Pengyi Yang

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Venues

Nature communications

Genome biology

Bioinformatics (Oxford, England)

Proteomics

Children's Medical Research Institute

University of Sydney (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Children's Medical Research Institute May 01 2019

Australia

Group Leader :: Computational Systems Biology Group

University of Sydney Jun 30 2017

Australia

Senior Lecturer and DECRA Fellow :: School of Mathematics and Statistics

University of Sydney Sep 01 2015 - Jun 29 2017

Australia

USyd Postdoctoral Research Fellow (DVC Research) :: School of Mathematics and Statistics

National Institutes of Health Jan 08 2013 - Aug 30 2015

United States

Research Fellow :: National Institute of Environmental Health Sciences; Stem Cells, Epigenetics & Gene Regulation; Systems Biology Group

Education History

University of Sydney

Australia

PHD :: School of Information Technologies

Publications

Manoj M Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
Interpretable deep learning in single-cell omics. Bioinformatics (Oxford, England) 40 (6) (2024)
Carissa Chen, Hani Jieun Kim, Pengyi Yang
Evaluating spatially variable gene detection methods for spatial transcriptomics data. Genome biology 25 (1) (2024)
Manoj M Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
Interpretable deep learning in single-cell omics. Bioinformatics (Oxford, England) 40 (6) (2024)
Carissa Chen, Hani Jieun Kim, Pengyi Yang
Evaluating spatially variable gene detection methods for spatial transcriptomics data. Genome biology 25 (1) (2024)
Manoj M Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
Interpretable deep learning in single-cell omics. Bioinformatics (Oxford, England) 40 (6) (2024)
Carissa Chen, Hani Jieun Kim, Pengyi Yang
Evaluating spatially variable gene detection methods for spatial transcriptomics data. Genome biology 25 (1) (2024)
Carissa Chen, Hani Jieun Kim, Pengyi Yang
Evaluating spatially variable gene detection methods for spatial transcriptomics data. Genome biology 25 (1) (2024)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Daniel Kim, Andy Tran, Hani Jieun Kim, Yingxin Lin, Jean Yee Hwa Yang, Pengyi Yang
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. NPJ systems biology and applications 9 (1) (2023)
Elijah Willie, Pengyi Yang, Ellis Patrick
The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data. Bioinformatics advances 3 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Chunlei Liu, Hao Huang, Pengyi Yang
Multi-task learning from multimodal single-cell omics with Matilda. Nucleic acids research (2023)
Di Xiao, Michael Lin, Chunlei Liu, Thomas A Geddes, James G Burchfield, Benjamin L Parker, Sean J Humphrey, Pengyi Yang
SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data. NAR genomics and bioinformatics 5 (4) (2023)
Hao Huang, Chunlei Liu, Manoj M Wagle, Pengyi Yang
Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis. Genome biology 24 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Daniel J Fazakerley, Julian van Gerwen, Kristen C Cooke, Xiaowen Duan, Elise J Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M Norris, Amber S Shun-Shion, James R Krycer, James G Burchfield, Pengyi Yang, Mark R Wade, Joseph T Brozinick, David E James, Sean J Humphrey
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nature communications 14 (1) (2023)
Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang, Jean Yee Hwa Yang
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinformatics (Oxford, England) 38 (20) (2022)
Andy Tran, Pengyi Yang, Jean Y H Yang, John Ormerod
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era. Briefings in functional genomics 21 (4) (2022)
Di Xiao, Hani Jieun Kim, Ignatius Pang, Pengyi Yang
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinformatics (Oxford, England) 38 (7) (2022)
Di Xiao, Carissa Chen, Pengyi Yang
Computational systems approach towards phosphoproteomics and their downstream regulation. Proteomics (2022)
Lijia Yu, Yue Cao, Jean Y H Yang, Pengyi Yang
Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data. Genome biology 23 (1) (2022)
Andy Tran, Pengyi Yang, Jean Yee Hwa Yang, John T Ormerod
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model. NAR genomics and bioinformatics 4 (1) (2022)
Yue Cao, Pengyi Yang, Jean Yee Hwa Yang
A benchmark study of simulation methods for single-cell RNA sequencing data. Nature communications 12 (1) (2021)
Ariadna Recasens, Sean J Humphrey, Michael Ellis, Monira Hoque, Ramzi H Abbassi, Brianna Chen, Mitchell Longworth, Elise J Needham, David E James, Terrance G Johns, Bryan W Day, Michael Kassiou, Pengyi Yang, Lenka Munoz
Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells. Cell death discovery 7 (1) (2021)
Dhirendra Kumar, Senthilkumar Cinghu, Andrew J Oldfield, Pengyi Yang, Raja Jothi
Decoding the function of bivalent chromatin in development and cancer. Genome research (2021)
Taiyun Kim, Owen Tang, Stephen T Vernon, Katharine A Kott, Yen Chin Koay, John Park, David E James, Stuart M Grieve, Terence P Speed, Pengyi Yang, Gemma A Figtree, John F O'Sullivan, Jean Yee Hwa Yang
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data. Nature communications 12 (1) (2021)
Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, Terence P Speed, David M Lin, Pengyi Yang, Jean Yee Hwa Yang
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Molecular systems biology 16 (6) (2021)
Pengyi Yang, Hao Huang, Chunlei Liu
Feature selection revisited in the single-cell era. Genome biology 22 (1) (2021)
Hani Jieun Kim, Kevin Y X Wang, Carissa Chen, Yingxin Lin, Patrick P L Tam, David M Lin, Jean Yee Hwa Yang, Pengyi Yang
Uncovering cell identity through differential stability with Cepo. Nature computational science 1 (12) (2021)
Sandeep Kaur, Timothy J Peters, Pengyi Yang, Laurence Don Wai Luu, Jenny Vuong, James R Krycer, Seán I O'Donoghue
Temporal ordering of omics and multiomic events inferred from time-series data. NPJ systems biology and applications 6 (1) (2020)
Ronnie Blazev, Christopher Ashwood, Jodie L Abrahams, Long H Chung, Deanne Francis, Pengyi Yang, Kevin I Watt, Hongwei Qian, Gregory A Quaife-Ryan, James E Hudson, Paul Gregorevic, Morten Thaysen-Andersen, Benjamin L Parker
Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development. Molecular & cellular proteomics : MCP (2020)
Thomas A Geddes, Taiyun Kim, Lihao Nan, James G Burchfield, Jean Y H Yang, Dacheng Tao, Pengyi Yang
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. BMC bioinformatics 20 (Suppl 19) (2019)
Andrew J Oldfield, Telmo Henriques, Dhirendra Kumar, Adam B Burkholder, Senthilkumar Cinghu, Damien Paulet, Brian D Bennett, Pengyi Yang, Benjamin S Scruggs, Christopher A Lavender, Eric Rivals, Karen Adelman, Raja Jothi
NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nature communications 10 (1) (2019)
Yingxin Lin, Shila Ghazanfar, Kevin Y X Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang, Jean Yee Hwa Yang
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proceedings of the National Academy of Sciences of the United States of America 116 (20) (2019)
Taiyun Kim, Irene Rui Chen, Benjamin L Parker, Sean J Humphrey, Ben Crossett, Stuart J Cordwell, Pengyi Yang, Jean Yee Hwa Yang
QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems. Proteomics 19 (13) (2019)
Taiyun Kim, Kitty Lo, Thomas A Geddes, Hani Jieun Kim, Jean Yee Hwa Yang, Pengyi Yang
scReClassify: post hoc cell type classification of single-cell rNA-seq data. BMC genomics 20 (Suppl 9) (2019)
Zhiduan Su, James G Burchfield, Pengyi Yang, Sean J Humphrey, Guang Yang, Deanne Francis, Sabina Yasmin, Sung-Young Shin, Dougall M Norris, Alison L Kearney, Miro A Astore, Jonathan Scavuzzo, Kelsey H Fisher-Wellman, Qiao-Ping Wang, Benjamin L Parker, G Gregory Neely, Fatemeh Vafaee, Joyce Chiu, Reichelle Yeo, Philip J Hogg, Daniel J Fazakerley, Lan K Nguyen, Serdar Kuyucak, David E James
Global redox proteome and phosphoproteome analysis reveals redox switch in Akt. Nature communications 10 (1) (2019)
Dougall M Norris, Pengyi Yang, James R Krycer, Daniel J Fazakerley, David E James, James G Burchfield
An improved Akt reporter reveals intra- and inter-cellular heterogeneity and oscillations in signal transduction. Journal of cell science 130 (16) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Pengyi Yang