Hongxu Ding - Publications, H-index & Citations

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Hongxu Ding

Department of Pharmacy Practice and Science

15H-index

72Paper Count

1.4KCitation Count

Published Papers 24

Publication Date

A reference-guided iterative approach to polish the nanopore sequencing basecalling for therapeutic RNA quality control

Communications Biology

IF5.1

2025-10-01

OAAI

Ziyuan Wang; Mei-Juan Tu; Ziyang Liu; Katherine K. Wang; Yinshan Fang; Ning Hao; Hao Helen Zhang; Jianwen Que; Xiaoxiao Sun; Ai-Ming Yu; Hongxu Ding

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Impact of Posttranscriptional Modifications in Novel Bioengineered RNAs

JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

IF3.8

2025-03-01

PREAI

Wang, Katherine; Tu, Mei-Juan; Wang, Ziyuan; Limbach, Patrick A.; Ding, Hongxu; Yu, Ai-Ming

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Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection

NATURE COMMUNICATIONS

IF15.7

2024-08-21

OAAI

Wang, Ziyuan; Fang, Yinshan; Liu, Ziyang; Hao, Ning; Zhang, Hao Helen; Sun, Xiaoxiao; Que, Jianwen; Ding, Hongxu

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General Capillary Endothelial Cells Undergo Reprogramming Into Arterial Endothelial Cells in Pulmonary Hypertension Through HIF-2α/Notch4 Pathway

CIRCULATION

IF38.6

2024-07-30

OAAI

Liu, Bin; Yi, Dan; Xia, Xiaomei; Ramirez, Karina; Zhao, Hanqiu; Cao, Yanhong; Tripathi, Ankit; Dong, Ryan; Gao, Anton; Ding, Hongxu; Qiu, Shenfeng; Kalinichenko, Vladimir V.; Zhao, You-Yang; Fallon, Michael B.; Dai, Zhiyu

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Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes

CELL REPORTS METHODS

IF4.5

2024-06-01

OAAI

Xue, Yuanqing; Friedl, Verena; Ding, Hongxu; Wong, Christopher K.; Stuart, Joshua M.

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The manatee variational autoencoder model for predicting gene expression alterations caused by transcription factor perturbations

SCIENTIFIC REPORTS

IF3.9

2024-05-23

OAAI

Yang, Ying; Seninge, Lucas; Wang, Ziyuan; Oro, Anthony; Stuart, Joshua M.; Ding, Hongxu

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(3-cell Jagged1 is sufficient but not necessary for islet Notch activity and insulin secretory defects in obese mice

MOLECULAR METABOLISM

IF6.6

2024-03-01

OAAI

Suda, Nina; Bartolome, Alberto; Liang, Jiani; Son, Jinsook; Yagishita, Yoko; Siebel, Christian; Accili, Domenico; Ding, Hongxu; Pajvani, Utpal B.

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Identification and pharmacological targeting of treatment-resistant, stem-like breast cancer cells for combination therapy

CANCER RESEARCH

IF16.6

2024-02-01

PREAI

Worley, Jeremy; Noh, Heeju; You, Daoqi; Turunen, Mikko M.; Ding, Hongxu; Paull, Evan; Griffin, Aaron T.; Grunn, Adina; Guillan, Kristina; Bush, Erin C.; Brosius, Samantha J.; Mundi, Prabhjot S.; Sims, Peter; Dalerba, Piero; Dela Cruz, Filemon S.; Kung, Andrew L.; Califano, Andrea

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E2F1 Mediates SOX17 Deficiency-Induced Pulmonary Hypertension

HYPERTENSION

IF8.2

2023-11-01

OAAI

Yi, Dan; Liu, Bin; Ding, Hongxu; Li, Shuai; Li, Rebecca; Pan, Jiakai; Ramirez, Karina; Xia, Xiaomei; Kala, Mrinalini; Ye, Qinmao; Lee, Won Hee; Frye, Richard E.; Wang, Ting; Zhao, Yutong; Knox, Kenneth S.; Glembotski, Christopher C.; Fallon, Michael B.; Dai, Zhiyu

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Development and validation of SSR markers related to flower color based on full-length transcriptome sequencing in Chrysanthemum

SCIENTIFIC REPORTS

IF3.9

2022-12-24

OAAI

Shi, Zhongya; Zhao, Wenqian; Li, Zhongai; Kang, Dongru; Ai, Penghui; Ding, Hongxu; Wang, Zicheng

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Airway basal cells show regionally distinct potential to undergo metaplastic differentiation

ELIFE

IF0

2022-09-30

OAAI

Zhou, Yizhuo; Yang, Ying; Guo, Lihao; Qian, Jun; Ge, Jian; Sinner, Debora; Ding, Hongxu; Califano, Andrea; Cardoso, Wellington, V

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Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

ELIFE

IF0

2022-04-06

OAAI

Bailey, Andrew D.; Talkish, Jason; Ding, Hongxu; Igel, Haller; Duran, Alejandra; Mantripragada, Shreya; Paten, Benedict; Ares, Manuel

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Notch-mediated Ephrin signaling disrupts islet architecture and β cell function

JCI INSIGHT

IF6.1

2022-03-22

OAAI

Bartolome, Alberto; Suda, Nina; Yu, Junjie; Zhu, Changyu; Son, Jinsook; Ding, Hongxu; Califano, Andrea; Accili, Domenico; Pajvani, Utpal B.

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BACH2 inhibition reverses β cell failure in type 2 diabetes models

JOURNAL OF CLINICAL INVESTIGATION

IF13.6

2021-12-15

OAAI

Son, Jinsook; Ding, Hongxu; Farb, Thomas B.; Efanov, Alexander M.; Sun, Jiajun; Core, Julie L.; Syed, Samreen K.; Lei, Zhigang; Wang, Qidi; Accili, Domenico; Califano, Andrea

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Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

NATURE COMMUNICATIONS

IF15.7

2021-11-11

OAAI

Ding, Hongxu; Anastopoulos, Ioannis; Bailey, Andrew D.; Stuart, Joshua; Paten, Benedict

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VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics

NATURE COMMUNICATIONS

IF15.7

2021-09-28

OAAI

Seninge, Lucas; Anastopoulos, Ioannis; Ding, Hongxu; Stuart, Joshua

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Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines

PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

IF3.3

2021-07-06

OAAI

Kang, Dong-ru; Zhu, Yi; Li, Shuai-lei; Ai, Peng-hui; Khan, Muhammad Ayoub; Ding, Hong-xu; Wang, Ying; Wang, Zi-cheng

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Biological process activity transformation of single cell gene expression for cross-species alignment

NATURE COMMUNICATIONS

IF15.7

2019-10-25

OAAI

Ding, Hongxu; Blair, Andrew; Yang, Ying; Stuart, Joshua M.

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Decoding the immunologic landscape of human clear cell renal carcinoma

CANCER RESEARCH

IF16.6

2019-07-01

PREAI

Chowdhury, Nivedita; Obradovic, Aleksandar; Aggen, David; Wang, Vinson; Guo, Xinzheng; DeCastro, Guarionex J.; Ding, Hongxu; Califano, Andrea; Drake, Charles G.

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Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer

CANCER DISCOVERY

IF33.3

2019-05-01

OAAI

Slotkin, Emily K.; Diolaiti, Daniel; Shukla, Neerav N.; Dela Cruz, Filemon S.; Clark, Jennifer J.; Gundem, Gunes; Yellapantula, Venkata D.; Levine, Max F.; You, Daoqi; Ma, Peilin; Pachhal, Sagarika; Sanchez, Glorymar Ibanez; Benayed, Ryma; Jungbluth, Achim A.; Smyth, Lillian M.; Mauguen, Audrey; Gushterova, Irena; Ding, Hongxu; Spraggon, Lee; Darnell, Robert; Califano, Andrea; Ladanyi, Marc; Papaemmanuil, Elli; Kung, Andrew L.; Hyman, David M.; Roberts, Stephen S.

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Research Directions