Selected Articles

• JD Lin*, YZ Ye, SR Wang, WY Kao, KT Lee. Bacillus subtilis natto NTU-18 attenuates atherosclerosis progression by modulating peripheral immune cell alterations. Applied Microbiology and Biotechnology, 109: 229, October, 2025. (Rank: Q1, 5-yr. IF=5.1), *Corresponding Author.

• KY Tai, CL Chen, S MY Fan, CH Kuan, CK Lin, HW Huang, HW Lee, SH Wang, NW Chang, JD Lin, CF Chang, KC Yang, MV Plikus, SJ Lin. Adipocyte lipolysis activates epithelial stem cells for hair regeneration through fatty acid metabolic signaling. Cell Metabolism (In Press). (Rank: Q1, 5-yr. IF=33.4).

• CL Jiang, PH Lai, PC Yang, CJ Lien, HP C Chu, JD Lin, SJ Lin, IS Yu, FJ Lin. Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and b-hydroxybutyrylome. Nature Metabolism (In Press). (Rank: Q1, 5-yr. IF=23.2).

• YH Chen, K Zaldana, F Yeung, I Vujkovic-Cvijin, AE Downie, JD Lin, Y Yang, C Herrmann, O Oyesola, F Rozenberg, RE Schwartz, D Kim, K Tio, Y Belkaid, P Loke, AL Graham, SB Koralov, K Cadwell. Rewilding catalyzes maturation of the humoral immune system. Science Advances, 11(10), March 2025. (Rank: Q1, 5-yr. IF=13.8, Citations≥7).

• YC Fan, YC Fong, CT Kuo, CW Li, WY Chen, JD Lin, F Burtin, M Linnebacher, QT Bui, KD Lee, YC Tsai. Tumor-derived interleukin-1 receptor antagonist exhibits immunosuppressive functions and promotes pancreatic cancer. Cell and Bioscience, 13(147), August, 2023. (Rank: Q1, BIOCHEMISTRY & MOLECULAR BIOLOGY , 5-yr. IF=7.9, Citations≥10).

• D G Loredan, J C Devlin, K A Lacey, N Howard, Z Chen, E E Zwack, JD Lin, K V Ruggles, K M Khanna, V J Torres, P Loke*. Single-cell analysis of CX3CR1+ cells reveals a pathogenic role for BIRC5+ myeloid proliferating cells driven by Staphylococcus aureus leukotoxins. Journal of Immunology, 211, July 2023. (Rank: Q2, IMMUNOLOGY, 5-yr. IF=5.2; Citations≥3).

• YH Chen*, F Yeung*, KA Lacey, K Zaldana, JD Lin#, GCW Bee, C McCauley, RS Barre, SH Liang, CB Hansen, AE Downie, K Tio, JN Weiser, VJ Torres, RJ Bennett, P Loke, AL Graham, K Cadwell. Rewilding of laboratory mice enhances granulopoiesis and immunity through intestinal fungal colonization. Science Immunology, 8(84), June 2023. (Rank: Q1, IMMUNOLOGY, 5-yr. IF=22, Citations≥38), *Co-first Author, #4th Author.  

• P Loke*, JD Lin*. Redefining inflammatory macrophage phenotypes across stages and tissues by single-cell transcriptomics. Science Immunology, 7(70), April 2022. (Rank: Q1, IMMUNOLOGY, 5-yr. IF=22, Citations≥24), *Corresponding Author. 

• JD Lin*, P Loke*. Helminth infections and cardiovascular diseases: A role for the microbiota and Møs? Journal of Leukocyte Biology, 110(6), September 2021. (Rank: Q2, HEMOTOLOGY, 5-yr. IF=5.4, Citations≥6), *Corresponding Author. 

• C McElrath, V Espinosa, JD Lin#, J Peng, R Sridhar, O Dutta, HC Tseng, S V Smirnov, H Risman, M J Sandoval, V Davra, YJ Chang, B P Pollack, R B Birge, M Galan, A Rivera, J E Durbin, S V Kotenko. Critical role of interferons in gastrointestinal injury repair. Nature Communication, 12(1), May 2021. (Rank: Q1, MULTIDISPLINARY SCIENCES, 5-yr. IF=17, Citations≥87), #3rd Author.  

• J C Devlin*, J Axelrad*, A M Hine*, S Chang, S Sarkar, JD Lin#, K V Ruggles, D Hudesman, K Cadwell, P Loke. Single-cell transcriptional survey of ileal-anal pouch immune cells from ulcerative colitis patients. Gastroenterology, 160(5), April 2021. (Rank: Q1, GASTROENTEROLOGY & HEPATOLOGY, 5-yr. IF=25.8, Citations≥62), *Co-first Author. #4th Author.  

• JD Lin, J C Devlin, F Yeung, C McCauley, J M. Leung, YH Chen, A Cronkite, C Hansen, C Drake-Dunn, K V. Ruggles, K Cadwell, A L Graham, P Loke. Rewilding Nod2 and Atg16l1 mutant mice uncover genetic and environmental contributions towards variation in microbial responses and immune cell composition. Cell Host & Microbe, 27(5), May 2020. (Rank: Q1, MICROBIOLOGY, 5-yr. IF=25.7, Citations≥93) 

• F Yeung*, YH Chen*, JD Lin*, J M Leung, C McCauley, J C. Devlin, C Hansen, A Cronkite, Z Stephens, C Drake-Dunn, Y Fulmer, B Shopsin, K V. Ruggles, J L. Round, P Loke, A L Graham, K Cadwell. Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host & Microbe, 27(5), May, 2020. (Rank: Q1, MICROBIOLOGY, 5-yr. IF=25.7, Citations≥162); *Co-first Author.

• JD Lin, H Nishi, J Poles, X Niu, C Mccauley, K Rahman, E J. Brown, S T Yeung, N Vozhilla, A Weinstock, S Ramsey, E A Fisher and P Loke. Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression. JCI insight, 4 (4), February, 2019. (Rank: Q1, MEDICINE, RESEARCH & EXPERIMENTAL, 5-yr. IF=8.6; Citations≥328) (Top 1% cited in "Clinical Medicine" field)

• U M Gundra, N M Girgis, M A Gonzalez, MS Tang, H J P Van Der Zande, JD Lin, M Ouimet, L J Ma, J Poles, N Vozhilla, E A Fisher, K J Moore, P Loke. Vitamin A mediates conversion of monocyte-derived macrophages into tissue-resident macrophages during alternative activation. Nature Immunology, 18 (6), June 2017. (Rank: Q1, IMMUNOLOGY, 5-yr. IF=29.6; Citations≥166)

• JD Lin, N Feng, A Sen, M Balan, HC Tseng, C McElrath, S V Smirnov, J Peng, L L Yasukawa, R K. Durbin, J E Durbin, H B Greenberg and S V. Kotenko. Distinct roles of type I and type III interferons in intestinal immunity to homologous and heterologous rotavirus infection. PLoS Pathog., 12 (4), April, 2016. (Rank: Q1, MICROBIOLOGY, 5-yr. IF=6.7; Citations≥216)

Conference Issues

• Role of Saa3 in macrophage ontogeny, differentiation, and polarization. YZ Ye, TY Chou, CL Jian, YY Sun, HF Juan, FJ Lin, JD Lin. (本人為通訊作者). 會議：39th生物醫學聯合學術年會, March 2025. (博士組壁報競賽特優獎)

• Nod2-mediated type 2 immunity and anti-inflammatory responses drive atherosclerosis regression following helminth infection. IH Lo, CJ Lien, JD Lin. (本人為通訊作者). 會議：39th生物醫學聯合學術年會, March 2025. (獲選大會口頭報告)

• Exploring microbiome-independent mechanisms of helminth infections in modulating atherosclerosis and immune responses. KH Chen, CS Chao, ST Chang, KT Lee, JD Lin. (本人為通訊作者). 會議：39th生物醫學聯合學術年會, March 2025.

• Nod2 deficiency attenuates atherosclerosis progression. HY Chen, KH Chen, JC Wang, JD Lin. (本人為通訊作者). 會議：39th生物醫學聯合學術年會, March 2025.

• Deciphering sex-dimorphic mechanisms of SAA3 in macrophage polarization and activation via simultaneous scRNA-seq and scATAC-seq. JC Wang, YZ Ye, TY Chou, JD Lin. (本人為通訊作者). 會議：39th生物醫學聯合學術年會, March 2025.

• Unraveling the immunological roles of Serum Amyloid A3 in aortic arches during atherosclerosis progression. TY Chou, IJ Lin, YZ Ye, CJ Lien, CH Yang, JD Lin. Journal of Immunology, 212(1 Supplement), May 2024. (SCI, 5-yr IF 4.2, 79/181, IMMUNOLOGY). (本人為通訊作者). 會議：IMMUNOLOGY2024, May 2024. (獲選於大會Block Symposia口頭演講並獲頒Trainee Abstract Award)

• Deciphering the links between microbiome and immune profiles by multi-omics analysis during aortic plaque progression and helminth-induced regression. JD Lin, YT Chen, PA Chao, IJ Lin, TY Chou, YZ Ye, CJ Lien, CH Yang,. Journal of Immunology, 212(1 Supplement), May 2024. (SCI, 5-yr IF 4.2, 79/181, IMMUNOLOGY). (本人為第一作者、通訊作者). 會議：IMMUNOLOGY2024, May 2024. (獲選於大會Block Symposia口頭演講並獲頒Early Career Faculty Travel Grant)

• Critical roles of serum amyloid A3 (SAA3) in modulating macrophage conversions and metabolic features. YZ Ye, TY Chou, IJ Lin, CJ Lien, CL Jian, YY Sun, HF Juan, FJ Lin, JD Lin. (本人為通訊作者). 會議：38th生物醫學聯合學術年會, March 2024. (碩士組口頭論文競賽特優獎)

• The possible immune modulating roles of microbiota during atherosclerosis progression with helminth infections. KH Chen, PA Chao, YT Chen, JC Wang, HY Chen, JD Lin. (本人為通訊作者). 會議：38th生物醫學聯合學術年會, March 2024. (獲選大會口頭報告) 

• Interrogate the gut-heart axis in helminth-induced aortic plaque regression during atherosclerosis. CJ Lien, PA Chao, YT Chen, IJ Lin, JD Lin. (本人為通訊作者). 會議：38th 生物醫學聯合學術年會, March 2024.

• Single-Cell Multi-Omics Analysis Identified the Roles of Serum Amyloid A3 (Saa3) in Regulating Macrophage Dynamics. YZ Ye, TY Chou, IJ Lin, CJ Lien, CL Jiang, CH Yang, PA Chao, YT Chen, YY Sun, HF Juan, FJ Lin, JD Lin. (本人為通訊作者). 會議：2022多體學及精準醫學聯合會議, October 2023. (獲選大會壁報獎)