Hongkai Ji

12.6k citations

126 papers · 7.1k indexed · 4 hit papers · h-index 37

Impact in

Aging top 1%
Molecular Biology top 1%
- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- FOXO transcription factor regulation
- Gene expression and cancer classification
- Hedgehog Signaling Pathway Studies
- Pluripotent Stem Cells Research

Papers in

Molecular Biology 88
- Genomics and Chromatin Dynamics 32
- Epigenetics and DNA Methylation 20
- Gene expression and cancer classification 19
- Single-cell and spatial transcriptomics 18
- RNA Research and Splicing 13
- Hedgehog Signaling Pathway Studies 9
- Gene Regulatory Network Analysis 8
Obstetrics and Gynecology 6

Co-authors: Zhicheng Ji Wing Hung Wong Steven A. Vokes Wing H. Wong Wenxiu Ma Andrew P. McMahon Hui Jiang R Myers
Journals: Nature Communications (9 papers)Bioinformatics (7 papers)Nucleic Acids Research (6 papers)Cell (4 papers)Proceedings of the National Academy of Sciences (4 papers)
Partner nations: United States China Taiwan

In The Last Decade

Hongkai Ji

123 papers receiving 7.1k citations

Hit Papers

align trajectories log scale

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis 2016 · 397 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2016 Nucleic Acids Research
2010 Developmental Cell
2008 Nature Biotechnology
2007 Cell

Peers

Countries citing papers authored by Hongkai Ji

Since Specialization

Citations

This map shows the geographic impact of Hongkai Ji's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Hongkai Ji with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Hongkai Ji more than expected).

Fields of papers citing papers by Hongkai Ji

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Hongkai Ji. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Hongkai Ji. The network helps show where Hongkai Ji may publish in the future.

Co-authors

The 25 scholars most cited alongside Hongkai Ji, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Hongkai Ji Line = papers co-authored together Hongkai Ji links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	TFE3 fusion oncoprotein condensates drive transcriptional reprogramming and cancer progression in translocation renal cell carcinoma Cell Reports ·Choon Leng So, Ye Jin Lee, Bujamin Vokshi, Wanlu Chen, Binglin Huang, Emily De Sousa, Yangzhenyu Gao, Marie E. Portuallo, Sumreen Begum, Kasturee Jagirdar, W. Marston Linehan, Vito W. Rebecca, Hongkai Ji, Eneda Toska, Danfeng Cai	2025	1
2	Maternal exposure to per- and polyfluoroalkyl substances and epitope level antibody response to vaccines against measles and rubella in children from the Boston birth cohort Environment International ·Xiumei Hong, William R. Morgenlander, Kari C. Nadeau, Guoying Wang, Pamela A Frischmeyer-Guerrerio, Colleen Pearson, William G. Adams, Hongkai Ji, H. Benjamin Larman, Xiaobin Wang	2025	1
3	Metabolomic profiles during early childhood and risk of food allergies and asthma in multiethnic children from a prospective birth cohort Journal of Allergy and Clinical Immunology ·Xiumei Hong, Kari C. Nadeau, Guoying Wang, Ben Larman, Kellie N. Smith, Colleen Pearson, Hongkai Ji, Pamela A. Frischmeyer‐Guerrerio, Liming Liang, Frank B. Hu, Xiaobin Wang	2024	6
4	Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo Nature Communications ·Xu Liao, Lican Kang, Yihao Peng, Xiaoran Chai, Peng Xie, Chengqi Lin, Hongkai Ji, Yuling Jiao, Jin Liu	2024	1
5	Emergency Myelopoiesis Distinguishes Multisystem Inflammatory Syndrome in Children From Pediatric Severe Coronavirus Disease 2019 The Journal of Infectious Diseases ·Katerina Roznik, T. Andargie, T Scott Johnston, Oren Gordon, Yi Wang, Nadine Peart Akindele, Deborah Persaud, Annukka A.R. Antar, Yukari C. Manabe, Weiqiang Zhou, Hongkai Ji, Sean Agbor-Enoh, Andrew H. Karaba, Elizabeth A. Thompson, Andrea L. Cox	2024	0
6	Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Optic Nerve Crush and Experimental Glaucoma International Journal of Molecular Sciences ·Casey Keuthan, Julie Schaub, Meihan Wei, Weixiang Fang, Sarah Quillen, Elizabeth Kimball, Thomas V. Johnson, Hongkai Ji, Donald J. Zack, Harry A. Quigley	2023	11
7	Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children Journal of Clinical Investigation ·T. Andargie, Katerina Roznik, Neelam Redekar, Tom Hill, Weiqiang Zhou, Zainab Apalara, Hyesik Kong, Oren Gordon, Rohan Meda, Woojin Park, Trevor S. Johnston, Yi Wang, Sheila M. Brady, Hongkai Ji, Jack A. Yanovski, Moon Kyoo Jang, Clarence M. Lee, Andrew H. Karaba, Andrea L. Cox, Sean Agbor-Enoh	2023	7
8	Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects Nature Communications ·Guanghao Qi, Benjamin J. Strober, Joshua M Popp, Rebecca Keener, Hongkai Ji, Alexis Battle	2023	12
9	NF-κB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells Nature Immunology ·Mingming Zhao, Prashant Chauhan, Cheryl A. Sherman‐Baust, Amit Singh, Mary Kaileh, Krystyna Mazan-Mamczarz, Hongkai Ji, Jaimy Joy, Satabdi Nandi, Supriyo De, Yongqing Zhang, Jinshui Fan, Kevin G. Becker, P’ng Loke, Weiqiang Zhou, Ranjan Sen	2023	14
10	Repeated exposure to heterologous hepatitis C viruses associates with enhanced neutralizing antibody breadth and potency Journal of Clinical Investigation ·Nicole Frumento, Alexis Figueroa, Tingchang Wang, Muhammad Zahid, Shuyi Wang, Guido Massaccesi, Georgia Stavrakis, James E. Crowe, Andrew I. Flyak, Hongkai Ji, Stuart C. Ray, George M. Shaw, Andrea L. Cox, Justin R. Bailey	2022	9
11	EGFR Activates a TAZ-Driven Oncogenic Program in Glioblastoma Cancer Research ·Minling Gao, Yi Fu, Weiqiang Zhou, Gege Gui, Bachuchu Lal, Yunqing Li, Shuli Xia, Hongkai Ji, Charles G. Eberhart, John Laterra, Mingyao Ying	2021	14
12	Fetal lipidome and incident risk of food allergy: A prospective birth cohort study Pediatric Allergy and Immunology ·Xiumei Hong, Liming Liang, Hongkai Ji, Pamela A. Frischmeyer‐Guerrerio, Guoying Wang, Colleen Pearson, Meir J. Stampfer, Frank B. Hu, Xiaobin Wang	2021	6
13	Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology Clinical Infectious Diseases ·Andrew H. Karaba, Weiqiang Zhou, Leon L. Hsieh, Alexis Figueroa, Guido Massaccesi, Richard E. Rothman, Katherine Fenstermacher, Lauren Sauer, Kathryn Shaw‐Saliba, Paul W. Blair, Matthew L. Robinson, Sherry Leung, Russell Wesson, Nada Alachkar, Ramy El–Diwany, Hongkai Ji, Andrea L. Cox	2021	29
14	Profiling Chromatin Accessibility at Single-Cell Resolution Genomics Proteomics & Bioinformatics ·Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo Anne Stratton, Arzina Jaffer, Nizar J. Bahlis, A. Sorana Morrissy, Jeff Biernaskie	2021	26
15	Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis Nature Biomedical Engineering ·Michael A. Koldobskiy, Garrett Jenkinson, Jordi Abante, Varenka A. Rodriguez DiBlasi, Weiqiang Zhou, Elisabet Pujadas, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, Challice L. Bonifant, Karen R. Rabin, Patrick A. Brown, Hongkai Ji, John Goutsias, Andrew P. Feinberg	2021	13
16	A prospective cohort study on the intersectionality of obesity, chronic disease, social factors, and incident risk of COVID-19 in US low-income minority middle-age mothers International Journal of Obesity ·Guoying Wang, Dana M. Foney, Jessica DiBari, Xiumei Hong, Nakiya Showell, Kwang Sik Kim, Hongkai Ji, Colleen Pearson, Gabrielle Mirolli, Serena Rusk, Josh Sharfstein, Tina L. Cheng, Barry Zuckerman, Xiaobin Wang	2021	7
17	Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells Nature Communications ·Xitiz Chamling, Alyssa Kallman, Weixiang Fang, Cynthia Berlinicke, Joseph Mertz, Prajwal Devkota, Itzy E. Morales Pantoja, Matthew D. Smith, Zhicheng Ji, Calvin Chang, Aniruddha M. Kaushik, Liben Chen, Katharine A. Whartenby, Peter A. Calabresi, Hai‐Quan Mao, Hongkai Ji, Tza‐Huei Wang, Donald J. Zack	2021	51
18	Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina Proceedings of the National Academy of Sciences ·David T. White, S. Sengupta, Meera Saxena, Qingguo Xu, Justin Hanes, Ding Ding, Hongkai Ji, Jeff S. Mumm	2017	114
19	HOXB7 Is an ERα Cofactor in the Activation of HER2 and Multiple ER Target Genes Leading to Endocrine Resistance Cancer Discovery ·Kideok Jin, Sunju Park, Wei Wen Teo, Preethi Korangath, Soonweng Cho, Takahiro Yoshida, Balázs Győrffy, Chirayu Goswami, Harikrishna Nakshatri, Leigh-Ann Cruz, Weiqiang Zhou, Hongkai Ji, Ying Su, Muhammad B. Ekram, Zhengsheng Wu, Tao Zhu, Kornélia Polyák, Saraswati Sukumar	2015	67
20	Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning Development ·Steven A. Vokes, Hongkai Ji, Scott McCuine, Toyoaki Tenzen, Shane Giles, Sheng Zhong, William J.R. Longabaugh, Eric H. Davidson, Wing Hung Wong, Andrew P. McMahon	2007	226

About Hongkai Ji

Hongkai Ji is a scholar working on Molecular Biology, Obstetrics and Gynecology, Cancer Research, Pediatrics, Perinatology and Child Health and Aging, having authored 126 papers that have together received 7.1k indexed citations. Recurring topics across this work include Genomics and Chromatin Dynamics (32 papers), Epigenetics and DNA Methylation (20 papers), Gene expression and cancer classification (19 papers), Single-cell and spatial transcriptomics (18 papers), RNA Research and Splicing (13 papers), Birth, Development, and Health (11 papers), Hedgehog Signaling Pathway Studies (9 papers) and Gene Regulatory Network Analysis (8 papers). The work is most often cited by research in Aging (193 citations), Molecular Biology (5.4k citations), Cancer Research (686 citations), Plant Science (1.2k citations) and Developmental Neuroscience (132 citations). Hongkai Ji has collaborated with scholars based in United States, China and Taiwan. Frequent co-authors include Zhicheng Ji, Wing Hung Wong, Steven A. Vokes, Wing H. Wong, Wenxiu Ma, Andrew P. McMahon, Hui Jiang, R Myers, David S. Johnson and Weiqiang Zhou. Their work appears in journals such as Nature Communications, Bioinformatics, Nucleic Acids Research, Cell and Proceedings of the National Academy of Sciences.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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