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1. Chen C, Kim HJ, Yang P
Carissa Chen, Hani Jieun Kim and Pengyi Yang: Evaluating spatially variable gene detection methods for spatial transcriptomics data, Genome Biology, 25 (2024), no. Open Access, Article 18 (21 pages).

2. Kim D, Tran A, Kim HJ, Lin Y, Yang YH, Yang P
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 (2023), Article number 51.

3. Yu L, Liu C, Yang YH, Yang P
Lijia Yu, Chunlei Liu, Jean Yee Hwa Yang, Pengyi Yang: Ensemble deep learning of embeddings for clustering multimodal single-cell omics data, Bioinformatics, 39 (2023), no. 6, Article btad382.

4. Xiao D, Lin M, Liu C, Geddes TA, Burchfield JG, Parker BL, Humphrey SJ, Yang P
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 (2023), no. 4, Article number Iqad099 (12 pages).

5. Willie E, Yang P, Patrick E
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 (2023), no. 1, Article vbad141 (12 pages).

6. Huang H, Liu C, Wagle MM, Yang P
Hao Huang, Chunlei Liu, Manoj M Wagle and Pengyi Yang: Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis, Genome Biology, 24 (2023), no. 1, Art. 259 (20 pages).

7. Patrick E, Canete NP, Iyengar SS, Harman AN, Sutherland GT, Yang P
Ellis Patrick, Nicolas P Canete, Sourish S Iyengar, Andrew N Harman, Greg T Sutherland, Pengyi Yang: Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments, Cytometry Part A, 103 (2023), no. 7, 593–599.

8. Fazakerley DJ, van Gerwen J, Cooke KC, Duan X, Needham EJ, Díaz-Vegas A, Madsen S, Norris DM, Shun-Shion AS, Krycer JR, Burchfield JG, Yang P, Wade MR, Brozinick JT, James DE, Humphrey SJ
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 and Sean J Humphrey: Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance, Nature Communications, Published Online (2023), no. 18 February 2023, 20 pages.

9. Liu C, Huang H, Yang P
Chunlei Liu, Hao Huang and Pengyi Yang: Multi-task learning from multimodal single-cell omics with Matilda, Nucleic Acids Research, 51 (2023), no. 8, e45.

10. Kim HJ, O'Hara-Wright M, Kim D, Loi TH, Lim BY, Jamieson RV, Gonzalez-Cordero A, Yang P
Hani Jieun Kim, Michelle O'Hara-Wright, Daniel Kim, To Ha Loi, Benjamin Y. Lim, Robyn V. Jamieson, Anai Gonzalez-Cordero and Pengyi Yang: Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids, Stem Cell Reports, 18 (2023), no. 1, 175–189.

11. Xiao D, Chen C, Yang P
Di Xiao, Carissa Chen, Pengyi Yang: Computational systems approach towards phosphoproteomics and their downstream regulation, Proteomics, 23 (2023), no. 3 - 4, Article number 2200068.

12. Xiao D, Kim HJ, Pang I, Yang P
Di Xiao, Hani Jieun Kim, Ignatius Pang and Pengyi Yang: Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities, Bioinformatics, 38 (2022), no. 7, 1956–1963.

13. Tran A, Yang P, Yang YH, Ormerod JT
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, Volume 21 (2022), Issue 4.

14. Tran A, Yang P, Yang YH, Ormerod JT
Andy Tran, Pengyi Yang, Jean Y H 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, Volume 4 (2022), Issue 1.

15. Cao Y, Lin Y, Patrick E, Yang P, Yang YH
Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang and Jean Yee Hwa Yang: scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction, Bioinformatics, 38 (Open Access) (2022), no. 20, 4745–4753.

16. Yang P, Tam PPL
Pengyi Yang and Patrick P L Tam: Mouse organogenesis atlas at single-cell resolution, Cell, 185 (2022), no. 10, 1625–1627.

17. Duan X, Norris DM, Humphrey SJ, Yang P, Cooke KC, Bultitude WP, Parker BL, Conway OJ, Burchfield JG, Krycer JR, Brodsky FM, James DE, Fazakerley DJ
Xiaowen Duan, Dougall M Norris, Sean J Humphrey, Pengyi Yang, Kristen C Cooke, Will P Bultitude, Benjamin L Parker, Olivia J Conway, James G Burchfield, James R Krycer, Frances M Brodsky, David E James and Daniel J Fazakerley: Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate, Biochemical Journal, 479 (2022), no. 11, 1237–1257.

18. Cao Y, Yang P, Yang YH
Yue Cao, Pengyi Yang & Jean Yee Hwa Yang: A benchmark study of simulation methods for single-cell RNA sequencing data, Nature Communications, 12 (2021), no. 1, 6911 (12 pages).

19. Kim T, Tang O, Vernon ST, Kitt KA, Koay YC, Park J, James DE, Grieve SM, Speed TP, Yang P, Figtree GA, O'Sullivan JF, Yang YH
Taiyun Kim, Owen Tang, Stephen T Vernon, Katharine A Kitt, 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 (Open Access) (2021), no. 1, Article no. 4992 (10 pages).

20. Kim HJ, Tam PPL, Yang P
Hani Jieun Kim, Patrick P L Tam, and Pengyi Yang: Defining cell identity beyond the premise of differential gene expression, Cell Regeneration, 10:20 (2021), no. 1, 3 pages.

21. Kim HJ, Kim T, Xiao D, Yang P
Hani Jieun Kim,Taiyun Kim, Di Xiao, and Pengyi Yang: Protocol for the processing and downstreamanalysis of phosphoproteomic data with PhosR, STAR Protocols, 2 (Open Access) (2021), no. 2, Article number 100585 – 22 pages.

22. Singh R, Cottle L, Loudovaris T, Xiao D, Yang P, Thomas HE, Kebede MA, Thorn P
Reena Singh, Louise Cottle, Thomas Loudovaris, Di Xiao, Pengyi Yang, Helen E Thomas, Melkam A Kebede, Peter Thorn: Enhanced structure and function of human pluripotent stem cell-derived beta-cells cultured on extracellular matrix, Stem Cells Translational Medicine, 10 (2021), no. 3, 492–505.

23. Norris DM, Yang P, Shin SY, Kearney AL, Kim HJ, Geddes TA, Senior AM, Fazakerley DJ, Nguyen LK, James DE, Burchfield JG
Dougall Norris, Pengyi Yang, Sung-Young Shin, Alison L Kearney, Hani Jieun Kim, Thomas Geddes, Alistair M Senior, Daniel J Fazakerley, Lan K Nguyen, David E James and James G Burchfield: Signaling Heterogeneity is Defined by Pathway Architecture and Intercellular Variability in Protein Expression, iScience (Open Access), 24 (2021), no. 2, Art. 102118 (24 pages).

24. Kim HJ, Kim T, Hoffman NJ, Xiao D, James DE, Humphrey SJ, Yang P
Hani Jieun Kim, Taiyun Kim, Nolan J. Hoffman, Di Xiao, David E. James, Sean J. Humphrey, Pengyi Yang: PhosR enables processing and functional analysis of phosphoproteomic data, Cell Reports, 34 (2021), no. 8, 108771.

25. Su X, Zhao L, Shi Y, Zhang R, Long Q, Bai S, Luo Q, Lin Y, Zou X, Ghazanfar S, Tao K, Yang G, Wang L, He KY, Cui X, He J, Wu JX, Han B, Yan B, Deng B, Wang N, Li X, Yang P, Hou S, Sun J, Yang YH, Chen J, Han ZG
Xianbin Su, Linan Zhao, Yi Shi, Rui Zhang, Qi Long, Shihao Bai, Qing Luo, Yingxin Lin, Xin Zou, Shila Ghazanfar, Kun Tao, Guoliang Yang, Lan Wang, Kun‑Yan He, Xiaofang Cui, Jian He, Jiao‑Xiang Wu, Bo Han, Bin Yan, Biao Deng, Na Wang, Xiaolin Li, Pengyi Yang, Shangwei Hou, Jielin Sun, Jean Y H Yang, Jinhong Chen and Ze‑Guang Han: Clonal evolution in liver cancer at single-cell and single-variant resolution, Journal of Hematology and Oncology, 14 (2021), no. 1, Article Number 22.

26. Cao Y, Geddes TA, Yang YH, Yang P
Yue Cao, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang: Ensemble deep learning in bioinformatics, Nature Machine Intelligence, 2 (2020), 500–508.

27. Lin Y, Cao Y, Kim HJ, Salim A, Speed TP, Lin DM, Yang P, Yang YH
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 (2020), e9389.

28. Kim HJ, Lin Y, Geddes TA, Yang P, Yang YH
Hani Jieun Kim, Yingxin Lin, Thomas A Geddes, Jean Yee Hwa Yang, Pengyi Yang: CiteFuse enables multi-modal analysis of CITE-seq data, Bioinformatics, 36 (2020), 4137–4143.

29. Tang T, Wu H, Bao W, Yang P, Yuan D, Zhou BB
Tao Tang, Hao Wu, Wei Bao, Pengyi Yang, Dong Yuan, Bing Bing Zhou: New parallel algorithms for all pairwise computation on large HPC clusters, 20th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT), 20th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT), NA (ed.), IEEE, Gold Coast, Australia, Australia, (2020), 199–204. ISBN 978-1-7281-2616-6/2640-6721.

30. Kaur S, Peters TJ, Yang P, Luu LDW, Vuong J, Krycer JR, O'Donoghue SI
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 (2020), 22.

31. Kim PS, Osteil P, Humphrey SJ, Cinghu S, Oldfield AJ, Patrick E, Wilkie EE, Peng G, Suo S, Jothi R, Tam PPL, Yang P
Hani Jieun Kim, Pierre Osteil, Sean J Humphrey, Senthilkumar Cinghu, Andrew J Oldfield, Ellis Patrick, Emilie E Wilkie, Guangdun Peng, Shengbao Suo, Raja Jothi, Patrick P L Tam, Pengyi Yang: Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning, Nucleic acids research, 48 (2020), no. 4, 1828–1842.

32. Azimi A, Yang P, Ali M, Howard V, Mann GJ, Kaufman KL, Fernandez-Penas P
Ali Azimi, Pengyi Yang, Marina Ali, Vicki Howard, Graham J Mann, Kimberley L Kaufman, Pablo Fernandez-Penas: Data Independent Acquisition Proteomic Analysis Can Discriminate between Actinic Keratosis, Bowen’s Disease, and Cutaneous Squamous Cell Carcinoma, Journal of Investigative Dermatology, 140 (2020), no. 1, 212–222.

33. Cao Y, Lin Y, Ormerod JT, Yang P, Yang YH, Lo KK
Yue Cao, Yingxin Lin, John T Ormerod, Pengyi Yang, Jean Y H Yang and Kitty K Lo: ScDC: Single cell differential composition analysis, BMC Bioinformatics, 20 (2019), no. Suppl 19:721, 12 pages.

34. Geddes TA, Kim T, Nan L, Burchfield JG, Yang YH, Tao D, Yang P
Thomas A Geddes, Taiyun Kim, Lihao Nan, James G Burchfield, Jean Y H Yang, Dacheng Tao and Pengyi Yang: Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis, BMC Bioinformatics, 20 (2019), no. Suppl 19:660, 11 pages.

35. Kim T, Lo KK, Geddes TA, Kim HJ, Yang YH, Yang P
Taiyun Kim, Kitty Lo, Thomas A Geddes, Hani Jieun Kim, Jean Yee Hwa Yang and Pengyi Yang: scReClassify: post hoc cell type classification of single-cell rNA-seq data, BMC Genomics, 20 (2019), no. Suppl 9:913, 10 pages.

36. Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang YH, Yang P
Yingxin Lin, Shila Ghazanfar, Dario Strbenac, Andy Wang, Ellis Patrick, David M Lin, Terence Speed, Jean YH Yang, Pengyi Yang: Evaluating stably expressed genes in single cells, GigaScience, 8 (2019), no. 9, giz106.

37. Kim T, Chen IR, Parker BL, Humphrey SJ, Crossett B, Cordwell SJ, Yang P, Yang YH
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 (2019), no. 13, 1900068 (4 pages).

38. de Ridder M, Klein K, Yang YH, Yang P, Lagopoulos J, Hickie I, Bennett MR, Jinman K
Michael de Ridder,Karsten Klein, Jean Yang, Pengyi Yang, Jim Lagopoulos, Ian Hickie, Max Bennett, Jinman Kim: An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity, Neuroinformatics, 17 (2019), no. 2, 211–223.

39. Lin Y, Ghazanfar S, Wang KYX, Gagnon-Bartsch JA, Lo KK, Su X, Han ZG, Ormerod JT, Speed TP, Yang P, Yang YH
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 and Jean Yee Hwa Yang: scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets, PNAS, 116 (2019), no. 20, 9775–9784.

40. Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang YH, James DE, Mann M, Jothi R
Pengyi Yang, Sean J Humphrey, Senthilkumar Cinghu, Rajneesh Pathania, Andrew J Oldfield, Dhirendra Kumar, Dinuka Perera, Jean Y H Yang, David E James, Matthias Mann, Raja Jothi: Multi-omic profiling reveals dynamics of the phased progression of pluripotency, Cell Systems, 8 (2019), no. 5, 427–445.

41. Yang P, Ormerod JT, Liu W, Ma C, Zomaya AY, Yang YH
Pengyi Yang , John T Ormerod, Wei Liu, Chendong Ma, Albert Y Zomaya and Jean Y H Yang: AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications, IEEE Transactions on Cybernetics, 49 (2019), no. 5, 1932–1943.

42. Parker B, Calkin A, Seldin M, Keating M, Tarling E, Yang P, Moody S, Liu Y, Zerenturk E, Needham EJ, Miller M, Clifford B, Morand P, Watt M, Meex R, Peng KY, Lee R, Jayawardana K, Pan C, Mellett N, Weir J, Lazarus R, Lusis A, Meikle P, James D, de Aguiar Vallim T, Drew B
Benjamin Parker, Anna Calkin, Marcus Seldin, Michael Keating, Elizabeth Tarling, Pengyi Yang, Sarah Moody, Yingying Liu, Eser Zerenturk, Elise Needham, Matthew Miller, Bethan Clifford, Pauline Morand, Matthew Watt, Ruth Meex, Kang-Yu Peng, Richard Lee, Kaushala Jayawardana, Calvin Pan, Natalie Mellett, Jacquelyn Weir, Ross Lazarus, Aldons Lusis, Peter Meikle, David James, Thomas de Aguiar Vallim and Brian Drew: An integrative systems genetic analysis of mammalian lipid metabolism, Nature, 567 (2019), 187–193.

43. O'Sullivan JF, Neylon A, Fahy EF, Yang P, McGorrian C, Blake GJ
John F O'Sullivan, Antoinette Neylon, Eoin F Fahy, Pengyi Yang, Catherine McGorrian, Gavin J Blake: MiR-93-5p is a novel predictor of coronary in-stent restenosis, Heart Asia, 11 (2019), no. 1, Art. 011134.

44. Kim T, Chen IR, Lin Y, Wang A, Yang YH, Yang P
Taiyun Kim, Irene R. Chen, Yingxin Lin, Andy Wang, Jean Y.H. Yang and Pengyi Yang: Impact of similarity metrics on single-cell RNA-seq data clustering, Briefings in Bioinformatics, (2018), EPub.

45. Yang P, Ormerod JT, Liu W, Ma C, Zomaya AY, Yang YH
Pengyi Yang, John T. Ormerod, Wei Liu, Chendong Ma, Albert Y. Zomaya and Jean Y. H. Yang: AdaSampling for positive-unlabeled and label noise learning with bioinformatics applications, IEEE Transactions on Cybernetics, 1 (2018), 1–12.

46. Fazakerley DJ, Chaudhuri R, Yang P, Maghzal GJ, Thomas KC, Krycer JR, Humphrey SJ, Parker BL, Fisher-Wellman KH, Meoli CC, Hoffman NJ, Diskin C, Birchfield JG, Cowley MJ, Kaplan WH, Modrusan Z, Kolumam G, Yang YH, Chen DL, Samocha-Bonet D, Greenfield JR, Hoehn KL, Stocker R, James DE
Daniel J Fazakerley, Rima Chaudhuri, Pengyi Yang, Ghassan J Maghzal, Kristen C Thomas, James R Krycer, Sean J Humphrey, Benjamin L Parker, Kelsey H Fisher-Wellman, Christopher C Meoli, Nolan J Hoffman, Ciana Diskin, James G Burchfield, Mark J Cowley, Warren Kaplan, Zora Modrusan, Ganesh Kolumam, Jean YH Yang, Daniel L Chen, Dorit Samocha-Bonet, Jerry R Greenfield, Kyle L Hoehn, Roland Stocker and David E James: Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance, eLIFE, 7 (2018), e32111.

47. Cinghu S, Yang P, Kosak JP, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R
Senthilkumar Cinghu, Pengyi Yang, Justin P Kosak, Amanda E Conway, Dhirendra Kumar, Andrew J Oldfield, Karen Adelman, Raja Jothi: Intragenic Enhancers Attenuate Host Gene Expression, Molecular Cell, 68 (2017), no. 1, 104–117.

48. Yang P, Liu W, Yang YH
Pengyi Yang, Wei Liu, Jean Yang: Positive unlabeled learning via wrapper-based adaptive sampling, Proceedings of the Twenty-Sixth International Joint Conference on Artificial Intelligence (IJCAI), The Twenty-Sixth International Joint Conference on Artificial Intelligence, Carles Sierra (ed.), International Joint Conferences on Artificial Intelligence, Melbourne, (2017), 3273–3279. ISBN 978-0-9992411-0-3.

49. Norris DM, Yang P, Krycer JR, Fazakerley DJ, James DE
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 (2017), no. 16, 2757–2766.

50. Yang P, Oldfield AJ, Kim T, Yang A, Yang YH, Ho JWK
Pengyi Yang, Andrew Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang and Joshua W K Ho: Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells, Bioinformatics, 33 (2017), no. 13, 1916–1920.

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