Joe Qi, PhD

Title(s)Professor, Laboratory Medicine
SchoolSchool of Medicine
Address185 Berry Street Bldg B, #2426
San Francisco CA 94158
Phone415-514-6831
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    University of California, San FranciscoPostdoctoral StudiesGraduate Division

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details 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. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurol Genet. 2024 Apr; 10(2):e200142. Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V. PMID: 38586598; PMCID: PMC10997208.
      View in: PubMed   Mentions:
    2. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. bioRxiv. 2024 Jan 25. Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. PMID: 38328093; PMCID: PMC10849466.
      View in: PubMed   Mentions:
    3. Complex Genomic Rearrangements Involving ETV6::ABL1 Gene Fusion in an Individual with Myeloid Neoplasm. Genes (Basel). 2023 09 23; 14(10). Qi Z, Smith C, Shah NP, Yu J. PMID: 37895201; PMCID: PMC10606058.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    4. Editorial: Unravelling the basis of non-invasive prenatal screening results. Front Genet. 2023; 14:1247764. De Falco L, Pelo E, Qi Z, Novelli A. PMID: 37529782; PMCID: PMC10390063.
      View in: PubMed   Mentions:
    5. Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening. Front Genet. 2023; 14:971087. Qi Z, Yu J. PMID: 36726805; PMCID: PMC9886268.
      View in: PubMed   Mentions:
    6. Genomic Features of Interstitial Deletions of Chromosome 9q in Acute Myeloid Leukemia. Cytogenet Genome Res. 2022; 162(3):119-123. Qi Z, Wen KW, Ki A, Prakash S, Kogan S, Yu J. PMID: 35675801; PMCID: PMC9677869.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. A genetically distinct pediatric subtype of primary CNS large B-cell lymphoma is associated with favorable clinical outcome. Blood Adv. 2022 05 24; 6(10):3189-3193. Güney E, Lucas CG, Qi Z, Yu J, Zhang R, Ohgami RS, Rubenstein JL, Boué DR, Schafernak K, Wertheim GB, Dahiya S, Giulino-Roth L, Attarbaschi A, Barth MJ, Kothari S, Abla O, Cohen AL, Mendez JS, Bollen A, Perry A, Tihan T, Pekmezci M, Solomon DA, Wen KW. PMID: 35157770; PMCID: PMC9131901.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    8. Distinct pathologic feature of myeloid neoplasm with t(v;11p15); NUP98 rearrangement. Hum Pathol. 2022 05; 123:11-19. Lauw MIS, Qi Z, Eversmeyer L, Prakash S, Wen KW, Yu J, Monaghan SA, Aggarwal N, Wang L. PMID: 35167894.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    9. Publisher Correction: Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med. 2021 Oct 12; 6(1):88. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. PMID: 34642307; PMCID: PMC8511154.
      View in: PubMed   Mentions:
    10. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med. 2021 Sep 23; 6(1):77. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. PMID: 34556655; PMCID: PMC8460793.
      View in: PubMed   Mentions: 15  
    11. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med. 2021 06 01; 13(1):98. Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, Prakash S, Simko J, Chiu CY. PMID: 34074327; PMCID: PMC8167833.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    12. [Experience and lessons on guiding and governing clinical applications of chromosome microarray analysis in the United States]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2021 May 10; 38(5):419-424. Xie X, Yu J, Qi Z, Bao L, Shen Y, Chen T, Li P. PMID: 33974247.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    13. Genomic analysis in myeloid sarcoma and comparison with paired acute myeloid leukemia. Hum Pathol. 2021 02; 108:76-83. Greenland NY, Van Ziffle JA, Liu YC, Qi Z, Prakash S, Wang L. PMID: 33232718.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    14. Gross morphologic appearance of chorionic villi and the risk of chromosomal abnormalities. Reprod Sci. 2021 02; 28(2):570-574. Sobhani NC, Cassidy AG, Qi Z, Yu J, Chetty S, Norton ME. PMID: 32989629.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    15. Acute myeloid leukemia with inv(16)(p13.1q22) and deletion of the 5'MYH11/3'CBFB gene fusion: a report of two cases and literature review. Mol Cytogenet. 2020; 13:4. Lv L, Yu J, Qi Z. PMID: 32015759; PMCID: PMC6990480.
      View in: PubMed   Mentions: 3  
    16. [Introduction of the American Board of Medical Genetics and Genomics (ABMGG) Certification Exams and maintenance of certification]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2019 Jan 10; 36(1):13-22. Qi Z, Xiang B, Tsai AC, Yu J. PMID: 30722087.
      View in: PubMed   Mentions:    Fields:    
    17. Investigating human placentation and pregnancy using first trimester chorionic villi. Placenta. 2018 05; 65:65-75. Hannibal RL, Cardoso-Moreira M, Chetty SP, Lau J, Qi Z, Gonzalez-Maldonado E, Cherry AM, Yu J, Norton ME, Baker JC. PMID: 29908643.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    18. Acute myeloid leukemia with t(14;21) involving RUNX1 and SYNE2: A novel favorable-risk translocation? Cancer Genet. 2017 Oct; 216-217:74-78. Foley N, Van Ziffle J, Yu J, Qi Z, Grenert JP, Yeh I, Bastian B, Kogan S, Mannis GN. PMID: 29025598.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    19. False negative fetal cell free DNA screening for microdeletion syndromes in the presence of an unbalanced translocation involving monosomy 4p. Prenat Diagn. 2017 04; 37(4):420-422. Qi Z, Madaan S, Chetty S, Yu J, Wiita AP. PMID: 28207935.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    20. The human chorion contains definitive hematopoietic stem cells from the fifteenth week of gestation. Development. 2017 04 15; 144(8):1399-1411. Muench MO, Kapidzic M, Gormley M, Gutierrez AG, Ponder KL, Fomin ME, Beyer AI, Stolp H, Qi Z, Fisher SJ, Bárcena A. PMID: 28255007; PMCID: PMC5399660.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    21. False positive cell free DNA screening for microdeletions due to non-pathogenic copy number variants. Prenat Diagn. 2016 Jun; 36(6):584-6. Mather CA, Qi Z, Wiita AP. PMID: 27061292.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    22. YAP Induces Human Naive Pluripotency. Cell Rep. 2016 Mar 15; 14(10):2301-12. Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song JS, Ramalho-Santos M. PMID: 26947063; PMCID: PMC4807727.
      View in: PubMed   Mentions: 95     Fields:    Translation:HumansCells
    23. TALENs Facilitate Single-step Seamless SDF Correction of F508del CFTR in Airway Epithelial Submucosal Gland Cell-derived CF-iPSCs. Mol Ther Nucleic Acids. 2016 Jan 05; 5:e273. Suzuki S, Sargent RG, Illek B, Fischer H, Esmaeili-Shandiz A, Yezzi MJ, Lee A, Yang Y, Kim S, Renz P, Qi Z, Yu J, Muench MO, Beyer AI, Guimarães AO, Ye L, Chang J, Fine EJ, Cradick TJ, Bao G, Rahdar M, Porteus MH, Shuto T, Kai H, Kan YW, Gruenert DC. PMID: 26730810; PMCID: PMC5012545.
      View in: PubMed   Mentions: 25  
    24. Trisomy Xp and partial tetrasomy Xq resulting from gain of a rearranged X chromosome in a female fetus: pathogenic or not? Mol Cytogenet. 2015; 8:53. Yiu M, Qi Z, Ki A, Yu J. PMID: 26213575; PMCID: PMC4513972.
      View in: PubMed   Mentions:
    25. Haploinsufficiency and triploinsensitivity of the same 6p25.1p24.3 region in a family. BMC Med Genomics. 2015 Jul 15; 8:38. Qi Z, Jeng LJ, Slavotinek A, Yu J. PMID: 26174853; PMCID: PMC4502905.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    26. BCL6 expression correlates with the t(1;19) translocation in B-lymphoblastic leukemia. Am J Clin Pathol. 2015 Apr; 143(4):547-57. Deucher AM, Qi Z, Yu J, George TI, Etzell JE. PMID: 25780007.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    27. Self-enforcing feedback activation between BCL6 and pre-B cell receptor signaling defines a distinct subtype of acute lymphoblastic leukemia. Cancer Cell. 2015 Mar 09; 27(3):409-25. Geng H, Hurtz C, Lenz KB, Chen Z, Baumjohann D, Thompson S, Goloviznina NA, Chen WY, Huan J, LaTocha D, Ballabio E, Xiao G, Lee JW, Deucher A, Qi Z, Park E, Huang C, Nahar R, Kweon SM, Shojaee S, Chan LN, Yu J, Kornblau SM, Bijl JJ, Ye BH, Ansel KM, Paietta E, Melnick A, Hunger SP, Kurre P, Tyner JW, Loh ML, Roeder RG, Druker BJ, Burger JA, Milne TA, Chang BH, Müschen M. PMID: 25759025; PMCID: PMC4618684.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    28. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jul 01; 111(26):9591-6. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. PMID: 24927590; PMCID: PMC4084478.
      View in: PubMed   Mentions: 150     Fields:    Translation:HumansCells
    29. Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet. 2013; 9(9):e1003821. Huang V, Zheng J, Qi Z, Wang J, Place RF, Yu J, Li H, Li LC. PMID: 24086155; PMCID: PMC3784563.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    30. Blood cell-derived induced pluripotent stem cells free of reprogramming factors generated by Sendai viral vectors. Stem Cells Transl Med. 2013 Aug; 2(8):558-66. Ye L, Muench MO, Fusaki N, Beyer AI, Wang J, Qi Z, Yu J, Kan YW. PMID: 23847002; PMCID: PMC3726135.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    31. Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming. Hum Mol Genet. 2012 May 01; 21(9):2054-67. Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi Z, Yu J, Yeh RF, Hebrok M, Ramalho-Santos M. PMID: 22286172; PMCID: PMC3315209.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    32. Endothelial lipase mediates HDL levels in normal and hyperlipidemic rabbits. J Atheroscler Thromb. 2012; 19(3):213-26. Zhang J, Yu Y, Nakamura K, Koike T, Waqar AB, Zhang X, Liu E, Nishijima K, Kitajima S, Shiomi M, Qi Z, Yu J, Graham MJ, Crooke RM, Ishida T, Hirata K, Hurt-Camejo E, Chen YE, Fan J. PMID: 22240910; PMCID: PMC3493565.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    33. Upregulation of Cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res. 2012 Feb; 40(4):1695-707. Huang V, Place RF, Portnoy V, Wang J, Qi Z, Jia Z, Yu A, Shuman M, Yu J, Li LC. PMID: 22053081; PMCID: PMC3287204.
      View in: PubMed   Mentions: 164     Fields:    Translation:AnimalsCells
    34. Transgenic expression of entire hepatitis B virus in mice induces hepatocarcinogenesis independent of chronic liver injury. PLoS One. 2011; 6(10):e26240. Na B, Huang Z, Wang Q, Qi Z, Tian Y, Lu CC, Yu J, Hanes MA, Kakar S, Huang EJ, Ou JH, Liu L, Yen TS. PMID: 22022578; PMCID: PMC3192172.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    35. Presence of complex t(6;9;22;15) four-way chromosome rearrangement plus rare t(1;6) translocation with favorable response to imatinib therapy in chronic myelogenous leukemia. Leuk Lymphoma. 2011 Nov; 52(11):2182-4. Lu CM, Zhou L, Feng S, Kohn PH, Qi Z, Yu J. PMID: 21718138.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    36. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May; 13(5):541-9. Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M. PMID: 21499256; PMCID: PMC3987913.
      View in: PubMed   Mentions: 313     Fields:    Translation:HumansCells
    37. Generation of induced pluripotent stem cells using site-specific integration with phage integrase. Proc Natl Acad Sci U S A. 2010 Nov 09; 107(45):19467-72. Ye L, Chang JC, Lin C, Qi Z, Yu J, Kan YW. PMID: 20974949; PMCID: PMC2984165.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    38. Methylation-mediated downregulation of the B-cell translocation gene 3 (BTG3) in breast cancer cells. Gene Expr. 2008; 14(3):173-82. Yu J, Zhang Y, Qi Z, Kurtycz D, Vacano G, Patterson D. PMID: 18590053; PMCID: PMC6042006.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    39. Prevalence of the C677T substitution of the methylenetetrahydrofolate reductase (MTHFR) gene in Wisconsin. Genet Med. 2003 Nov-Dec; 5(6):458-9. Qi Z, Hoffman G, Kurtycz D, Yu J. PMID: 14614398.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
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