{"id":19,"date":"2021-05-18T16:07:48","date_gmt":"2021-05-18T16:07:48","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/jilab\/?page_id=19"},"modified":"2026-03-23T16:36:50","modified_gmt":"2026-03-23T16:36:50","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/jilab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<p>[et_pb_section fb_built=&#8221;1&#8243; admin_label=&#8221;Section&#8221; _builder_version=&#8221;4.16&#8243; global_colors_info=&#8221;{}&#8221;][et_pb_row _builder_version=&#8221;4.16&#8243; background_size=&#8221;initial&#8221; background_position=&#8221;top_left&#8221; background_repeat=&#8221;repeat&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_column type=&#8221;4_4&#8243; _builder_version=&#8221;4.16&#8243; custom_padding=&#8221;|||&#8221; global_colors_info=&#8221;{}&#8221; custom_padding__hover=&#8221;|||&#8221;][et_pb_text _builder_version=&#8221;4.16&#8243; background_size=&#8221;initial&#8221; background_position=&#8221;top_left&#8221; background_repeat=&#8221;repeat&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<h1>Publications<\/h1>\n<h1><span style=\"font-size: 30px\"><\/span><\/h1>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong>2026<\/strong><\/span><\/p>\n<ul>\n<li><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Restrepo P, Wilder A, Houser A, Sandhu HS, Ramirez A, Hren MG, Gill R, Kazmi A, Chen L, Nigro A, Imanishi I, Demircioglu D, Hasson D, Soto A, McQuillan S, Gonzalez-Kozlova E, Brody R, Ungar B, Kasper M, Lu CP, Torina P, Lewin JM, Gnjatic S, Ma S, <strong><span style=\"text-decoration: underline\">Ji AL<\/span><\/strong>. Single-cell spatial transcriptomic analysis of human skin anatomy. <strong><em>Nature Genetics <\/em><\/strong>2026. <a href=\"https:\/\/doi.org\/10.1038\/s41588-026-02552-8\">https:\/\/doi.org\/10.1038\/s41588-026-02552-8<\/a><\/span><\/span><\/span><\/span><span style=\"font-size: x-large\"><strong><\/strong><\/span>\n<ul>\n<li><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Browse data accompanying the manuscript interactively with our <a href=\"https:\/\/rstudio-connect.hpc.mssm.edu\/humanskin-spatialcensus\/\">Human Skin MERFISH Atlas<\/a>.<\/span><\/span><\/span><\/span><\/li>\n<li><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Featured &#8220;News and Views&#8221; commentary: <a href=\"https:\/\/www.nature.com\/articles\/s41588-026-02555-5\">A refined blueprint for human skin.<\/a><\/span><\/span><\/span><\/span><\/li>\n<li><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Read the Mount Sinai Press Release: <a href=\"https:\/\/www.mountsinai.org\/about\/newsroom\/2026\/mount-sinai-researchers-identify-unique-coordination-among-cell-types-that-support-healthy-human-skin\">https:\/\/www.mountsinai.org\/about\/newsroom\/2026\/mount-sinai-researchers-identify-unique-coordination-among-cell-types-that-support-healthy-human-skin<\/a>.<\/span><\/span><\/span><\/span><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\"><\/span><\/span><\/span><\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Silva I, Nigro A, Yeroushalmi O, <strong><span style=\"text-decoration: underline\">Ji AL<\/span><\/strong>. Characterization of inflammatory skin conditions and autoimmune conditions in solid organ transplant patients at a large metropolitan academic center. <em><strong>JAAD International<\/strong><\/em> 24:271-273 2026.<\/span><\/span><\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong>2025<\/strong><\/span><\/p>\n<ul>\n<li><span style=\"font-size: large\">Imanishi I*, Gill R*, Wilder A, Restrepo R, Nair A, Cho I, Krueger JG, Guttman-Yassky E, Kim BS, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. A basophil-fibroblast pro-inflammatory axis fuels type 2 skin inflammation. <strong><em>Cell Reports<\/em><\/strong> 2025 Aug 26;44(8):115114.\u00a0<a href=\"https:\/\/www.cell.com\/cell-reports\/fulltext\/S2211-1247(25)00885-X\">https:\/\/www.cell.com\/cell-reports\/fulltext\/S2211-1247(25)00885-X.<\/a><\/span>\n<ul>\n<li><span style=\"font-size: large\">Featured in commentary in AAD DermWorld: <a href=\"https:\/\/www.medpagetoday.com\/reading-room\/aad\/atopic-dermatitis\/118406\">https:\/\/www.medpagetoday.com\/reading-room\/aad\/atopic-dermatitis\/118406<\/a><\/span><span style=\"font-size: large\">\u00a0<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-size: large\">Kim G, Siprashvili Z, Yang X, Meyers JM, <span style=\"text-decoration: underline\"><strong>Ji A<\/strong><\/span>, Khavari PA, Ducoli L. In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth. <strong><em>Journal of Investigative Dermatology<\/em><\/strong> 2025, <a href=\"https:\/\/doi.org\/10.1016\/j.jid.2025.04.038\">https:\/\/doi.org\/10.1016\/j.jid.2025.04.038<\/a>.<\/span><\/li>\n<li><span style=\"font-size: large\">Hren MG, Silva I, Gulati N, Ungar J, Lewin J, <span style=\"text-decoration: underline\"><strong>Ji A<\/strong><\/span>. Utilization of an Email-Based Referral System to Streamline Skin Cancer Screenings Among Solid Organ Transplant Recipients. <strong><em>Journal of Cutaneous Medicine and Surgery<\/em><\/strong> 2025, <a href=\"https:\/\/doi.org\/10.1177\/12034754251336200\">https:\/\/doi.org\/10.1177\/1203475425133620<\/a>.<\/span><\/li>\n<li><span style=\"font-size: large\">Kazmi A, Gill R, Restrepo P, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. The spatial and single-cell landscape of skin: Charting the multiscale regulation of skin immune function. <strong><em>Seminars in Immunology<\/em><\/strong>, 78: 101958, 2025.<\/span><\/li>\n<li><span style=\"font-size: large\">Lopez-Pajares V, Bhaduri A, Zhao Y, Gowrishankar G, Donohue L, Guo MG, Siphrashvili Z, Miao W, Nguyen DT, Li AM, Shanderson RL, Meyers RM, Guerrero A, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>, Garcia OS, Tao S, Meservey LM, Yang X, Gambhir SS, Ye J, Khavari PA. Glucose modulates transcription factor dimerization to enable tissue differentiation. <strong><em>Cell Stem Cell<\/em><\/strong> 2025 32, 1-16.<br \/><\/span><\/li>\n<li><span style=\"font-size: large\">Silva I, Kazmi A, Hren MG, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. Analysis of Race in Time to Keratinocyte Carcinoma in Solid Organ Transplant Recipients: Results of a Single-Institution Study. <strong><em>Journal of the American Academy of Dermatology<\/em><\/strong> 2025 <em>Mar <\/em>2:S0190-9622(25)00392-5. doi: 10.1016\/j.jaad.2025.02.085. Online ahead of print. PubMed PMID: 40037497.<\/span><\/li>\n<\/ul>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong>2024<\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<ul>\n<li><span style=\"font-size: large\">Hren MG, Del Duca E, He H, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>, Guttman-Yassky E. Algorithms in allergy: Diagnosis and management of atopic dermatitis in adulthood. <strong><em>Allergy<\/em><\/strong>, 00:1-3, 2024. <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/all.16315\">[link]<\/a><br \/><\/span><\/li>\n<li><span style=\"font-size: large\">Cho I, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. Type 1 innate lymphoid cells: a biomarker and therapeutic candidate in sarcoidosis. <strong><em>The Journal of Clinical Investigation<\/em><\/strong>, 134(17), 2024. <a href=\"https:\/\/www.jci.org\/articles\/view\/183708\">[link]<\/a><br \/><\/span><\/li>\n<li><span style=\"font-size: large\">Trier, AM, Ver Heul A, Fredman A, Le V, Wang, Z, Auyeung K, Meixiong J, Lovato P, Holtzman MJ, Wang F, Dong X, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>, Kim BS. IL-33 Potentiates Histaminergic Itch. <strong><em>Journal of Allergy and Clinical Immunology<\/em><\/strong> 153(3):852-859.e3, 2024. <a href=\"https:\/\/www.jacionline.org\/article\/S0091-6749(23)01465-3\/fulltext\">[link]<\/a><\/span><\/li>\n<\/ul>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong><\/strong><\/span><\/p>\n<p><span style=\"font-size: x-large\"><strong>2023<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><span style=\"font-size: large\">Chen L, Chang D, Tandukar B, Deivendran D, Cho R, Cheng J, Bastian BC, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. <strong><em>Genome Biology<\/em><\/strong> 2023 24: 273. <a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-023-03121-6\">[link]<\/a><br \/><\/span><\/li>\n<li><span style=\"font-size: large\">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, <strong><\/strong><span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. Single-cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. <em><strong>Journal of Investigative Dermatology<\/strong><\/em> 2023\u00a0May 2;S0022-202X(23)02040-7. doi: 10.1016\/j.jid.2023.02.040. Online ahead of print. PubMed PMID: 37142187.<em>\u00a0<\/em><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0022202X23020407?dgcid=author\">[link]<\/a><\/span>\n<ul>\n<li><span style=\"font-size: large\">Browse data <span style=\"color: #000000\">accompanying<\/span> the manuscript with our <a href=\"https:\/\/rstudio-connect.hpc.mssm.edu\/hmsbrowser\/\">Human-Mouse Skin Browser<\/a><\/span><\/li>\n<li><span style=\"font-size: large\">Browse spatial data with our <a href=\"https:\/\/human-skin-browser.ds.czbiohub.org\">Human Skin Browser<\/a> (username: demo; password: <span class=\"css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0\">YjJKBAbhUF9Ug<\/span>)<\/span><\/li>\n<li><span style=\"font-size: large\">Highlighted in JID Commentary. <a href=\"https:\/\/doi.org\/10.1016\/j.jid.2023.03.1678\">https:\/\/doi.org\/10.1016\/j.jid.2023.03.1678<\/a><br \/><\/span><\/li>\n<\/ul>\n<p><span style=\"font-size: large\"><\/span><\/p>\n<\/li>\n<li><span style=\"font-size: large\">Houser AE, Kazmi A, Nair AK, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>. The Use of Single Cell RNA-seq and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. <em><strong>JID Innovations<\/strong><\/em> 2023, <a href=\"https:\/\/doi.org\/10.1016\/j.xjidi.2023.100198\">https:\/\/doi.org\/10.1016\/j.xjidi.2023.100198<\/a>.<\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: x-large\"><strong>2022<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><span style=\"font-size: large\">Han J, Correa da Rosa J, Owji S, Yassky D, Luu Y, Estrada Y, Ungar J, <strong><span style=\"text-decoration: underline\">Ji A<\/span><\/strong>, Krueger JG, Gulati N. Skin proteomic analysis of immune activation associated with regression of melanoma metastases induced by diphencyprone.<em><strong> JAAD International<\/strong><\/em> 2022 9, 65-68. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36147215\/\">PMID:36147215<\/a>.<\/span><\/li>\n<li><span style=\"font-size: large\">Erickson A, He M, Berglund E, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstr\u00e5hle L, Bergenstr\u00e5hle J, Larsson L, Galicia LA, Shamikh A, Bascami E, St\u00e5hl TSD, Rajakumar T, Doultsinos D, Thrane K, <strong><span style=\"text-decoration: underline\">Ji AL<\/span><\/strong>, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J<i>.<\/i> Spatially resolved clonal copy number alterations in benign and malignant tissue. <strong><i>Nature<\/i><\/strong> 608<b>, <\/b>360\u2013367 (2022). <a href=\"https:\/\/www.nature.com\/articles\/s41586-022-05023-2\">[link]<\/a><\/span><\/li>\n<li><span style=\"font-size: large\">Pi\u00f1eiro AJ*, Houser AE*,<span style=\"text-decoration: underline\"><strong> Ji AL<\/strong><\/span>. Research Techniques Made Simple: Spatial Transcriptomics. <em><strong>Journal of Investigative Dermatology<\/strong><\/em>, 142(4): 993-1001, 2022. <a href=\"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-content\/uploads\/sites\/389\/2022\/07\/1-s2.0-S0022202X21026312-main.pdf\" rel=\"attachment wp-att-179\">[pdf]<\/a><\/span><\/li>\n<li><span style=\"font-size: large\">Bergenstr\u00e5hle, L, He, B, Bergenstr\u00e5hle, J, Abalo X, Mirzazadeh R, Thrane K, <span style=\"text-decoration: underline\"><strong>Ji AL<\/strong><\/span>, Andersson A, Larsson L, Stakenborg N, Boeckxstaens G, Khavari P, Zou J, Lundeberg J, Maaskola J<i>.<\/i> Super-resolved spatial transcriptomics by deep data fusion. <strong><i>Nature Biotechnology<\/i><\/strong><i>, <\/i>40: 476\u2013479, 2022. <a href=\"https:\/\/doi.org\/10.1038\/s41587-021-01075-3\">https:\/\/doi.org\/10.1038\/s41587-021-01075-3<\/a><\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: x-large\"><strong>2021<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><span style=\"font-size: large\">Longo SL, Guo MG, <strong><u>Ji AL<\/u><\/strong>, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. <em><strong>Nature Reviews Genetics, <\/strong><\/em>2021,\u00a0<a href=\"https:\/\/doi.org\/10.1038\/s41576-021-00370-8\">https:\/\/doi.org\/10.1038\/s41576-021-00370-8<\/a>.<\/span><\/li>\n<li><span style=\"font-size: large\">Porter DF, Miao W, Yang X, Goda GA, <strong><u>Ji AL<\/u><\/strong>, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. <strong><em>Nature Communications,<\/em><\/strong> 12(1):1569, 2021. <a href=\"https:\/\/www.nature.com\/articles\/s41467-021-21623-4\">[link]<\/a><\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: x-large\"><strong>2020<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><span style=\"font-size: large\"><strong><u>Ji AL<\/u><\/strong><u>*<\/u>, Rubin AJ*, Thrane K*, Jiang S*, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstr\u00e5hle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clav\u00e9 X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. <strong><em>Cell<\/em><\/strong>, 182:497-514, 2020. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867420306723\">[link]<\/a><\/span>\n<ul>\n<li><span style=\"font-size: large\">Editor&#8217;s Choice,\u00a0<em>Science Translational Medicine<\/em>. <a href=\"https:\/\/www.science.org\/doi\/10.1126\/scitranslmed.abd3609\">doi: 10.1126\/scitranslmed.abd3609<\/a><\/span><\/li>\n<li><span style=\"font-size: large\">Featured on <a href=\"https:\/\/med.stanford.edu\/news\/all-news\/2020\/06\/skin-cancer-growth-driven-by-subset-of-cellular-masterminds.html\">Stanford Medicine News<\/a> and <a href=\"https:\/\/www.prnewswire.com\/news-releases\/groundbreaking-stanford-skin-cancer-study-uses-multi-omics-approach-including-ionpath-high-definition-spatial-proteomics-301098977.html\">PR Newswire<\/a><\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: x-large\"><strong>2019 and Prior<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><span style=\"font-size: large\">Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, <strong><u>Ji AL<\/u><\/strong>, 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. <strong><em>Cell<\/em><\/strong>, 176:361-376, 2019. <a href=\"https:\/\/www.cell.com\/cell\/pdf\/S0092-8674(18)31514-9.pdf\">[link]<\/a><\/span><\/li>\n<li><span style=\"font-size: large\"><strong><u>Ji AL<\/u><\/strong>, Bichakjian CK, Swetter SM. Molecular Profiling in Cutaneous Melanoma. <strong><em>Journal of the National Comprehensive Cancer Network: JNCCN<\/em><\/strong>, 14(4):475-80, 2016. <a href=\"https:\/\/jnccn.org\/view\/journals\/jnccn\/14\/4\/article-p475.xml\">[link]<\/a><\/span><\/li>\n<li><span style=\"font-size: large\">Obenauf AC, Zou Y*, <strong><u>Ji AL<\/u><\/strong><u>*,<\/u> Vanharanta S, Shu W, Shi H, Kong X, Bosenberg MC, Wiesner T, Rosen N, Lo RS, Massagu\u00e9 J. Therapy-induced tumour secretomes promote resistance and tumour progression. <strong><em>Nature<\/em><\/strong>, 520(7547):368-72, 2015. <a href=\"https:\/\/www.nature.com\/articles\/nature14336\">[link]<\/a><\/span><\/li>\n<li><span style=\"font-size: large\"><strong><u>Ji AL<\/u><\/strong><u>*<\/u><strong>, <\/strong>Baze MR*, Davis SA, Feldman SR, Fleischer AB Jr. Ambulatory Melanoma Care Patterns in The United States. <strong><em>Journal of Skin Cancer<\/em><\/strong> (2013):689261, 2013.<\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: large\">*Authors contributed equally to this work.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<h1><span style=\"font-size: xx-large\">Preprints<\/span><\/h1>\n<p>&nbsp;<\/p>\n<div class=\"highwire-cite-title\">\n<ul>\n<li class=\"highwire-cite-metadata\"><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Restrepo P, Wilder A, Houser A, Ramirez A, Hren MG, Gill R, Kazmi A, Chen L, Demircioglu D, Hasson D, Soto A, McQuillan S, Gonzalez-Kozlova E, Brody R, Ungar B, Kasper M, Torina P, Lewin JM, Gnjatic S, Ma S, <strong><span style=\"text-decoration: underline\">Ji AL<\/span><\/strong>. A single-cell spatial transcriptomic census of human skin anatomy. bioRxiv 2025.09.22.676865; doi:<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2025.09.22.676865v1\">https:\/\/doi.org\/10.1101\/2025.09.22.676865<\/a><\/span><\/span><\/span><\/span><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\"><\/span><\/span><\/span><\/span><\/li>\n<li class=\"highwire-cite-metadata\"><span style=\"font-size: large\"><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">Chen L<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"1\"><span class=\"nlm-surname\">Chang D<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"2\"><span class=\"nlm-surname\">Tandukar B<\/span><\/span>, D<span class=\"highwire-citation-author\" data-delta=\"3\"><span class=\"nlm-surname\">eivendran D<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"4\"> <span class=\"nlm-surname\">Cho R<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"5\"><span class=\"nlm-surname\">Cheng J<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"6\"><span class=\"nlm-surname\">Bastian BC<\/span><\/span>, <span style=\"text-decoration: underline\"><strong><span class=\"highwire-citation-author\" data-delta=\"7\"><span class=\"nlm-surname\">Ji AL<\/span><\/span><\/strong><\/span>, <span class=\"highwire-citation-author\" data-delta=\"8\"><span class=\"nlm-surname\">Shain AH<\/span><\/span><\/span>. Visualizing somatic alterations in spatial transcriptomics data of skin cancer. <span class=\"highwire-cite-metadata-journal highwire-cite-metadata\">bioRxiv <\/span><span class=\"highwire-cite-metadata-pages highwire-cite-metadata\">2022.12.05.519162; <\/span><span class=\"highwire-cite-metadata-doi highwire-cite-metadata\"><span class=\"doi_label\">doi:<\/span> <a href=\"https:\/\/doi.org\/10.1101\/2022.12.05.519162\">https:\/\/doi.org\/10.1101\/2022.12.05.519162 <\/a><\/span><\/span><\/li>\n<li class=\"highwire-cite-metadata\"><span style=\"font-size: large\"><span class=\"highwire-cite-metadata-doi highwire-cite-metadata\"><\/span>L<span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first\" data-delta=\"0\"><span class=\"nlm-surname\">opez-Pajares V<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"1\"><span class=\"nlm-surname\">Bhaduri A<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"2\"> <span class=\"nlm-surname\">Zhao Y<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"3\"><span class=\"nlm-surname\">Gowrishankar G<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"4\"><span class=\"nlm-surname\">Donohue L<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"5\"><span class=\"nlm-surname\">Guo MG<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"6\"><span class=\"nlm-surname\">Siprashvili Z<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"7\"><span class=\"nlm-surname\">Miao W<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"8\"> <span class=\"nlm-surname\">Nguyen DT<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"9\"> <span class=\"nlm-surname\">Li AM<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"10\"><span class=\"nlm-surname\">Shanderson RL<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"11\"> <span class=\"nlm-surname\">Meyers RM<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"12\"><span class=\"nlm-surname\">Guerrero A<\/span><\/span>, <span style=\"text-decoration: underline\"><strong><span class=\"highwire-citation-author\" data-delta=\"13\"><span class=\"nlm-surname\">Ji AL<\/span><\/span><\/strong><\/span>,<span class=\"highwire-citation-author\" data-delta=\"14\"> <span class=\"nlm-surname\">Garcia OS<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"15\"> <span class=\"nlm-surname\">Tao S<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"16\"><span class=\"nlm-surname\">Meservey LM<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"17\"> <span class=\"nlm-surname\">Yang X<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"18\"><span class=\"nlm-surname\">Gambhir SS<\/span><\/span>,<span class=\"highwire-citation-author\" data-delta=\"19\"> <span class=\"nlm-surname\">Ye J<\/span><\/span>, <span class=\"highwire-citation-author\" data-delta=\"20\"><span class=\"nlm-surname\">Khavari PA<\/span><\/span><\/span>. Glucose modulates transcription factor dimerization to enable tissue differentiation. <span class=\"highwire-cite-metadata-journal highwire-cite-metadata\">bioRxiv <\/span><span class=\"highwire-cite-metadata-pages highwire-cite-metadata\">2022.11.28.518222; <\/span><span class=\"highwire-cite-metadata-doi highwire-cite-metadata\"><span class=\"doi_label\">doi:<\/span> <a href=\"https:\/\/doi.org\/10.1101\/2022.11.28.518222\">https:\/\/doi.org\/10.1101\/2022.11.28.518222<\/a><\/span><\/span><\/li>\n<\/ul>\n<\/div>\n<p>&nbsp;<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Publications 2026 Restrepo P, Wilder A, Houser A, Sandhu HS, Ramirez A, Hren MG, Gill R, Kazmi A, Chen L, Nigro A, Imanishi I, Demircioglu D, Hasson D, Soto A, McQuillan S, Gonzalez-Kozlova E, Brody R, Ungar B, Kasper M, Lu CP, Torina P, Lewin JM, Gnjatic S, Ma S, Ji AL. Single-cell spatial transcriptomic [&hellip;]<\/p>\n","protected":false},"author":470,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"<ul><li>Longo SL, Guo MG, <strong><u>Ji AL<\/u><\/strong>, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. <em><strong>Nature Reviews Genetics, <\/strong><\/em>2021,\u00a0<em>in press<\/em>.<\/li><li>Porter DF, Miao W, Yang X, Goda GA, <strong><u>Ji AL<\/u><\/strong>, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. <strong><em>Nature Communications,<\/em><\/strong> 12(1):1569, 2021.<\/li><li><strong><u>Ji AL<\/u><\/strong><u>*<\/u>, Rubin AJ*, Thrane K*, Jiang S*, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstr\u00e5hle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clav\u00e9 X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. <strong><em>Cell<\/em><\/strong>, 182:497-514, 2020.<ul><li>Comment in Sci. Trans. Med. doi: 10.1126\/scitranslmed.abd3609<\/li><\/ul><\/li><li>Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, <strong><u>Ji AL<\/u><\/strong>, 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. <strong><em>Cell<\/em><\/strong>, 176:361-376, 2019.<\/li><li><strong><u>Ji AL<\/u><\/strong>, Bichakjian CK, Swetter SM. Molecular Profiling in Cutaneous Melanoma. <strong><em>Journal of the National Comprehensive Cancer Network: JNCCN<\/em><\/strong>, 14(4):475-80, 2016.<\/li><li>Obenauf AC, Zou Y*, <strong><u>Ji AL<\/u><\/strong><u>*,<\/u> Vanharanta S, Shu W, Shi H, Kong X, Bosenberg MC, Wiesner T, Rosen N, Lo RS, Massagu\u00e9 J. Therapy-induced tumour secretomes promote resistance and tumour progression. <strong><em>Nature<\/em><\/strong>, 520(7547):368-72, 2015.<\/li><li><strong><u>Ji AL<\/u><\/strong><u>*<\/u><strong>, <\/strong>Baze MR*, Davis SA, Feldman SR, Fleischer AB Jr. Ambulatory Melanoma Care Patterns in The United States. <strong><em>Journal of Skin Cancer<\/em><\/strong> (2013):689261, 2013.<\/li><\/ul><p>*Authors contributed equally to this work.<\/p>","_et_gb_content_width":"","footnotes":""},"class_list":["post-19","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/pages\/19","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/users\/470"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/comments?post=19"}],"version-history":[{"count":52,"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/pages\/19\/revisions"}],"predecessor-version":[{"id":473,"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/pages\/19\/revisions\/473"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/jilab\/wp-json\/wp\/v2\/media?parent=19"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}