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Youping Deng, PhD

TitleCo-Director, Genomics and Bioinformatics Shared Resource
Faculty RankProfessor
InstitutionUniversity of Hawaii
DepartmentQuantitative Health Sciences
AddressJohn A. Burns School of Medicine
University of Hawaii at Manoa
651 Ilalo Street
Honolulu HI 96813
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Qin Y, Maggio A, Hawkins D, Beaudry L, Kim A, Pan D, Gong T, Fu Y, Yang H, Deng Y. Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform. Brief Bioinform. 2024 Jul 23; 25(Supplement_1). PMID: 39041913.
      Citations: 1     Fields:    Translation:HumansCells
    2. Kuehu DL, Fu Y, Nasu M, Yang H, Khadka VS, Deng Y. Use of Microalgae-Derived Astaxanthin to Improve Cytoprotective Capacity in the Ileum of Heat-Induced Oxidative Stressed Broilers. Animals (Basel). 2024 Jun 29; 14(13). PMID: 38998041.
      Citations:    
    3. Feng Z, Fu Y, Deng Y. Enhancing visibility and inclusivity of queer scientists to advance equality in academia. Patterns (N Y). 2024 Jun 14; 5(6):101008. PMID: 39005484.
      Citations:    
    4. Chen Y, Gao Z, Mohd-Ibrahim I, Yang H, Wu L, Fu Y, Deng Y. Pan-cancer analyses of bromodomain containing 9 as a novel therapeutic target reveals its diagnostic, prognostic potential and biological mechanism in human tumours. Clin Transl Med. 2024 02; 14(2):e1543. PMID: 38303608.
      Citations: 1     Fields:    Translation:HumansCells
    5. Nasu M, Khadka VS, Jijiwa M, Kobayashi K, Deng Y. Exploring Optimal Biomarker Sources: A Comparative Analysis of Exosomes and Whole Plasma in Fasting and Non-Fasting Conditions for Liquid Biopsy Applications. Int J Mol Sci. 2023 Dec 27; 25(1). PMID: 38203541.
      Citations: 2     Fields:    Translation:HumansCells
    6. Liu S, Zhong H, Zhu J, Wu Y, Deng Y, Wu L. Regulome-wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk. Int J Cancer. 2024 Feb 15; 154(4):670-678. PMID: 37850323.
      Citations: 1     Fields:    Translation:HumansCells
    7. Fu Y, Wu K, Wang Z, Yang H, Chen Y, Wu L, Yanagihara R, Hedges JR, Wang H, Deng Y. Effectiveness of various COVID-19 vaccine regimens among 10.4 million patients from the National COVID Cohort Collaborative during Pre-Delta to Omicron periods - United States, 11 December 2020 to 30 June 2022. Vaccine. 2023 10 06; 41(42):6339-6349. PMID: 37741761.
      Citations:    Fields:    Translation:HumansCells
    8. Maison DP, Deng Y, Gerschenson M. SARS-CoV-2 and the host-immune response. Front Immunol. 2023; 14:1195871. PMID: 37404823.
      Citations: 8     Fields:    Translation:HumansCells
    9. Burkhart JG, Wu G, Song X, Raimondi F, McWeeney S, Wong MH, Deng Y. Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. Patterns (N Y). 2023 Jul 14; 4(7):100758. PMID: 37521042.
      Citations:    
    10. Khadka VS, Nasu M, Deng Y, Jijiwa M. Circulating microRNA Biomarker for Detecting Breast Cancer in High-Risk Benign Breast Tumors. Int J Mol Sci. 2023 Apr 20; 24(8). PMID: 37108716.
      Citations: 5     Fields:    Translation:Humans
    11. Wang JY, Liu K, Wang YB, Deng YB, Sun J. Effects of norepinephrine on plaque hypoxia in atherosclerotic rabbits. Front Cardiovasc Med. 2023; 10:1121413. PMID: 36873394.
      Citations:    
    12. Yang WS, Caliva MJ, Khadka VS, Tiirikainen M, Matter ML, Deng Y, Ramos JW. RSK1 and RSK2 serine/threonine kinases regulate different transcription programs in cancer. Front Cell Dev Biol. 2022; 10:1015665. PMID: 36684450.
      Citations:    
    13. Chen Y, Qin Y, Fu Y, Gao Z, Deng Y. Integrated Analysis of Bulk RNA-Seq and Single-Cell RNA-Seq Unravels the Influences of SARS-CoV-2 Infections to Cancer Patients. Int J Mol Sci. 2022 Dec 10; 23(24). PMID: 36555339.
      Citations: 2     Fields:    Translation:HumansCells
    14. Wang JY, Sun J, Deng YB, Wang YB, Liu K. Effects of Norepinephrine on Renal Cortical and Medullary Blood Flow in Atherosclerotic Rabbits. Curr Med Sci. 2022 Dec; 42(6):1172-1177. PMID: 36083378.
      Citations:    Fields:    Translation:Animals
    15. Mahmanzar M, Houseini ST, Rahimian K, Namini AM, Gholamzad A, Tokhanbigli S, Sisakht MM, Farhadi A, Kuehu DL, Deng Y. The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends. bioRxiv. 2022 Jul 19. PMID: 35898341.
      Citations:    
    16. Adhikari B, Lee CN, Khadka VS, Deng Y, Fukumoto G, Thorne M, Caires K, Odani J, Mishra B. RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy. BMC Genomics. 2022 Jul 07; 23(1):494. PMID: 35799127.
      Citations: 6     Fields:    Translation:Animals
    17. Gao Z, Jijiwa M, Nasu M, Borgard H, Gong T, Xu J, Chen S, Fu Y, Chen Y, Hu X, Huang G, Deng Y. Comprehensive landscape of tRNA-derived fragments in lung cancer. Mol Ther Oncolytics. 2022 Sep 15; 26:207-225. PMID: 35892120.
      Citations:    
    18. Fu Y, Hu L, Ren HW, Zuo Y, Chen S, Zhang QS, Shao C, Ma Y, Wu L, Hao JJ, Wang CZ, Wang Z, Yanagihara R, Deng Y. Corrigendum to "Prognostic Factors for COVID-19 Hospitalized Patients with Preexisting Type 2 Diabetes". Int J Endocrinol. 2022; 2022:9838923. PMID: 35833192.
      Citations:    
    19. Gao LY, Ran HT, Deng YB, Luo BM, Zhou P, Chen W, Zhang YH, Li JC, Wang HY, Jiang YX. Gail model and fifth edition of ultrasound BI-RADS help predict axillary lymph node metastasis in breast cancer-A multicenter prospective study. Asia Pac J Clin Oncol. 2023 Apr; 19(2):e71-e79. PMID: 35593663.
      Citations: 1     Fields:    Translation:Humans
    20. Chen S, Gao Z, Hu L, Zuo Y, Fu Y, Wei M, Zitello E, Huang G, Deng Y. Association of Septic Shock with Mortality in Hospitalized COVID-19 Patients in Wuhan, China. Adv Virol. 2022; 2022:3178283. PMID: 35502304.
      Citations:    
    21. Urena F, Ma C, Hoffmann FW, Nunes LGA, Urschitz J, Moisyadi S, Khadka VS, Deng Y, Hoffmann PR. T-cell activation decreases miRNA-15a/16 levels to promote MEK1-ERK1/2-Elk1 signaling and proliferative capacity. J Biol Chem. 2022 03; 298(3):101634. PMID: 35085550.
      Citations: 4     Fields:    Translation:AnimalsCells
    22. Gong T, Borgard H, Zhang Z, Chen S, Gao Z, Deng Y. Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. Small Methods. 2022 03; 6(3):e2101251. PMID: 35064762.
      Citations: 10     Fields:    Translation:HumansCells
    23. Fu Y, Hu L, Ren HW, Zuo Y, Chen S, Zhang QS, Shao C, Ma Y, Wu L, Hao JJ, Wang CZ, Wang Z, Yanagihara R, Deng Y. Prognostic Factors for COVID-19 Hospitalized Patients with Preexisting Type 2 Diabetes. Int J Endocrinol. 2022; 2022:9322332. PMID: 35047039.
      Citations:    
    24. Zhan S, Siu J, Wang Z, Yu H, Bezabeh T, Deng Y, Du W, Fei P. Focal Point of Fanconi Anemia Signaling. Int J Mol Sci. 2021 Nov 30; 22(23). PMID: 34884777.
      Citations: 9     Fields:    Translation:HumansCells
    25. Bartlett B, Gao Z, Schukking M, Menor M, Khadka VS, Fabbri M, Fei P, Deng Y. The miRNA Profile of Inflammatory Colorectal Tumors Identify TGF-? as a Companion Target for Checkpoint Blockade Immunotherapy. Front Cell Dev Biol. 2021; 9:754507. PMID: 34722540.
      Citations:    
    26. Zitello E, Hernandez B, Deng Y. Viral Etiology of Solid Tumors and Immunotherapy. Gastroenterology. 2022 02; 162(2):659-660. PMID: 34582894.
      Citations:    Fields:    Translation:Humans
    27. Rodriguez RM, Menor M, Hernandez BY, Deng Y, Khadka VS. Bacterial Diversity Correlates with Overall Survival in Cancers of the Head and Neck, Liver, and Stomach. Molecules. 2021 Sep 17; 26(18). PMID: 34577130.
      Citations: 5     Fields:    Translation:HumansCells
    28. Sah N, Kuehu DL, Khadka VS, Deng Y, Jha R, Wasti S, Mishra B. RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen. BMC Genomics. 2021 May 01; 22(1):318. PMID: 33932994.
      Citations: 5     Fields:    Translation:HumansAnimals
    29. Chen Y, Zitello E, Guo R, Deng Y. The function of LncRNAs and their role in the prediction, diagnosis, and prognosis of lung cancer. Clin Transl Med. 2021 04; 11(4):e367. PMID: 33931980.
      Citations: 46     Fields:    Translation:Humans
    30. Marikawa Y, Menor M, Deng Y, Alarcon VB. Regulation of endoplasmic reticulum stress and trophectoderm lineage specification by the mevalonate pathway in the mouse preimplantation embryo. Mol Hum Reprod. 2021 03 24; 27(4). PMID: 33677573.
      Citations: 4     Fields:    Translation:HumansAnimals
    31. Ma C, Hoffmann FW, Marciel MP, Page KE, Williams-Aduja MA, Akana ENL, Gojanovich GS, Gerschenson M, Urschitz J, Moisyadi S, Khadka VS, Rozovsky S, Deng Y, Horgen FD, Hoffmann PR. Upregulated ethanolamine phospholipid synthesis via selenoprotein I is required for effective metabolic reprogramming during T cell activation. Mol Metab. 2021 05; 47:101170. PMID: 33484950.
      Citations: 14     Fields:    Translation:AnimalsCells
    32. Niu Z, Tian JW, Ran HT, Ren WD, Chang C, Yuan JJ, Kang CS, Deng YB, Wang H, Luo BM, Guo SL, Zhou Q, Xue ES, Zhan WW, Zhou Q, Li J, Zhou P, Zhang CQ, Chen M, Gu Y, Xu JF, Chen W, Zhang YH, Wang HQ, Li JC, Wang HY, Jiang YX. Risk-predicted dual nomograms consisting of clinical and ultrasound factors for downgrading BI-RADS category 4a breast lesions - A multiple centre study. J Cancer. 2021; 12(1):292-304. PMID: 33391426.
      Citations:    
    33. Gao LY, Gu Y, Tian JW, Ran HT, Ren WD, Chang C, Yuan JJ, Kang CS, Deng YB, Luo BM, Zhou Q, Zhan WW, Zhou Q, Li J, Zhou P, Zhang CQ, Chen M, Gu Y, Guo JF, Chen W, Zhang YH, Li JC, Wang HY, Jiang YX. Gail Model Improves the Diagnostic Performance of the Fifth Edition of Ultrasound BI-RADS for Predicting Breast Cancer: A Multicenter Prospective Study. Acad Radiol. 2022 01; 29 Suppl 1:S1-S7. PMID: 33384211.
      Citations: 7     Fields:    Translation:Humans
    34. Rodriguez RM, Khadka VS, Menor M, Hernandez BY, Deng Y. Tissue-associated microbial detection in cancer using human sequencing data. BMC Bioinformatics. 2020 Dec 03; 21(Suppl 9):523. PMID: 33272199.
      Citations: 7     Fields:    Translation:Humans
    35. Fu Y, Ling Z, Arabnia H, Deng Y. Current trend and development in bioinformatics research. BMC Bioinformatics. 2020 Dec 03; 21(Suppl 9):538. PMID: 33272214.
      Citations: 16     Fields:    Translation:Humans
    36. Gu Y, Tian JW, Ran HT, Ren WD, Chang C, Yuan JJ, Kang CS, Deng YB, Wang H, Luo BM, Guo SL, Zhou Q, Xue ES, Zhan WW, Zhou Q, Li J, Zhou P, Zhang CQ, Chen M, Gu Y, Xu JF, Chen W, Zhang YH, Wang HQ, Li JC, Wang HY, Jiang YX. The Utility of the Fifth Edition of the BI-RADS Ultrasound Lexicon in Category 4 Breast Lesions: A Prospective Multicenter Study in China. Acad Radiol. 2022 01; 29 Suppl 1:S26-S34. PMID: 32768352.
      Citations: 5     Fields:    Translation:Humans
    37. Williams AL, Khadka VS, Anagaran MCT, Lee K, Avelar A, Deng Y, Shohet RV. miR-125 family regulates XIRP1 and FIH in response to myocardial infarction. Physiol Genomics. 2020 08 01; 52(8):358-368. PMID: 32716698.
      Citations: 2     Fields:    Translation:AnimalsCells
    38. Zhao T, Khadka VS, Deng Y. Identification of lncRNA biomarkers for lung cancer through integrative cross-platform data analyses. Aging (Albany NY). 2020 07 16; 12(14):14506-14527. PMID: 32675385.
      Citations: 13     Fields:    Translation:Humans
    39. Gao LY, Gu Y, Xu W, Tian JW, Yin LX, Ran HT, Ren WD, Mu YM, Zhang JY, Chang C, Yuan JJ, Kang CS, Deng YB, Wang H, Xie XY, Luo BM, Guo SL, Zhou Q, Xue ES, Zhan WW, Jiao T, Zhou Q, Li J, Zhou P, Huang PT, Xue HY, Zhang CQ, Chen M, Jing XX, Gu Y, Guo JF, Ding HY, Xu JF, Chen W, Liu L, Zhang YH, Wang HQ, Mu ZP, Li JC, Wang HY, Jiang YX. Can Combined Screening of Ultrasound and Elastography Improve Breast Cancer Identification Compared with MRI in Women with Dense Breasts-a Multicenter Prospective Study. J Cancer. 2020; 11(13):3903-3909. PMID: 32328194.
      Citations:    
    40. Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J. 2020; 18:631-641. PMID: 32257046.
      Citations:    
    41. Zhou LQ, Wu XL, Huang SY, Wu GG, Ye HR, Wei Q, Bao LY, Deng YB, Li XR, Cui XW, Dietrich CF. Lymph Node Metastasis Prediction from Primary Breast Cancer US Images Using Deep Learning. Radiology. 2020 01; 294(1):19-28. PMID: 31746687.
      Citations: 107     Fields:    Translation:Humans
    42. Marikawa Y, Chen HR, Menor M, Deng Y, Alarcon VB. Exposure-based assessment of chemical teratogenicity using morphogenetic aggregates of human embryonic stem cells. Reprod Toxicol. 2020 01; 91:74-91. PMID: 31711903.
      Citations: 16     Fields:    Translation:HumansCells
    43. Seale LA, Khadka VS, Menor M, Xie G, Watanabe LM, Sasuclark A, Guirguis K, Ha HY, Hashimoto AC, Peplowska K, Tiirikainen M, Jia W, Berry MJ, Deng Y. Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice. Nutrients. 2019 Oct 26; 11(11). PMID: 31717805.
      Citations: 4     Fields:    Translation:AnimalsCells
    44. Deng Y, Zhu Y, Wang H, Khadka VS, Hu L, Ai J, Dou Y, Li Y, Dai S, Mason CE, Wang Y, Jia W, Zhang J, Huang G, Jiang B. Ratio-Based Method To Identify True Biomarkers by Normalizing Circulating ncRNA Sequencing and Quantitative PCR Data. Anal Chem. 2019 05 21; 91(10):6746-6753. PMID: 31002238.
      Citations: 16     Fields:    Translation:HumansAnimals
    45. Menor M, Zhu Y, Wang Y, Zhang J, Jiang B, Deng Y. Development of somatic mutation signatures for risk stratification and prognosis in lung and colorectal adenocarcinomas. BMC Med Genomics. 2019 01 31; 12(Suppl 1):24. PMID: 30704450.
      Citations: 9     Fields:    Translation:Humans
    46. Siriwardhana C, Khadka VS, Chen JJ, Deng Y. Development of a miRNA-seq based prognostic signature in lung adenocarcinoma. BMC Cancer. 2019 Jan 08; 19(1):34. PMID: 30621620.
      Citations: 20     Fields:    Translation:HumansCells
    47. Fang R, Zhu Y, Khadka VS, Zhang F, Jiang B, Deng Y. The Evaluation of Serum Biomarkers for Non-small Cell Lung Cancer (NSCLC) Diagnosis. Front Physiol. 2018; 9:1710. PMID: 30555348.
      Citations:    
    48. Sah N, Kuehu DL, Khadka VS, Deng Y, Peplowska K, Jha R, Mishra B. RNA sequencing-based analysis of the laying hen uterus revealed the novel genes and biological pathways involved in the eggshell biomineralization. Sci Rep. 2018 11 15; 8(1):16853. PMID: 30443032.
      Citations: 25     Fields:    Translation:AnimalsCells
    49. Mao YH, Deng YB, Liu YN, Wei X, Bi XJ, Tang QY, Wang YB, Wang XY. Contrast Echocardiographic Perfusion Imaging in Clinical Decision-Making for Cardiac Masses in Patients With a History of Extracardiac Malignant Tumor. JACC Cardiovasc Imaging. 2019 04; 12(4):754-756. PMID: 30448137.
      Citations: 3     Fields:    Translation:Humans
    50. Marciel MP, Khadka VS, Deng Y, Kilicaslan P, Pham A, Bertino P, Lee K, Chen S, Glibetic N, Hoffmann FW, Matter ML, Hoffmann PR. Correction: Selenoprotein K deficiency inhibits melanoma by reducing calcium flux required for tumor growth and metastasis. Oncotarget. 2018 07 20; 9(56):30937. PMID: 30112120.
      Citations: 1     Fields:    
    51. Marciel MP, Khadka VS, Deng Y, Kilicaslan P, Pham A, Bertino P, Lee K, Chen S, Glibetic N, Hoffmann FW, Matter ML, Hoffmann PR. Selenoprotein K deficiency inhibits melanoma by reducing calcium flux required for tumor growth and metastasis. Oncotarget. 2018 03 02; 9(17):13407-13422. PMID: 29568366.
      Citations: 16     Fields:    
    52. Deng Y, Wang H, Hamamoto R, Duan S, Pirooznia M, Bai Y. Functional Genomics, Genetics, and Bioinformatics 2016. Biomed Res Int. 2016; 2016:2625831. PMID: 27995138.
      Citations: 1     Fields:    Translation:Humans
    53. Tang QY, Guo LD, Wang WX, Zhou W, Liu YN, Liu HY, Li L, Deng YB. Usefulness of contrast perfusion echocardiography for differential diagnosis of cardiac masses. Ultrasound Med Biol. 2015 Sep; 41(9):2382-90. PMID: 26087885.
      Citations: 8     Fields:    Translation:Humans
    54. Yao GH, Deng Y, Liu Y, Xu MJ, Zhang C, Deng YB, Ren WD, Li ZA, Tang H, Zhang QB, Mu YM, Fang LG, Zhang M, Yin LX, Zhang Y. Echocardiographic measurements in normal chinese adults focusing on cardiac chambers and great arteries: a prospective, nationwide, and multicenter study. J Am Soc Echocardiogr. 2015 May; 28(5):570-9. PMID: 25753502.
      Citations: 31     Fields:    Translation:Humans
    55. Sun J, Deng YB, Liu K, Wang YB. Effects of noradrenaline and adenosine triphosphate on the degree on contrast enhancement in a rabbit model of atherosclerosis during contrast-enhanced ultrasonography. Ultrasound Med Biol. 2014 Nov; 40(11):2655-61. PMID: 25218451.
      Citations: 3     Fields:    Translation:Animals
    56. Zhu Y, Deng YB, Liu YN, Bi XJ, Sun J, Tang QY, Deng Q. Use of carotid plaque neovascularization at contrast-enhanced US to predict coronary events in patients with coronary artery disease. Radiology. 2013 Jul; 268(1):54-60. PMID: 23440321.
      Citations: 10     Fields:    Translation:Humans
    57. Wang C, Deng YB, Zhu Y, Liu YN, Bi XJ. Evaluation of subtle myocardial noncompaction by contrast echocardiography in patients with hypertrophic cardiomyopathy and its relationship with regional ventricular systolic dysfunction. J Ultrasound Med. 2012 Oct; 31(10):1551-7. PMID: 23011618.
      Citations: 7     Fields:    Translation:Humans
    58. Xiong L, Deng YB, Zhu Y, Liu YN, Bi XJ. Correlation of carotid plaque neovascularization detected by using contrast-enhanced US with clinical symptoms. Radiology. 2009 May; 251(2):583-9. PMID: 19304920.
      Citations: 46     Fields:    Translation:Humans
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