Ji Lab

Publications

 

2024

  • Hren MG, Del Duca E, He H, Ji AL, Guttman-Yassky E. Algorithms in allergy: Diagnosis and management of atopic dermatitis in adulthood. Allergy, 00:1-3, 2024. [link]
  • Cho I, Ji AL. Type 1 innate lymphoid cells: a biomarker and therapeutic candidate in sarcoidosis. The Journal of Clinical Investigation, 134(17), 2024. [link]
  • Trier, AM, Ver Heul A, Fredman A, Le V, Wang, Z, Auyeung K, Meixiong J, Lovato P, Holtzman MJ, Wang F, Dong X, Ji AL, Kim BS. IL-33 Potentiates Histaminergic Itch. Journal of Allergy and Clinical Immunology 153(3):852-859.e3, 2024. [link]

2023

 

  • Chen L, Chang D, Tandukar B, Deivendran D, Cho R, Cheng J, Bastian BC, Ji AL, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biology 2023 24: 273. [link]
  • Thrane K*, Winge MCG*, Wang H, Chen L, Guo MG, Andersson A, Abalo XM, Yang X, Kim DS, Longo SK, Soong BY, Meyers JM, Reynolds DL, McGeever A, Demircioglu D, Hasson D, Mirzazadeh R, Rubin AJ, Bae GH, Karkanias J, Rieger K, Lundeberg J, Ji AL. Single-cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. Journal of Investigative Dermatology 2023 May 2;S0022-202X(23)02040-7. doi: 10.1016/j.jid.2023.02.040. Online ahead of print. PubMed PMID: 37142187. [link]

  • Houser AE, Kazmi A, Nair AK, Ji AL. The Use of Single Cell RNA-seq and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. JID Innovations 2023, https://doi.org/10.1016/j.xjidi.2023.100198.

 

2022

 

  • Han J, Correa da Rosa J, Owji S, Yassky D, Luu Y, Estrada Y, Ungar J, Ji A, Krueger JG, Gulati N. Skin proteomic analysis of immune activation associated with regression of melanoma metastases induced by diphencyprone. JAAD International 2022 9, 65-68. PMID:36147215.
  • Erickson A, He M, Berglund E, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstråhle L, Bergenstråhle J, Larsson L, Galicia LA, Shamikh A, Bascami E, Ståhl TSD, Rajakumar T, Doultsinos D, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022). [link]
  • Piñeiro AJ*, Houser AE*, Ji AL. Research Techniques Made Simple: Spatial Transcriptomics. Journal of Investigative Dermatology, 142(4): 993-1001, 2022. [pdf]
  • Bergenstråhle, L, He, B, Bergenstråhle, J, Abalo X, Mirzazadeh R, Thrane K, Ji AL, Andersson A, Larsson L, Stakenborg N, Boeckxstaens G, Khavari P, Zou J, Lundeberg J, Maaskola J. Super-resolved spatial transcriptomics by deep data fusion. Nature Biotechnology, 40: 476–479, 2022. https://doi.org/10.1038/s41587-021-01075-3

 

2021

 

  • Longo SL, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nature Reviews Genetics, 2021, https://doi.org/10.1038/s41576-021-00370-8.
  • Porter DF, Miao W, Yang X, Goda GA, Ji AL, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. Nature Communications, 12(1):1569, 2021. [link]

 

2020

 

  • Ji AL*, Rubin AJ*, Thrane K*, Jiang S*, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell, 182:497-514, 2020. [link]

 

2019 and Prior

 

  • Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA. Couple Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell, 176:361-376, 2019. [link]
  • Ji AL, Bichakjian CK, Swetter SM. Molecular Profiling in Cutaneous Melanoma. Journal of the National Comprehensive Cancer Network: JNCCN, 14(4):475-80, 2016. [link]
  • Obenauf AC, Zou Y*, Ji AL*, Vanharanta S, Shu W, Shi H, Kong X, Bosenberg MC, Wiesner T, Rosen N, Lo RS, Massagué J. Therapy-induced tumour secretomes promote resistance and tumour progression. Nature, 520(7547):368-72, 2015. [link]
  • Ji AL*, Baze MR*, Davis SA, Feldman SR, Fleischer AB Jr. Ambulatory Melanoma Care Patterns in The United States. Journal of Skin Cancer (2013):689261, 2013.

 

*Authors contributed equally to this work.

 

 

Preprints

 

  • Chen L, Chang D, Tandukar B, Deivendran D, Cho R, Cheng J, Bastian BC, Ji AL, Shain AH. Visualizing somatic alterations in spatial transcriptomics data of skin cancer. bioRxiv 2022.12.05.519162; doi: https://doi.org/10.1101/2022.12.05.519162
  • Lopez-Pajares V, Bhaduri A, Zhao Y, Gowrishankar G, Donohue L, Guo MG, Siprashvili Z, Miao W, Nguyen DT, Li AM, Shanderson RL, Meyers RM, Guerrero A, Ji AL, Garcia OS, Tao S, Meservey LM, Yang X, Gambhir SS, Ye J, Khavari PA. Glucose modulates transcription factor dimerization to enable tissue differentiation. bioRxiv 2022.11.28.518222; doi: https://doi.org/10.1101/2022.11.28.518222