Jeffrey Cheng, MD, PhD

Title(s)Associate Professor, Dermatology
SchoolSchool of Medicine
Address1701 Divisadero, #283
San Francisco CA 94115
Phone415-353-7891
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    Collapse Biography 
    Collapse Education and Training
    University of Texas SouthwesternM.D.2006School of Medicine

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Precision medicine approaches to chronic inflammatory skin disease of older veterans
    Veterans Health Administration I01CX002608Jul 1, 2023 - Jun 30, 2027
    Single Cell Transcriptomic Classification of Inflammatory Skin Disease
    LEO Foundation Dec 1, 2022 - Nov 30, 2025
    Role: Principal Investigator
    Spatial Analysis of Alopecia Areata Inflammation
    Pfizer Global Medical Grants Aug 1, 2021 - Jul 31, 2023
    Role: Principal Investigator
    Role of DNA Methylation and Hydroxymethylation in Epidermal Homeostasis
    NIH K08AR067243Aug 1, 2015 - Jul 31, 2021
    Role: Principal Investigator

    Collapse ORNG Applications 
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    Collapse Publications
    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. Short cell cycle duration is a phenotype of human epidermal stem cells. Stem Cell Res Ther. 2024 Mar 13; 15(1):76. Xiao T, Eze UC, Charruyer-Reinwald A, Weisenberger T, Khalifa A, Abegaze B, Schwab GK, Elsabagh RH, Parenteau TR, Kochanowski K, Piper M, Xia Y, Cheng JB, Cho RJ, Ghadially R. PMID: 38475896; PMCID: PMC10935907.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response. Sci Immunol. 2024 Jan 26; 9(91):eadi2848. Wu D, Hailer AA, Wang S, Yuan M, Chan J, El Kurdi A, Han D, Ali H, D'Angio B, Mayer A, Rahim M, Kondo A, Klufas D, Kim E, Shain AH, Choi J, Bhutani T, Simpson G, Grekin RC, Ricardo-Gonzalez R, Purdom E, North JP, Cheng JB, Cho RJ. PMID: 38277466.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biol. 2023 Nov 30; 24(1):273. Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. PMID: 38037084; PMCID: PMC10688493.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. GLUT3 promotes macrophage signaling and function via RAS-mediated endocytosis in atopic dermatitis and wound healing. J Clin Invest. 2023 11 01; 133(21). Yu DM, Zhao J, Lee EE, Kim D, Mahapatra R, Rose EK, Zhou Z, Hosler C, El Kurdi A, Choe JY, Abel ED, Hoxhaj G, Westover KD, Cho RJ, Cheng JB, Wang RC. PMID: 37721853; PMCID: PMC10617774.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    5. Optimizing Single T-Cell Transcriptomic Discrimination of Atopic Dermatitis Versus Psoriasis Vulgaris. J Invest Dermatol. 2023 Oct 23. Taylor MA, El Kurdi A, Hailer A, Wang S, Yuan M, Mukhopadhyay S, Bhutani T, North JP, Cho RJ, Cheng JB. PMID: 37879399.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Isolation of human cutaneous immune cells for single-cell RNA sequencing. STAR Protoc. 2023 Apr 28; 4(2):102239. Hailer AA, Wu D, El Kurdi A, Yuan M, Cho RJ, Cheng JB. PMID: 37120815; PMCID: PMC10173011.
      View in: PubMed   Mentions:    Fields:    
    7. Transcriptomics aids differentiation of IL-23 overactivity in a patient with atypical skin and joint disease. Lancet. 2023 04 22; 401(10385):1381. Hakimi M, North JP, Taylor MA, Hailer A, Liu Y, Kim E, Morehead K, Shinkai K, Bhutani T, Cheng JB, Cho RJ. PMID: 37087172.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    8. A Novel Potential Role for Monocytes Revealed by Single Cell Analysis of Immunotherapy Induced Immune Related Adverse Events. Cancers (Basel). 2022 Nov 02; 14(21). Garrison Z, Chang M, Hornick N, Yu WY, Cheng JB, Kulkarni RP. PMID: 36358824; PMCID: PMC9657437.
      View in: PubMed   Mentions: 1  
    9. Circulating biomarkers of response to immunotherapy and immune-related adverse events. Expert Rev Mol Diagn. 2022 Sep; 22(9):855-865. Garrison Z, Hornick N, Cheng J, Kulkarni RP. PMID: 36193802.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    10. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. Cell Rep Med. 2022 08 16; 3(8):100715. Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SBV, Cheng JB, Cho RJ. PMID: 35977472; PMCID: PMC9418858.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. Defining Patient-Level Molecular Heterogeneity in Psoriasis Vulgaris Based on Single-Cell Transcriptomics. Front Immunol. 2022; 13:842651. Liu Y, Wang H, Cook C, Taylor MA, North JP, Hailer A, Shou Y, Sadik A, Kim E, Purdom E, Cheng JB, Cho RJ. PMID: 35958578; PMCID: PMC9360479.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    12. Spectral clustering of single-cell multi-omics data on multilayer graphs. Bioinformatics. 2022 07 11; 38(14):3600-3608. Zhang S, Leistico JR, Cho RJ, Cheng JB, Song JS. PMID: 35652725; PMCID: PMC9272806.
      View in: PubMed   Mentions: 2     Fields:    
    13. Classification of human chronic inflammatory skin disease based on single-cell immune profiling. Sci Immunol. 2022 04 15; 7(70):eabl9165. Liu Y, Wang H, Taylor M, Cook C, Martínez-Berdeja A, North JP, Harirchian P, Hailer AA, Zhao Z, Ghadially R, Ricardo-Gonzalez RR, Grekin RC, Mauro TM, Kim E, Choi J, Purdom E, Cho RJ, Cheng JB. PMID: 35427179; PMCID: PMC9301819.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    14. Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation. iScience. 2020 Oct 23; 23(10):101582. Liu Y, Cook C, Sedgewick AJ, Zhang S, Fassett MS, Ricardo-Gonzalez RR, Harirchian P, Kashem SW, Hanakawa S, Leistico JR, North JP, Taylor MA, Zhang W, Man MQ, Charruyer A, Beliakova-Bethell N, Benz SC, Ghadially R, Mauro TM, Kaplan DH, Kabashima K, Choi J, Song JS, Cho RJ, Cheng JB. PMID: 33205009; PMCID: PMC7648132.
      View in: PubMed   Mentions: 17  
    15. Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data. Phys Rev E. 2020 Jul; 102(1-1):012409. Zhang S, Leistico JR, Cook C, Liu Y, Cho RJ, Cheng JB, Song JS. PMID: 32794969; PMCID: PMC7437020.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    16. Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators. Front Genet. 2019; 10:775. Finnegan A, Cho RJ, Luu A, Harirchian P, Lee J, Cheng JB, Song JS. PMID: 31552090; PMCID: PMC6733986.
      View in: PubMed   Mentions: 29  
    17. A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes. J Invest Dermatol. 2019; 139(6):1264-1273. Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ, Mully T, Golovato J, Gray M, Mauro TM, Purdom E, Kim EA, Sbitany H, Bhutani T, Vaske CJ, Benz SC, Cho RJ, Cheng JB.
    18. Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX. Pigment Cell Melanoma Res. 2019 07; 32(4):500-509. Hejna M, Moon WM, Cheng J, Kawakami A, Fisher DE, Song JS. PMID: 30548162; PMCID: PMC6555698.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    19. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Rep. 2018 10 23; 25(4):871-883. Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ. PMID: 30355494; PMCID: PMC6367716.
      View in: PubMed   Mentions: 115     Fields:    Translation:HumansCells
    20. Emergence and Evolution of Mutational Hotspots in Sun-Damaged Skin. J Invest Dermatol. 2018 01; 138(1):16-17. Cheng JB, Cho RJ. PMID: 29273145; PMCID: PMC6053279.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    21. Induced Pluripotent Stem Cell Differentiation and Three-Dimensional Tissue Formation Attenuate Clonal Epigenetic Differences in Trichohyalin. Stem Cells Dev. 2016 09 15; 25(18):1366-75. Petrova A, Capalbo A, Jacquet L, Hazelwood-Smith S, Dafou D, Hobbs C, Arno M, Farcomeni A, Devito L, Badraiq H, Simpson M, McGrath JA, Di WL, Cheng JB, Mauro TM, Ilic D. PMID: 27460132; PMCID: PMC5035378.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    22. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed   Mentions: 3026     Fields:    Translation:HumansCells
    23. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18; 6:6351. Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. PMID: 25690954; PMCID: PMC4346612.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    24. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat Commun. 2014 Nov 25; 5:5442. Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB. PMID: 25421844; PMCID: PMC4385735.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    25. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep. 2014 Nov 20; 9(4):1228-34. Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ. PMID: 25456125; PMCID: PMC4254608.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    26. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014 04 15; 30(8):1172-1174. Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ. PMID: 24371156.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    27. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell. 2013 Aug 15; 154(4):888-903. Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA. PMID: 23953118; PMCID: PMC3962256.
      View in: PubMed   Mentions: 193     Fields:    Translation:HumansAnimalsCells
    28. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013 Sep; 23(9):1522-40. Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T. PMID: 23804400; PMCID: PMC3759728.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansCells
    29. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 2013 Sep; 23(9):1541-53. Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T. PMID: 23804401; PMCID: PMC3759729.
      View in: PubMed   Mentions: 82     Fields:    Translation:HumansCells
    30. Genetics and epigenetics of the skin meet deep sequence. J Invest Dermatol. 2012 Mar; 132(3 Pt 2):923-32. Cheng JB, Cho RJ. PMID: 22237701; PMCID: PMC4099064.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    31. Mammalian wax biosynthesis. I. Identification of two fatty acyl-Coenzyme A reductases with different substrate specificities and tissue distributions. J Biol Chem. 2004 Sep 03; 279(36):37789-97. Cheng JB, Russell DW. PMID: 15220348; PMCID: PMC2757098.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansAnimalsCells
    32. Mammalian wax biosynthesis. II. Expression cloning of wax synthase cDNAs encoding a member of the acyltransferase enzyme family. J Biol Chem. 2004 Sep 03; 279(36):37798-807. Cheng JB, Russell DW. PMID: 15220349; PMCID: PMC2743083.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    33. Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase. Proc Natl Acad Sci U S A. 2004 May 18; 101(20):7711-5. Cheng JB, Levine MA, Bell NH, Mangelsdorf DJ, Russell DW. PMID: 15128933; PMCID: PMC419671.
      View in: PubMed   Mentions: 244     Fields:    Translation:HumansCells
    34. De-orphanization of cytochrome P450 2R1: a microsomal vitamin D 25-hydroxilase. J Biol Chem. 2003 Sep 26; 278(39):38084-93. Cheng JB, Motola DL, Mangelsdorf DJ, Russell DW. PMID: 12867411; PMCID: PMC4450819.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansAnimalsCells
    35. Molecular genetics of 3beta-hydroxy-Delta5-C27-steroid oxidoreductase deficiency in 16 patients with loss of bile acid synthesis and liver disease. J Clin Endocrinol Metab. 2003 Apr; 88(4):1833-41. Cheng JB, Jacquemin E, Gerhardt M, Nazer H, Cresteil D, Heubi JE, Setchell KD, Russell DW. PMID: 12679481.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    36. A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3' end. Mol Cell Biol. 1999 Jan; 19(1):567-76. Mitchell JR, Cheng J, Collins K. PMID: 9858580; PMCID: PMC83914.
      View in: PubMed   Mentions: 230     Fields:    Translation:HumansAnimalsCells
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