and Hulin Wu. ImmuneData: an integrated data discovery system for immunology data repositories. Database 2022 (2022).
    122. Yang, Yiping, Hongjian Zhu, and Dejian Lai. Estimating Conditional Power for Sequential Monitoring of Covariate Adaptive Randomized Designs: The Fractional Brownian Motion Approach. Fractal and Fractional 5, no. 3 (2021): 114.
    123. Dharia, Priyadarshani, Michael D. Swartz, M. Brooke Bernhardt, Han Chen, M. Monica Gramatges, Philip J. Lupo, Austin L. Brown, and Michael E. Scheurer. Clinical and demographic factors contributing to asparaginase-associated toxicities in children with acute lymphoblastic leukemia. Leukemia & Lymphoma 63, no. 12 (2022): 2948-2954.
    124. Kumar, Akshat, Heath Goodrum, Ashley Kim, Carly Stender, Kirk Roberts, and Elmer V. Bernstam. Closing the loop: automatically identifying abnormal imaging results in scanned documents. Journal of the American Medical Informatics Association 29, no. 5 (2022): 831-840.
    125. Si, Yuqi, Elmer V. Bernstam, and Kirk Roberts. Generalized and transferable patient language representation for phenotyping with limited data. Journal of Biomedical Informatics 116 (2021): 103726.
    126. Swartz, Maria C., Zakkoyya H. Lewis, Rachel R. Deer, Anna L. Stahl, Michael D. Swartz, Ursela Christopherson, Karen Basen-Engquist, Stephanie J. Wells, H. Colleen Silva, and Elizabeth J. Lyons. Feasibility and Acceptability of an Active Video Game–Based Physical Activity Support Group (Pink Warrior) for Survivors of Breast Cancer: Randomized Controlled Pilot Trial. JMIR cancer 8, no. 3 (2022): e36889.
    127. Li, Z., Li, R., Zhou, Y., Rasmy, L., Zhi, D., Zhu, P., Dono, A., Jiang, X., Xu, H., Esquenazi, Y., Zheng, W. J.: Prediction of Brain Metastases Development in Lung Cancer Patients by Explainable AI from Electronic Health Records, Journal of Clinical Oncology Clinical Cancer Informatics, accepted, 2023.
    128. Chandra Sekhar Amara, Karthik Reddy Kami Reddy, Yang Yuntao, Yuen San Chan, Danthasinghe Waduge Badrajee Piyarathna, Lacey Elizabeth Dobrolecki, David J H Shih, Zhongcheng Shi, Jun Xu, Shixia Huang, Matthew J Ellis, Andrea B Apolo, Leomar Y Ballester, Jianjun Gao, Donna E Hansel, Yair Lotan, H. Courtney Hodges, Seth P Lerner, Chad J Creighton, Arun Sreekumar, W. Jim Zheng, Pavlos Msaouel, Shyam M Kavuri and Nagireddy Putluri: The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer, Nature Communication, 2024 Feb 14;15(1):1373. doi: 10.1038/s41467-024-45132-2. PMID: 38355560; PMCID: PMC10867091.
    129. Xiaohua Ye, David J. H. Shih, Zhiqiang Ku, Junping Hong, Diane F. Barrett, Richard E. Rupp, Ningyan Zhang, Tong-Ming Fu, W. Jim Zheng, Zhiqiang An: Transcriptional signature of durable effector T cells elicited by a replication defective HCMV vaccine, npj Vaccines, 2024 Apr 1;9(1):70. doi: 10.1038/s41541-024-00860-w. PMID: 38561339; PMCID: PMC10984989.
    130. Zhao Li, Qiang Wei, Liang-Chin Huang, Jianfu Li, Yan Hu, Yao-Shun Chuang, Jianping He, Avisha Das, Vipina Kuttichi Keloth, Yuntao Yang, Chiamaka S Diala, Kirk E Roberts, Cui Tao, Xiaoqian Jiang, W. Jim Zheng, Hua Xu: Ensemble pretrained language models to extract biomedical knowledge from literature, Journal of the American Medical Informatics Association, 2024 Mar 23:ocae061. doi: 10.1093/jamia/ocae061. Epub ahead of print. PMID: 38520725.