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Pengyi Yang

the university of sydney

46H-index
194Paper Count
7.5KCitation Count
Published Papers 75
Publication Date
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SwitchClass distinguishes baseline- and perturbation-aligned features across intermediate molecular states
errCell Reports Methods
IF4.5
err2026-08-12
err0
errOAAI
errDi Xiao; Siqu Long; Pengyi Yang
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Computational blueprints for cell fate programming
errStem Cell Reports
IF5.1
err2026-05-28
err0
errOAAI
errPengyi Yang
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Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids
errNature Communications
IF15.7
err2026-04-25
err0
errOAAI
errBenjamin Y. Lim; Carissa Chen; Anna Fredericks; Elham Nilli; Santiago Mesa Mora; Megan Weatherstone; To Ha Loi; Peter Newman; Nader Aryamanesh; Hala Zreiqat; Patrick Tam; Pengyi Yang; Anai Gonzalez-Cordero
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Interpretable deep generative ensemble learning for single-cell omics with Hydra
errMolecular Systems Biology
IF7.7
err2026-04-11
err0
errOAAI
errManoj M Wagle; Chunlei Liu; Zunpeng Liu; Yongheng Wang; Manolis Kellis; Ellis Patrick; Pengyi Yang
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Phosphoproteomics of aged insulin-resistant bone identifies P70S6K phosphorylation of AFF4 as a gene-specific transcriptional regulator
errNature Communications
IF15.7
err2025-12-31
err0
errOAAI
errMriga Dutt; Luoping Liao; Hani Jieun Kim; Ronnie Blazev; Audrey Chan; Hitesh Kore; Ayenachew Bezawork-Geleta; Li Dong; Isela Sarahi Rivera; Natalie K. Y. Wee; Jeffrey Molendijk; Julian P. H. Wong; Vanessa R. Haynes; Veronica Uribe; Gordon S. Lynch; Kelly A. Smith; Magdalene K. Montgomery; Matthew J. Watt; Pengyi Yang; Garron T. Dodd; Stephin J. Vervoort; Natalie A. Sims; Benjamin L. Parker
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Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma
errNature Communications
IF15.7
err2025-12-15
err0
errOAAI
errGeorge L. Joun; Emma G. Kempe; Brianna Chen; Jayden R. Sterling; Ramzi H. Abbassi; Dana Friess; Matthew Singleton; Chandra Choudhury; Oana C. Marian; W. Daniel du Preez; Ariadna Recasens; Teleri Clark; Tian Y. Du; Jason K. K. Low; Hani Kim; Pengyi Yang; Jasmine Khor; Monira Hoque; Dinesh C. Indurthi; Mani Kuchibhotla; Ranjith Palanisamy; William T. Jorgensen; Andrew P. Montgomery; Jennifer R. Baker; Sarah L. Higginbottom; Eva Tomaskovic-Crook; Jeremy M. Crook; Lipin Loo; Bryan W. Day; G. Gregory Neely; Ernesto Guccione; Terrance G. Johns; Michael Kassiou; Yuchen Feng; Lachlan Harris; Anthony S. Don; Lenka Munoz
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Connecting cilium, stress response, and proteostasis abnormalities inform variant and therapy assessment in RPGRIP1 retinal organoids
errStem Cell Reports
IF5.1
err2025-11-20
err0
errOAAI
errTo Ha Loi; Anson Cheng; Hani Jieun Kim; Milan Fernando; Benjamin M. Nash; Nader Aryamanesh; John R. Grigg; Pengyi Yang; Anai Gonzalez-Cordero; Robyn V. Jamieson
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BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures
errScience Advances
IF12.5
err2025-10-31
err0
PREAI
errHilary S. Y. Toh; Lisheng Xu; Carissa Chen; Pengyi Yang; Alfred X. Sun; John F. Ouyang
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errSave
Pinoresinol Diglucoside Alleviates Ovariectomy-induced Osteoporosis by Modulating the “Microbiota–Gut–Bone” Axis
errBiochemical and Biophysical Research Communications
IF2.2
err2025-10-25
err0
PREAI
errNing Li; Huan Pei; Miao Luo; Li Deng; Xiaoliang Zhang; Cong Ma; Funeng Wang; Pengyi Yang; Deguang Li; Lvyu Li; Yuan Ma
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errSave
Multitask benchmarking of single-cell multimodal omics integration methods
errNature Methods
IF32.1
err2025-10-13
err0
errOAAI
errChunlei Liu; Sichang Ding; Hani Jieun Kim; Siqu Long; Di Xiao; Shila Ghazanfar; Pengyi Yang
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errSave
SpaNorm: spatially-aware normalization for spatial transcriptomics data
errGENOME BIOLOGY
IF9.4
err2025-04-29
err0
errOAAI
errSalim, Agus; Bhuva, Dharmesh D.; Chen, Carissa; Tan, Chin Wee; Yang, Pengyi; Davis, Melissa J.; Yang, Jean Y. H.
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Lineage contribution of the mesendoderm progenitors in the gastrulating mouse embryo
errDevelopmental Cell
IF8.7
err2025-03-24
err0
PREAI
errV. Pragathi Masamsetti; Nazmus Salehin; Hani Jieun Kim; Nicole Santucci; Megan Weatherstone; Riley McMahon; Lee L. Marshall; Hilary Knowles; Jane Sun; Josh B. Studdert; Nader Aryamanesh; Ran Wang; Naihe Jing; Pengyi Yang; Pierre Osteil; Patrick P.L. Tam
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errSave
Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation
errCELL REPORTS
IF6.9
err2024-05-01
err0
errOAAI
errChen, Carissa; Lee, Scott; Zyner, Katherine G.; Fernando, Milan; Nemeruck, Victoria; Wong, Emilie; Marshall, Lee L.; Wark, Jesse R.; Aryamanesh, Nader; Tam, Patrick P. L.; Graham, Mark E.; Gonzalez-Cordero, Anai; Yang, Pengyi
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errSave
Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm
errDEVELOPMENTAL CELL
IF8.7
err2024-03-01
err1
PREAI
errWu, Zhixuan; Shen, Sophie; Mizikovsky, Dalia; Cao, Yuanzhao; Naval-Sanchez, Marina; Tan, Siew Zhuan; Alvarez, Yanina D.; Sun, Yuliangzi; Chen, Xiaoli; Zhao, Qiongyi; Kim, Daniel; Yang, Pengyi; Hill, Timothy A.; Jones, Alun; Fairlie, David P.; Pebay, Alice; Hewitt, Alex W.; Tam, Patrick P. L.; White, Melanie D.; Nefzger, Christian M.; Palpant, Nathan J.
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Evaluating spatially variable gene detection methods for spatial transcriptomics data
errGENOME BIOLOGY
IF9.4
err2024-01-15
err3
errOAAI
errChen, Carissa; Kim, Hani Jieun; Yang, Pengyi
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Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis
errGENOME BIOLOGY
IF9.4
err2023-11-10
err4
errOAAI
errHuang, Hao; Liu, Chunlei; Wagle, Manoj M.; Yang, Pengyi
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SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data
errgenomics proteomics bioinformatics
IF2.8
err2023-11-06
err0
errOAAI
errXiao, Di; Lin, Michael; Liu, Chunlei; Geddes, Thomas A.; Burchfield, James G.; Parker, Benjamin L.; Humphrey, Sean J.; Yang, Pengyi
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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
errNPJ SYSTEMS BIOLOGY AND APPLICATIONS
IF3.5
err2023-10-19
err23
errOAAI
errKim, Daniel; Tran, Andy; Kim, Hani Jieun; Lin, Yingxin; Yang, Jean Yee Hwa; Yang, Pengyi
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Vascular senescence and leak are features of the early breakdown of the blood-brain barrier in Alzheimer's disease models
errGEROSCIENCE
IF5.4
err2023-10-02
err23
errOAAI
errTing, Ka Ka; Coleman, Paul; Kim, Hani Jieun; Zhao, Yang; Mulangala, Jocelyne; Cheng, Ngan Ching; Li, Wan; Gunatilake, Dilini; Johnstone, Daniel M.; Loo, Lipin; Neely, G. Gregory; Yang, Pengyi; Gotz, Jurgen; Vadas, Mathew A.; Gamble, Jennifer R.
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Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2023-04-24
err2
errOAAI
errCao, Yue; Ghazanfar, Shila; Yang, Pengyi; Yang, Jean
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Research Directions

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Co-authors
Cooperation Journals
M
Matthias Mann
H-index: 250 · Papers: 1.4K
M
Manolis Kellis
H-index: 139 · Papers: 1.1K
D
David E. James
H-index: 108 · Papers: 576
T
Terence P. Speed
H-index: 108 · Papers: 640
E
Erik A. Richter
H-index: 107 · Papers: 660
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