Publications

  1. Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N. SenNet recommendations for detecting senescent cells in different tissues. Nat Rev Mol Cell Biol. 2024 Dec; 25 (12):1001-1023 Epub 2024 June 03
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  2. Liu J, Wang K, Zhu Q, Zhang Y, Chen Y, Lou Z, Yuan J. USP19 regulates DNA methylation damage repair and confers temozolomide resistance through MGMT stabilization. CNS Neurosci Ther. 2024 Apr; 30 (4):e14711
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  3. Robino JJ, Plekhanov AP, Zhu Q, Jensen MD, Scherer PE, Roberts CT, Varlamov O. Adipose Tissue Analysis Toolkit (ATAT) for automated analysis of adipocyte size and extracellular matrix in white adipose tissue. Obesity (Silver Spring). 2024 Apr; 32 (4):723-732 Epub 2024 Feb 06
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  4. Lin D, Zhu Q, Zhang S, Zhou F, Zhao L, Wang Q, Chen W, Chen H, Lin X, Feng H, Zhong Q, Chen J, Lin Z, Li X, Xiao W, Zhou Y, Wang J, Li J, Chen W. Postoperative myopic shift and visual acuity rehabilitation in patients with bilateral congenital cataracts. Front Med (Lausanne). 2024; 11:1406287 Epub 2024 May 02
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  5. Gurkar AU, Gerencser AA, Mora AL, Nelson AC, Zhang AR, Lagnado AB, Enninful A, Benz C, Furman D, Beaulieu D, Jurk D, Thompson EL, Wu F, Rodriguez F, Barthel G, Chen H, Phatnani H, Heckenbach I, Chuang JH, Horrell J, Petrescu J, Alder JK, Lee JH, Niedernhofer LJ, Kumar M, Konigshoff M, Bueno M, Sokka M, Scheibye-Knudsen M, Neretti N, Eickelberg O, Adams PD, Hu Q, Zhu Q, Porritt RA, Dong R, Peters S, Victorelli S, Pengo T, Khaliullin T, Suryadevara V, Fu X, Bar-Joseph Z, Ji Z, Passos JF. Spatial mapping of cellular senescence: emerging challenges and opportunities. Nat Aging. 2023 Jul; 3 (7):776-790 Epub 2023 July 03
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  6. Singh KP, Cooper BA, Tofthagen CS, Fryer JD, Singh P, Pituch K, Zhu Q, Gu H, Hammer MJ, Conley YP, Levine JD, Miaskowski C. Higher Levels of Stress and Neuropsychological Symptoms Are Associated With a High Nausea Profile in Patients With Cancer Receiving Chemotherapy. Oncol Nurs Forum. 2023 Jun 15; 50 (4):461-473
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  7. Huang J, Wu C, Kloeber JA, Gao H, Gao M, Zhu Q, Chang Y, Zhao F, Guo G, Luo K, Dai H, Liu S, Huang Q, Kim W, Zhou Q, Zhu S, Wu Z, Tu X, Yin P, Deng M, Wang L, Yuan J, Lou Z. SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology. Mol Cell. 2023 Apr 6; 83 (7):1043-1060.e10 Epub 2023 Feb 27
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  8. Zhou Q, Huang J, Zhang C, Zhao F, Kim W, Tu X, Zhang Y, Nowsheen S, Zhu Q, Deng M, Chen Y, Qin B, Luo K, Liu B, Lou Z, Mutter RW, Yuan J. Author Correction: The bromodomain containing protein BRD-9 orchestrates RAD51-RAD54 complex formation and regulates homologous recombination-mediated repair. Nat Commun. 2022 Nov 23; 13 (1):7190
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  9. Zeng X, Zhao F, Cui G, Zhang Y, Deshpande RA, Chen Y, Deng M, Kloeber JA, Shi Y, Zhou Q, Zhang C, Hou J, Kim W, Tu X, Yan Y, Xu Z, Chen L, Gao H, Guo G, Liu J, Zhu Q, Cao Y, Huang J, Wu Z, Zhu S, Yin P, Luo K, Mer G, Paull TT, Yuan J, Tao K, Lou Z. METTL16 antagonizes MRE11-mediated DNA end resection and confers synthetic lethality to PARP inhibition in pancreatic ductal adenocarcinoma. Nat Cancer. 2022 Sep; 3 (9):1088-1104 Epub 2022 Sept 22
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  10. Singh K, Pituch K, Zhu Q, Gu H, Ernst B, Tofthagen C, Brewer M, Kober KM, Cooper BA, Paul SM, Conley YP, Hammer M, Levine JD, Miaskowski C. Distinct Nausea Profiles Are Associated With Gastrointestinal Symptoms in Oncology Patients Receiving Chemotherapy. Cancer Nurs. 2022 Mar 2 Epub 2022 Mar 02
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  11. Gonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC Jr, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. Cell Mol Gastroenterol Hepatol. 2022; 14 (1):35-53 Epub 2022 Apr 01
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  12. Zhou Q, Huang J, Zhang C, Zhao F, Kim W, Tu X, Zhang Y, Nowsheen S, Zhu Q, Deng M, Chen Y, Qin B, Luo K, Liu B, Lou Z, Mutter RW, Yuan J. Author Correction: The bromodomain containing protein BRD-9 orchestrates RAD51–RAD54 complex formation and regulates homologous recombination-mediated repair (Nature Communications, (2020), 11, 1, (2639), 10.1038/s41467-020-16443-x). Nature Communications. 2022; 13 (1):7190
  13. Zhu Q, Huang J, Huang H, Li H, Yi P, Kloeber JA, Yuan J, Chen Y, Deng M, Luo K, Gao M, Guo G, Tu X, Yin P, Zhang Y, Su J, Chen J, Lou Z. RNF19A-mediated ubiquitination of BARD1 prevents BRCA1/BARD1-dependent homologous recombination. Nat Commun. 2021 Nov 17; 12 (1):6653
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  14. Zhang Y, Yang Q, Zeng X, Wang M, Dong S, Yang B, Tu X, Wei T, Xie W, Zhang C, Guo Q, Kloeber JA, Cao Y, Guo G, Zhou Q, Zhao F, Huang J, Liu L, Zhang K, Wang M, Yin P, Luo K, Deng M, Kim W, Hou J, Shi Y, Zhu Q, Chen L, Hu S, Yue J, Pi G, Lou Z. MET Amplification Attenuates Lung Tumor Response to Immunotherapy by Inhibiting STING. Cancer Discov. 2021 Nov; 11 (11):2726-2737 Epub 2021 June 07
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  15. Singh KP, Kober KM, Ernst B, Sachdev J, Brewer M, Zhu Q, Gu H, Melisko M, Paul SM, Cooper BA, Hammer M, Conley YP, Levine JD, Miaskowski C. Multiple Gastrointestinal Symptoms Are Associated With Chemotherapy-Induced Nausea in Patients With Breast Cancer. Cancer Nurs. 2021 Jun 28 Epub 2021 June 28
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  16. Zhou Q, Howard ME, Tu X, Zhu Q, Denbeigh JM, Remmes NB, Herman MG, Beltran CJ, Yuan J, Greipp PT, Boughey JC, Wang L, Johnson N, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. Inhibition of ATM Induces Hypersensitivity to Proton Irradiation by Upregulating Toxic End Joining. Cancer Res. 2021 Jun 15; 81 (12):3333-3346 Epub 2021 Feb 17
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  17. Guo G, Gao M, Gao X, Zhu B, Huang J, Tu X, Kim W, Zhao F, Zhou Q, Zhu S, Wu Z, Yan Y, Zhang Y, Zeng X, Zhu Q, Yin P, Luo K, Sun J, Deng M, Lou Z. Reciprocal regulation of RIG-I and XRCC4 connects DNA repair with RIG-I immune signaling. Nat Commun. 2021 Apr 12; 12 (1):2187
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  18. Gao M, Guo G, Huang J, Hou X, Ham H, Kim W, Zhao F, Tu X, Zhou Q, Zhang C, Zhu Q, Liu J, Yan Y, Xu Z, Yin P, Luo K, Weroha J, Deng M, Billadeau DD, Lou Z. DOCK7 protects against replication stress by promoting RPA stability on chromatin. Nucleic Acids Res. 2021 Apr 06; 49(6):3322-3337.
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  19. Shen C, Zhu Q, Dong F, Wang W, Fan B, Li K, Chen J, Hu S, He Z, Li X. Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing. Front Cell Infect Microbiol. 2021; 11:723781 Epub 2021 Nov 17
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  20. Wang J, Clay-Gilmour AI, Karaesmen E, Rizvi A, Zhu Q, Yan L, Preus L, Liu S, Wang Y, Griffiths E, Stram DO, Pooler L, Sheng X, Haiman C, Van Den Berg D, Webb A, Brock G, Spellman S, Pasquini M, McCarthy P, Allan J, Stolzel F, Onel K, Hahn T, Sucheston-Campbell LE. Genome-Wide Association Analyses Identify Variants in IRF4 Associated With Acute Myeloid Leukemia and Myelodysplastic Syndrome Susceptibility. Front Genet. 2021; 12:554948 Epub 2021 June 17
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  21. Chen VL, Yeh ML, Yang JD, Leong J, Huang DQ, Toyoda H, Chen YL, Guy J, Maeda M, Tsai PC, Huang CF, Yasuda S, Le AK, Dang H, Giama NH, Ali HA, Zhang N, Wang X, Jun DW, Tseng CH, Hsu YC, Huang JF, Dai CY, Chuang WL, Zhu Q, Dan YY, Schwartz M, Roberts LR, Yu ML, Nguyen MH. Effects of Cirrhosis and Diagnosis Scenario in Metabolic-Associated Fatty Liver Disease-Related Hepatocellular Carcinoma. Hepatol Commun. 2021 Jan; 5 (1):122-132 Epub 2020 Sept 24
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  22. Yan Y, Xu Z, Huang J, Guo G, Gao M, Kim W, Zeng X, Kloeber JA, Zhu Q, Zhao F, Luo K, Lou Z. The deubiquitinase USP36 Regulates DNA replication stress and confers therapeutic resistance through PrimPol stabilization. Nucleic Acids Res. 2020 Dec 16; 48 (22):12711-12726
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  23. Yan Y, Guo G, Huang J, Gao M, Zhu Q, Zeng S, Gong Z, Xu Z. Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance. J Hematol Oncol. 2020 Sep 14; 13 (1):124 Epub 2020 Sept 14
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  24. Huang J, Zhou Q, Gao M, Nowsheen S, Zhao F, Kim W, Zhu Q, Kojima Y, Yin P, Zhang Y, Guo G, Tu X, Deng M, Luo K, Qin B, Machida Y, Lou Z. Tandem Deubiquitination and Acetylation of SPRTN Promotes DNA-Protein Crosslink Repair and Protects against Aging. Mol Cell. 2020 Sep 3; 79 (5):824-835.e5 Epub 2020 July 09
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  25. Zhou Q, Huang J, Zhang C, Zhao F, Kim W, Tu X, Zhang Y, Nowsheen S, Zhu Q, Deng M, Chen Y, Qin B, Luo K, Liu B, Lou Z, Mutter RW, Yuan J. The bromodomain containing protein BRD-9 orchestrates RAD51-RAD54 complex formation and regulates homologous recombination-mediated repair. Nat Commun. 2020 May 26; 11 (1):2639
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  26. Zhu Q, Jiang J, Gendron TF, McAlonis-Downes M, Jiang L, Taylor A, Diaz Garcia S, Ghosh Dastidar S, Rodriguez MJ, King P, Zhang Y, La Spada AR, Xu H, Petrucelli L, Ravits J, Da Cruz S, Lagier-Tourenne C, Cleveland DW. Reduced C9ORF72 function exacerbates gain of toxicity from ALS/FTD-causing repeat expansion in C9orf72. Nat Neurosci. 2020 May; 23 (5):615-624 Epub 2020 Apr 13
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  27. He Y, Gu Z, Zhu Q, Chen M, He C, Huang Y, Li Q, Di W. CA125 over-release behavior following a 75-g oral glucose test as a predictive biomarker of multidrug resistance in patients with ovarian cancer. Int J Cancer. 2019 Sep 15; 145 (6):1690-1700 Epub 2019 Mar 23
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  28. Honigbaum S, Zhu Q, Layman A, Anders RA, Schwarz KB. Abundant Expression of Lysyl Oxidase-like 2 Protein in Intrahepatic Bile Ducts of Infants With Biliary Atresia. J Pediatr Gastroenterol Nutr. 2019 Sep; 69 (3):344-350
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  29. Wang L, Feng Y, Xie X, Wu H, Su XN, Qi J, Xin W, Gao L, Zhang Y, Shah VH, Zhu Q. Neuropilin-1 aggravates liver cirrhosis by promoting angiogenesis via VEGFR2-dependent PI3K/Akt pathway in hepatic sinusoidal endothelial cells. EBioMedicine. 2019 May; 43:525-536 Epub 2019 May 03
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  30. Kim AK, Gani F, Layman AJ, Besharati S, Zhu Q, Succaria F, Engle EL, Bhaijee F, Goggins MB, Llosa NJ, Pawlik TM, Yarchoan M, Jaffee EM, Simons HC, Taube JM, Anders RA. Multiple Immune-Suppressive Mechanisms in Fibrolamellar Carcinoma. Cancer Immunol Res. 2019 May; 7 (5):805-812 Epub 2019 Mar 22
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  31. Nandy S, Mostafa A, Hagemann IS, Powell MA, Amidi E, Robinson K, Mutch DG, Siegel C, Zhu Q. Evaluation of Ovarian Cancer: Initial Application of Coregistered Photoacoustic Tomography and US. Radiology. 2018 Dec; 289 (3):740-747 Epub 2018 Sept 11
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  32. Zhu Q, Yan L, Liu Q, Zhang C, Wei L, Hu Q, Preus L, Clay-Gilmour AI, Onel K, Stram DO, Pooler L, Sheng X, Haiman CA, Zhu X, Spellman SR, Pasquini M, McCarthy PL, Liu S, Hahn T, Sucheston-Campbell LE. Exome chip analyses identify genes affecting mortality after HLA-matched unrelated-donor blood and marrow transplantation. Blood. 2018 May 31; 131 (22):2490-2499 Epub 2018 Apr 02
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  33. Karaesmen E, Rizvi AA, Preus LM, McCarthy PL, Pasquini MC, Onel K, Zhu X, Spellman S, Haiman CA, Stram DO, Pooler L, Sheng X, Zhu Q, Yan L, Liu Q, Hu Q, Webb A, Brock G, Clay-Gilmour AI, Battaglia S, Tritchler D, Liu S, Hahn T, Sucheston-Campbell LE. Replication and validation of genetic polymorphisms associated with survival after allogeneic blood or marrow transplant. Blood. 2017 Sep 28; 130 (13):1585-1596 Epub 2017 Aug 15
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  34. Clay-Gilmour AI, Hahn T, Preus LM, Onel K, Skol A, Hungate E, Zhu Q, Haiman CA, Stram DO, Pooler L, Sheng X, Yan L, Liu Q, Hu Q, Liu S, Battaglia S, Zhu X, Block AW, Sait SNJ, Karaesmen E, Rizvi A, Weisdorf DJ, Ambrosone CB, Tritchler D, Ellinghaus E, Ellinghaus D, Stanulla M, Clavel J, Orsi L, Spellman S, Pasquini MC, McCarthy PL, Sucheston-Campbell LE. Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. Blood Adv. 2017 Sep 12; 1 (20):1717-1728 Epub 2017 Sept 08
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  35. Fan L, Zhu Q, Liu L, Zhu C, Huang H, Lu S, Liu P. CXCL13 is androgen-responsive and involved in androgen induced prostate cancer cell migration and invasion. Oncotarget. 2017 Aug 8; 8 (32):53244-53261 Epub 2017 June 07
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  36. He Y, Zhu Q, Chen M, Huang Q, Wang W, Li Q, Huang Y, Di W. The changing 50% inhibitory concentration (IC50) of cisplatin: a pilot study on the artifacts of the MTT assay and the precise measurement of density-dependent chemoresistance in ovarian cancer. Oncotarget. 2016 Oct 25; 7 (43):70803-70821
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  37. Jiang J, Zhu Q, Gendron TF, Saberi S, McAlonis-Downes M, Seelman A, Stauffer JE, Jafar-Nejad P, Drenner K, Schulte D, Chun S, Sun S, Ling SC, Myers B, Engelhardt J, Katz M, Baughn M, Platoshyn O, Marsala M, Watt A, Heyser CJ, Ard MC, De Muynck L, Daughrity LM, Swing DA, Tessarollo L, Jung CJ, Delpoux A, Utzschneider DT, Hedrick SM, de Jong PJ, Edbauer D, Van Damme P, Petrucelli L, Shaw CE, Bennett CF, Da Cruz S, Ravits J, Rigo F, Cleveland DW, Lagier-Tourenne C. Gain of Toxicity from ALS/FTD-Linked Repeat Expansions in C9ORF72 Is Alleviated by Antisense Oligonucleotides Targeting GGGGCC-Containing RNAs. Neuron. 2016 May 4; 90 (3):535-50 Epub 2016 Apr 21
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  38. Guo A, Racz R, Hur J, Lin Y, Xiang Z, Zhao L, Rinder J, Jiang G, Zhu Q, He Y. Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. J Biomed Semantics. 2016; 7:29 Epub 2016 May 21
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  39. Zhu Q, Liu H, Chute CG, Ferber M. EHR based Genetic Testing Knowledge Base (iGTKB) Development. BMC Med Inform Decis Mak. 2015 Nov 25; 15(Suppl 4):S3.
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  40. Xu J, Rasmussen LV, Shaw PL, Jiang G, Kiefer RC, Mo H, Pacheco JA, Speltz P, Zhu Q, Denny JC, Pathak J, Thompson WK, Montague E. Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. J Am Med Inform Assoc. 2015 Nov; 22 (6):1251-60 Epub 2015 July 29
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  41. Mo H, Thompson WK, Rasmussen LV, Pacheco JA, Jiang G, Kiefer R, Zhu Q, Xu J, Montague E, Carrell DS, Lingren T, Mentch FD, Ni Y, Wehbe FH, Peissig PL, Tromp G, Larson EB, Chute CG, Pathak J, Denny JC, Speltz P, Kho AN, Jarvik GP, Bejan CA, Williams MS, Borthwick K, Kitchner TE, Roden DM, Harris PA. Desiderata for computable representations of electronic health records-driven phenotype algorithms. J Am Med Inform Assoc. 2015 Nov; 22 (6):1220-30 Epub 2015 Sept 05
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  42. Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015 Jun; 55:206-17 Epub 2015 Apr 24
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  43. Zhang X, Zhu Q, Tian T, Zhao C, Zang J, Xue T, Sun B. Identification of RNAIII-binding proteins in Staphylococcus aureus using tethered RNAs and streptavidin aptamers based pull-down assay. BMC Microbiol. 2015 May 15; 15:102
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  44. Rasmussen LV, Kiefer RC, Mo H, Speltz P, Thompson WK, Jiang G, Pacheco JA, Xu J, Zhu Q, Denny JC, Montague E, Pathak J. A Modular Architecture for Electronic Health Record-Driven Phenotyping. AMIA Jt Summits Transl Sci Proc. 2015; 2015:147-51 Epub 2015 Mar 25
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  45. Zhang Y, Zhu Q, Liu H. Next generation informatics for big data in precision medicine era. BioData Min. 2015; 8:34 Epub 2015 Nov 03
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  46. Wang L, Liu H, Chute CG, Zhu Q. Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. BioData Min. 2015; 8:9 Epub 2015 Feb 25
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  47. Zhou Z, Zhu Q, Zhao H, Zhang L, Ma W, Gao F. Techniques to improve the accuracy of presampling MTF measurement in digital X-ray imaging based on constrained spline regression. IEEE Trans Biomed Eng. 2014 Apr; 61 (4):1339-49
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  48. Wang L, Liu H, Chute CG, Zhu Q. Cancer based pharmacogenomics network for drug repurposing. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2014; 8643:639-51.
  49. Ayvaz S, Zhu Q, Hochheiser H, Brochhausen M, Horn J, Dumontier M, Samwald M, Boyce RD. Drug-drug interaction data source survey and linking. AMIA Jt Summits Transl Sci Proc. 2014; 2014:16 Epub 2014 Apr 07
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  50. Freimuth RR, Wix K, Zhu Q, Siska M, Chute CG. Evaluation of RxNorm for Medication Clinical Decision Support. AMIA Annu Symp Proc. 2014; 2014:554-63 Epub 2014 Nov 14
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  51. Freimuth RR, Zhu Q, Pathak J, Chute CG. Simplifying complex clinical element models to encourage adoption. AMIA Jt Summits Transl Sci Proc. 2014; 2014:26-31 Epub 2014 Apr 07
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  52. Wang L, Liu H, Chute C, Zhu Q. Cancer Based Pharmacogenomics Network for Drug Repurposing. PAKDD proceeding. 2014.
  53. Zhu Q, Tao C, Shen F, Chute CG. Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging Web ontology language (OWL) and cheminformatics approaches. Pac Symp Biocomput. 2014; 172-82
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  54. Zhu Q, Freimuth RR, Pathak J, Durski MJ, Chute CG. Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. J Biomed Inform. 2013 Aug; 46 (4):690-6 Epub 2013 May 29
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  55. Zhu Q, Jiang G, Wang L, Chute CG. Standardized Drug and Pharmacological Class Network Construction. Proceedings of ICBO - International Conference on Biomedical Ontology. 2013 Jul 6-12.
  56. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG. A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J Am Med Inform Assoc. 2013 May 01; 20(3):554-62. Epub 2012 Dec 25.
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  57. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study. J Biomed Inform. 2013 Apr; 46 (2):286-93 Epub 2012 Nov 29
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  58. Zhu Q, Jiang G, Wang L, Chute CG. Standardized drug and pharmacological class network construction. CEUR Workshop Proceedings. 2013; 1061.
  59. Zhu Q, Freimuth RR, Pathak J, Chute CG. Using clinical element models for pharmacogenomic study data standardization. AMIA Jt Summits Transl Sci Proc. 2013; 2013:292-6 Epub 2013 Mar 18
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  60. Jiang G, Wang C, Zhu Q, Chute CG. A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome. AMIA Jt Summits Transl Sci Proc. 2013; 2013:88-92 Epub 2013 Mar 18
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  61. Zhu Q, Freimuth RR, Pathak J, Chute CG. PharmGKB Drug Data Normalization with NDF-RT. AMIA Jt Summits Transl Sci Proc. 2013; 2013:180 Epub 2013 Mar 18
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  62. Hassanzadeh O, Zhu Q, Freimuth R, Boyce R. Extending the "web of drug identity" with knowledge extracted from United States product labels. AMIA Jt Summits Transl Sci Proc. 2013; 2013:64-8 Epub 2013 Mar 18
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  63. Zhu Q, Jiang G, Wang L, Chute CG. Standardized drug and pharmacological class network construction. Stud Health Technol Inform. 2013; 192:1125
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  64. Zhu Q, Jiang G, Chute CG. Profiling structured product labeling with NDF-RT and RxNorm. J Biomed Semantics. 2012 Dec 20; 3 (1):16
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  65. Zhu Q, Tao C, Ding Y, Chute CG. Time-related patient data retrieval for the case studies from the pharmacogenomics research network. J Med Syst. 2012 Nov; 36 Suppl 1:S37-42 Epub 2012 Oct 18
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  66. Zhu Q, Jiang G, Chute CG. Profiling Structured Product Labeling Using NDF-RT and RxNorm Proceedings of ICBO - International Conference on Biomedical Ontology. Graz Austria July 21-25,. July 21-25, 2012 (Accepted).
  67. Zhu Q, Zou L, Jagavelu K, Simonetto DA, Huebert RC, Jiang ZD, DuPont HL, Shah VH. Intestinal decontamination inhibits TLR4 dependent fibronectin-mediated cross-talk between stellate cells and endothelial cells in liver fibrosis in mice. J Hepatol. 2012 Apr; 56 (4):893-9 Epub 2011 Dec 13
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  68. Pathak J, Weiss LC, Durski MJ, Zhu Q, Freimuth RR, Chute CG. Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results. Pac Symp Biocomput. 2012; 400-9
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  69. Zhu Q, Sun Y, Challa S, Ding Y, Lajiness MS, Wild DJ. Semantic inference using chemogenomics data for drug discovery. BMC Bioinformatics. 2011; 12:256. Epub 2011 Jun 23.
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  70. Zhu Q, Challa S, Purohit P, Sun Y, Lajiness MS, Wild DJ, Ding Y. Using Web Technologies for Integrative Drug Discovery. Web Intelligence and Intelligent Agent Technology (WI-IAT), 2010 IEEE/WIC/ACM International Conference on.. Sept 2010; 1: 188-91.
  71. Chen B, Ding Y, Wang H, Wild DJ, Dong X, Sun Y, Zhu Q, Sankaranarayanan M. Chem2Bio2RDF: A Linked Open Data Portal for Systems Biology. Web Intelligence and Intelligent Agent Technology (WI-IAT), 2010 IEEE/WIC/ACM International Conference on. Sept 2010; 1:232-9.
  72. Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics. 2010; 11:255. Epub 2010 May 17.
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  73. Zhu Q, Lajiness MS, Ding Y, Wild DJ. WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications. J Cheminform. 2010; 2:6. Epub 2010 Aug 20.
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  74. Zhu Q, Yao J, Yuan S, Li F, Chen H, Cai W, Liao Q. Superstructure searching algorithm for generic reaction retrieval. J Chem Inf Model. 2005 Sep-Oct; 45(5):1214-22.
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  75. Zhu Q, Yao J, Li F, Chen H, Yuan S. A Novel Approach to Acquire Reaction Knowledge by Classification of Reaction Data. Acta Chimica Sinica. 2004; 62:112.
  76. Zhu Q, Yao J, Li F, Chen H, Yuan S. Comparison of the R-Group Similarity. Acta Chimica Sinica. 2004; 62:1585.