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Ali Naji

university of pennsylvania

80H-index
529Paper Count
2.3WCitation Count
Published Papers 200
Publication Date
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Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes
errScience Immunology
IF16.3
err2025-11-21
err0
errOAAI
errMaryam Abedi; Priyadarshini Rai; Yeqiao Zhou; Chengyang Liu; Isabelle Johnson; Aditi Chandra; Maria Fasolino; Susan Rostami; Wei Wang; Zaw Min; Yanjing Li; Ming Yu; Atishay Jay; Vung Lian; Michael Silverman; Klaus H. Kaestner; Ali Naji; Robert B. Faryabi; Golnaz Vahedi
errShare
errSave
Dr. Clyde F. Barker (1932-2025)
errCLINICAL TRANSPLANTATION
IF1.9
err2025-11-19
err0
PREAI
errNaji, Ali
errShare
errSave
Capturing Nonlocal Effects in Fractional Dynamics: Riesz Derivatives as a New Frontier in Modeling Complex Diffusion and Pattern Formation
errMATHEMATICAL METHODS IN THE APPLIED SCIENCES
IF1.8
err2025-09-01
err0
PREAI
errAlqhtani, Manal; Owolabi, Kolade M.; Saad, Khaled M.; Naji, Akram A.; Pindza, Edson
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errSave
Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals
errCell Reports
IF6.9
err2025-07-29
err0
errOAAI
errRicardo D'Oliveira Albanus; Xiaoshan Zhang; Zeping Zhao; Henry J. Taylor; Xuming Tang; Yuling Han; Peter Orchard; Arushi Varshney; Tuo Zhang; Nandini Manickam; Michael R. Erdos; Narisu Narisu; Leland Taylor; Xiaxia Saavedra; Xinyi Liu; Aaron Zhong; Bo Li; Ting Zhou; Ali Naji; Chengyang Liu; Francis S. Collins; Stephen C.J. Parker; Shuibing Chen
errShare
errSave
ChemPerturb-seq screen identifies a small molecule cocktail enhancing human beta cell survival after subcutaneous transplantation
errCell Stem Cell
IF20.4
err2025-06-24
err0
PREAI
errJ. Jeya Vandana; Jiajun Zhu; Alice Maria Giani; Tuo Zhang; Lauretta A. Lacko; Dongliang Leng; D. Leland Taylor; Brian N. Lee; Zhaowei Han; Tiancheng Jiao; Yuanhao Huang; Meiqi Zhao; Xinyi Liu; Angie Chi Nok Chong; Dongxiang Xue; Zihe Meng; Jenny Z. Xiang; Chendong Pan; Wei Wang; Ali Naji; Todd Evans; Jie Liu; Francis S. Collins; Chengyang Liu; Shuibing Chen
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errSave
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset
errNATURE COMMUNICATIONS
IF15.7
err2025-05-18
err0
errOAAI
errGolden, Gregory J.; Wu, Vincent H.; Hamilton, Jacob T.; Amses, Kevin R.; Shapiro, Melanie R.; Japp, Alberto Sada; Liu, Chengyang; Pampena, M. Betina; Kuri-Cervantes, Leticia; Knox, James J.; Gardner, Jay S.; Atkinson, Mark A.; Brusko, Todd M.; Prak, Eline T. Luning; Kaestner, Klaus H.; Naji, Ali; Betts, Michael R.
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errSave
Biliary atresia susceptibility gene EFEMP1 regulates extrahepatic bile duct elastic fiber formation and mechanics
errJHEP REPORTS
IF7.5
err2025-01-01
err0
errOAAI
errGupta, Kapish; Llewellyn, Jessica; Roberts, Emilia; Liu, Chengyang; Naji, Ali; Assoian, Richard K.; Wells, Rebecca G.
errShare
errSave
β-Cell Secretory Capacity Predicts Metabolic Outcomes Over 6 Years After Human Islet Transplantation
errDIABETES
IF7.5
err2024-12-04
err0
PREAI
errFlatt, Anneliese J.; Matus, Austin M.; Gallop, Robert J.; Markmann, Eileen; Dalton-Bakes, Cornelia; Peleckis, Amy J.; Liu, Chengyang; Naji, Ali; Rickels, Michael R.
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errSave
The IsletTester Mouse: An Immunodeficient Model With Stable Hyperglycemia for the Study of Human Islets
errDIABETES
IF7.5
err2024-11-21
err0
PREAI
errWaite, Eric L.; Tigue, Mark; Yu, Ming; Lahori, Deeksha; Kelly, Kai; May, Catherine Lee; Naji, Ali; Roman, Jeffrey; Doliba, Nicolai; Avrahami, Dana; Nguyen-Ngoc, Kim-Vy; Sander, Maike; Glaser, Benjamin; Kaestner, Klaus H.
errShare
errSave
Human vascularized macrophage-islet organoids to model immune-mediated pancreatic R cell pyroptosis upon viral infection
errCELL STEM CELL
IF20.4
err2024-11-01
err1
errOAAI
errYang, Liuliu; Han, Yuling; Zhang, Tuo; Dong, Xue; Ge, Jian; Roy, Aadita; Zhu, Jiajun; Lu, Tiankun; Vandana, J. Jeya; de Silva, Neranjan; Robertson, Catherine C.; Xiang, Jenny Z.; Pan, Chendong; Sun, Yanjie; Que, Jianwen; Evans, Todd; Liu, Chengyang; Wang, Wei; Naji, Ali; Parker, Stephen C. J.; Schwartz, Robert E.; Chen, Shuibing
errShare
errSave
Human Peripancreatic Adipose Tissue Paracrine Signaling Impacts Insulin Secretion, Blood Flow, and Gene Transcription
errJOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
IF5.1
err2024-11-01
err1
errOAAI
errBergman, Bryan C.; Berry, Karin Zemski; Garfield, Amanda; Keller, Amy; Zarini, Simona; Bowen, Sophia; Mckenna, Colleen; Kahn, Darcy; Pavelka, Jay; Macias, Emily; Uhlson, Charis; Johnson, Chris; Russ, Holger A.; Viesi, Carlos H.; Seldin, Marcus; Liu, Chengyang; Doliba, Nicolai M.; Schoen, Jonathan; Rothchild, Kevin; Hazel, Kweku; Naji, Ali
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errSave
Three-Dimensional Imaging of the Enteric Nervous System in Human Pediatric Colon Reveals New Features of Hirschsprung's Disease
errGASTROENTEROLOGY
IF25.1
err2024-08-01
err1
errOAAI
errEisenberg, Joshua D.; Bradley, Rebecca P.; Graham, Kahleb D.; Ceron, Rachel H.; Lemke, Amanda M.; Wilkins, Benjamin J.; Naji, Ali; Heuckeroth, Robert O.
errShare
errSave
Immunosuppression withdrawal in living-donor renal transplant recipients following induction with antithymocyte globulin and rituximab: Results of a prospective clinical trial
errAMERICAN JOURNAL OF TRANSPLANTATION
IF8.2
err2024-07-01
err0
PREAI
errMarkmann, James F.; Burrell, Bryna E.; Bromberg, Jonathan S.; Hartono, Choli; Kaufman, Dixon B.; Possselt, Andrew M.; Naji, Ali; Bridges, Nancy D.; Breeden, Cynthia; Kanaparthi, Sai; Pardo, Jorge; Kopetskie, Heather; Mason, Kristen; Lim, Noha; Chandran, Sindhu
errShare
errSave
Exploring Intrinsic Features of Human Pancreatic a- and ßCell Physiology Using Pseudoislets
errDIABETES
IF7.5
err2024-06-14
err0
PREAI
errRozo, Andrea V.; Roman, Jefferey; Qin, Wei; Liu, Chengyang; Naji, Ali; Kaestner, Klaus H.; Hoshi, Toshinori; Stoffers, Doris A.; Doliba, Nicolai M.
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errSave
AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics
errNATURE COMMUNICATIONS
IF15.7
err2024-05-03
err3
errOAAI
errMongia, Aanchal; Zohora, Fatema Tuz; Burget, Noah G.; Zhou, Yeqiao; Saunders, Diane C.; Wang, Yue J.; Brissova, Marcela; Powers, Alvin C.; Kaestner, Klaus H.; Vahedi, Golnaz; Naji, Ali; Schwartz, Gregory W.; Faryabi, Robert B.
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errSave
Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets
errCELL REPORTS MEDICINE
IF10.6
err2024-05-01
err2
errOAAI
errPatil, Abhijeet R.; Schug, Jonathan; Liu, Chengyang; Lahori, Deeksha; Descamps, Helene C.; Naji, Ali; Kaestner, Klaus H.; Faryabi, Robert B.; Vahedi, Golnaz
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errSave
NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing
errBMC GENOMICS
IF3.7
err2024-04-30
err0
errOAAI
errXie, Gengqiang; Toledo, Maria Pilar; Hu, Xue; Yong, Hyo Jeong; Sanchez, Pamela Sandoval; Liu, Chengyang; Naji, Ali; Irianto, Jerome; Wang, Yue J.
errShare
errSave
Circulating T cell specific extracellular vesicle profiles in cardiac allograft acute cellular rejection
errAMERICAN JOURNAL OF TRANSPLANTATION
IF8.2
err2024-03-01
err1
PREAI
errKorutla, Laxminarayana; Hoffman, Jessica R.; Rostami, Susan; Hu, Robert; Korutla, Varun; Markmann, Caroline; Mullan, Clancy; Sotolongo, Alex; Habertheuer, Andreas; Romano, Connie; Acker, Michael; Sen, Sounok; Agarwal, Divyansh; Jayaraman, Arun; Li, Bo; Davis, Michael E.; Naji, Ali; Vallabhajosyula, Prashanth
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errSave
A fetal wound healing program after intrauterine bile duct injury may contribute to biliary atresia
errJOURNAL OF HEPATOLOGY
IF33
err2023-12-01
err9
errOAAI
errde Jong, Iris E. M.; Hunt, Mallory L.; Chen, Dongning; Du, Yu; Llewellyn, Jessica; Gupta, Kapish; Li, David; Erxleben, Dorothea; Rivas, Felipe; Hall, Adam R.; Furth, Emma E.; Naji, Ali; Liu, Chengyang; Dhand, Abhishek; Burdick, Jason A.; Davey, Marcus G.; Flake, Alan W.; Porte, Robert J.; Russo, Pierre A.; Gaynor, J. William; Wells, Rebecca G.
errShare
errSave
Immunotherapy targeting B cells and long-lived plasma cells effectively eliminates pre-existing donor-specific allo-antibodies
errCELL REPORTS MEDICINE
IF10.6
err2023-12-01
err5
errOAAI
errZhang, Zheng; Markmann, Caroline; Yu, Ming; Agarwal, Divyansh; Rostami, Susan; Wang, Wei; Liu, Chengyang; Zhao, Huiwu; Ochoa, Trini; Parvathaneni, Kalpana; Xu, Xiaoming; Li, Eric; Gonzalez, Vanessa; Khadka, Roman; Hoffmann, Jennifer; Knox, James J.; Scholler, John; Marcellus, Brooke; Allman, David; Fraietta, Joseph A.; Samelson-Jones, Benjamin; Milone, Michael C.; Monos, Dimitri; Garfall, Alfred L.; Naji, Ali; Bhoj, Vijay G.
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Research Directions

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Co-authors
Cooperation Journals
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Francis S. Collins
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Steven G. Deeks
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David D. Ho
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