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Zhicheng Ji

Department of Biostatistics and Bioinformatics

29H-index
175Paper Count
4.4KCitation Count
Published Papers 48
Publication Date
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LLM-based cell type annotation harmonization across single-cell studies using GCTHarmony
errGenome Biology
IF9.4
err2026-08-04
err0
errOAAI
errXingyuan Zhang; Zhicheng Ji
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errSave
Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity
errBioinformatics
IF5.4
err2026-04-22
err0
errOAAI
errHaotian Zhuang; Xin Gai; Anru R Zhang; Wenpin Hou; Zhicheng Ji; Pixu Shi; null
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errSave
PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns
errGenome Biology
IF9.4
err2026-02-12
err0
errOAAI
errHaotian Zhuang; Zhicheng Ji
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errSave
Identifying cell-type-specific spatially variable genes with ctSVG
errGenome Biology
IF9.4
err2025-12-08
err0
errOAAI
errHaotian Zhuang; Xinyi Shang; Wenpin Hou; Zhicheng Ji
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errSave
Transcriptome-wide association studies at cell-state level using single-cell eQTL data
errCell Genomics
IF9
err2025-11-03
err0
errOAAI
errGuanghao Qi; Eardi Lila; Zhicheng Ji; Ali Shojaie; Alexis Battle; Wei Sun
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errSave
Advancing biological understanding of cellular senescence with computational multiomics
errNature Genetics
IF0
err2025-09-15
err0
PREAI
errSheng Li; Paula A. Agudelo Garcia; Constantin Aliferis; Michael J. Becich; Jazmin Calyeca; Benjamin D. Cosgrove; Jennifer Elisseeff; Negin Farzad; Elana J. Fertig; Carolyn Glass; Liangcai Gu; Qianjiang Hu; Zhicheng Ji; Melanie Königshoff; Nathan K. LeBrasseur; Dongmei Li; Anjun Ma; Qin Ma; Vilas Menon; Jacob T. Mitchell; Ana L. Mora; Sushma Nagaraj; Andrew C. Nelson; Laura J. Niedernhofer; Mauricio Rojas; Hash Brown Taha; Jinhua Wang; Siyuan Wang; Pei-Hsun Wu; Jichun Xie; Ming Xu; Miao Yu; Xu Zhang; Yue Zhao; Peter D. Adams; Cristina Aguayo-Mazzucato; Darren J. Baker; Christopher Benz; David A. Bernlohr; Marta Bueno; Jin Chen; Bennett G. Childs; Jeffrey H. Chuang; Dongjun Chung; Mythili Dileepan; Li Ding; Mingze Dong; Francesca Duncan; Archibald Enninful; William F. Flynn; Ana Catarina Franco; David Furman; Vesna Garovic; Stephanie Halene; Allison B. Herman; Ann V. Hertzel; Kanako Iwasaki; Hyeongseon Jeon; Jeon Woong Kang; Shilpita Karmakar; James L. Kirkland; Ron Korstanje; Erich Kummerfeld; Jun Hee Lee; Yang Liu; Yao Lu; Jose Lugo-Martinez; Helene Martini; Simon Melov; Nicolas Musi; João F. Passos; Samuel T. Peters; Irfan Rahman; Ramalakshmi Ramasamy; Alexandra N. Rindone; Paul D. Robbins; Paul Robson; Jhonny Rodriguez-Lopez; Lorena Rosas; Nadia Rosenthal; Marissa J. Schafer; Birgit Schilling; Elizabeth L. Schmidt; Kevin Schneider; Kaustav Sengupta; Jian Shu; Peter T. C. So; Li Sun; Tamar Tchkonia; Marcos G. Teneche; Natalia Vanegas; Julia Wang; Juan Xie; Shanshan Yin; Ke Zhang; Quan Zhu; Rong Fan
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Smmit: A pipeline for integrating multiple single-cell multi-omics samples
errComputational and Structural Biotechnology Journal
IF4.1
err2025-09-01
err0
errOAAI
errChangxin Wan; Zhicheng Ji
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errSave
Benchmarking large language models for genomic knowledge with GeneTuring
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2025-09-01
err0
errOAAI
errShang, Xinyi; Liao, Xu; Ji, Zhicheng; Hou, Wenpin
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errSave
Assessing Large Multimodal Models for One-Shot Learning and Interpretability in Biomedical Image Classification
errADVANCED INTELLIGENT SYSTEMS
IF6.1
err2025-04-06
err0
errOAAI
errHou, WP; Liu, Q; Ma, HF; Qu, YL; Ji, ZC
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errSave
Comparing Large Language Models and Human Programmers for Generating Programming Code
errADVANCED SCIENCE
IF14.1
err2024-12-30
err0
errOAAI
errHou, WP; Ji, ZC
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errSave
A systematic evaluation of computational methods for cell segmentation
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2024-08-18
err0
errOAAI
errWang, Yuxing; Zhao, Junhan; Xu, Hongye; Han, Cheng; Tao, Zhiqiang; Zhou, Dawei; Geng, Tong; Liu, Dongfang; Ji, Zhicheng
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errSave
SifiNet: a robust and accurate method to identify feature gene sets and annotate cells
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-04-22
err0
errOAAI
errGao, Qi; Ji, Zhicheng; Wang, Liuyang; Owzar, Kouros; Li, Qi-Jing; Chan, Cliburn; Xie, Jichun
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errSave
Spatial transcriptomics reveals segregation of tumor cell states in glioblastoma and marked immunosuppression within the perinecrotic niche
errACTA NEUROPATHOLOGICA COMMUNICATIONS
IF5.7
err2024-04-22
err2
errOAAI
errLiu, Mengyi; Ji, Zhicheng; Jain, Vaibhav; Smith, Vanessa L.; Hocke, Emily; Patel, Anoop P.; McLendon, Roger E.; Ashley, David M.; Gregory, Simon G.; Lopez, Giselle Y.
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errSave
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
errNATURE METHODS
IF32.1
err2024-03-25
err24
errOAAI
errHou, Wenpin; Ji, Zhicheng
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errSave
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples
errNATURE COMMUNICATIONS
IF15.7
err2023-11-10
err13
errOAAI
errHou, Wenpin; Ji, Zhicheng; Chen, Zeyu; Wherry, E. John; Hicks, Stephanie C.; Ji, Hongkai
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errSave
Secreted FrizzledRelated Protein 1 Mediates Adipogenic Differentiation of Vascular Cell Adhesion Protein 1 Fibroadipogenic Progenitors in the Ischemic Limb
errCIRCULATION
IF38.6
err2023-11-07
err0
PREAI
errDai, Qunsheng; Wan, Changxin; Fei, Kaileen; Xu, Yueyuan; Peters, Derek; Garrett, Brianna; Otto, James; Kontos, Christopher D.; Ji, Zhicheng; Diao, Yarui; Southerland, Kevin W.
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Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response
errSCIENCE IMMUNOLOGY
IF16.3
err2023-09-29
err16
errOAAI
errDykema, Arbor G.; Zhang, Jiajia; Cheung, Laurene S.; Connor, Sydney; Zhang, Boyang; Zeng, Zhen; Cherry, Christopher M.; Li, Taibo; Caushi, Justina X.; Nishimoto, Marni; Munoz, Andrew J.; Ji, Zhicheng; Hou, Wenpin; Zhan, Wentao; Singh, Dipika; Zhang, Tianbei; Rashid, Rufiaat; Mitchell-Flack, Marisa; Bom, Sadhana; Tam, Ada; Ionta, Nick; Aye, Thet H. K.; Wang, Yi; Sawosik, Camille A.; Tirado, Lauren E.; Tomasovic, Luke M.; Vandyke, Derek; Spangler, Jamie B.; Anagnostou, Valsamo; Yang, Stephen; Spicer, Jonathan; Rayes, Roni; Taube, Janis; Brahmer, Julie R.; Forde, Patrick M.; Yegnasubramanian, Srinivasan; Ji, Hongkai; Pardoll, Drew M.; Smith, Kellie N.
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Nuclear PTEN Regulates Thymidylate Biosynthesis in Human Prostate Cancer Cell Lines
errMETABOLITES
IF3.7
err2023-08-11
err2
errOAAI
errLoh, Zoe N.; Wang, Mu-En; Wan, Changxin; Asara, John M.; Ji, Zhicheng; Chen, Ming
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errSave
DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat
errNEURON
IF15
err2023-04-01
err14
errOAAI
errLiu, Yang; Huang, Zhiyuan; Liu, Honghe; Ji, Zhicheng; Arora, Amit; Cai, Danfeng; Wang, Hongjin; Liu, Mingming; Simko, Eric A. J.; Zhang, Yanjun; Periz, Goran; Liu, Zhe; Wang, Jiou
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JAK-STAT activation contributes to cytotoxic T cell-mediated basal cell death in human chronic lung allograft dysfunction
errJCI INSIGHT
IF6.1
err2023-03-22
err7
errOAAI
errKhatri, Aaditya; Todd, Jamie L. .; Kelly, Fran L. .; Nagler, Andrew; Ji, Zhicheng; Jain, Vaibhav; Gregory, Simon G.; Weinhold, Kent J.; Palmer, Scott M.
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Research Directions

No research directions
Co-authors
Cooperation Journals
F
Frank B. Hu
H-index: 244 · Papers: 1.9K
J
Jedd D. Wolchok
H-index: 173 · Papers: 1.4K
D
Drew M. Pardoll
H-index: 164 · Papers: 892
E
E. John Wherry
H-index: 142 · Papers: 638
李丁 cover
李丁 (Li Ding)
H-index: 135 · Papers: 1.1K
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