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1. Lin Y, Wu TY, Chen X, Wan S, Chao B, Xin J, Yang YH, Wong WH, Wang RYX
Yingxin Lin, Tung-Yu Wu, Xi Chen, Sheng Wan, Brian Chao, Jingxue Xin, Jean Y H Yang, Wing H Wong and Y X Rachel Wang: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE, Genome Research, 34 (2024), no. 1, 119–133.

2. Dakic A, Wu JQ, Wang T, Huynh K, Mellett N, Duong T, Beyene HB, Magliano DJ, Shaw JE, Carrington MJ, Inouye M, Yang YH, Figtree GA, Curran JE, Blangero J, Simes J, Meikle CGPJ
Aleksandar Dakic, Jingqin Wu, Tingting Wang , Kevin Huynh, Natalie Mellett, Thy Duong, Habtamu B Beyene, Dianna J Magliano, Jonathan E Shaw, Melinda J Carrington, Michael Inouye, Jean Y Yang, Gemma A Figtree, Joanne E Curran, John Blangero, John Simes , Corey Giles & Peter J Meikle: Imputation of plasma lipid species to facilitate integration of lipidomic datasets, Nature Communications, 15 (2024), no. 1, Article 1540 (14 pages).

3. Tran A, Wang A, Mickaill J, Strbenac D, Larance M, Vernon ST, Grieve SM, Figtree GA, Patrick E, Yang YH
Andy Tran, Andy Wang, Jamie Mickaill, Dario Strbenac, Mark Larance, Stephen T. Vernon, Stuart M. Grieve, Gemma A. Figtree, Ellis Patrick and Jean Yee Hwa Yang: Construction and optimization of multi-platform precision pathways for precision medicine, Scientific reports, 14 (2024), Article 4248 (11 pages).

4. Fu X, Lin Y, Lin DM, Mechtersheimer D, Wang C, Ameen F, Ghazanfar S, Patrick E, Yang YH
Xiaohang Fu, Yingxin Lin, David M. Lin, Daniel Mechtersheimer, Chuhan Wang, Farhan Ameen, Shila Ghazanfar, Ellis Patrick, Jinman Kim & Jean Y. H. Yang: BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data, Nature Communications, 15 (2024), Article 509 (17 pages).

5. 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.

6. Zhang Y, Hu A, Lin Y, Cao Y, Muller S, Wong G, Yang YH
Yunwei Zhang, Anne Hu, Yingxin Lin, Yue Cao, Samuel Muller, Germaine Wong & Jean Yee Hwa Yang: simKAP: simulation framework for the kidney allocation process with decision making model, Scientific Reports, 13 (2023), Article number 16367.

7. 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.

8. Fu X, Patrick E, Yang YH, Feng DD, Kim J
Xiaohang Fu, Ellis Patrick, Jean Y H Yang, David Dagan Feng, Jinman Kim: Deep multimodal graph-based network for survival prediction from highly multiplexed images and patient variables, Computers in Biology and Medicine, (2023), N/A.

9. Hao J, Zou J, Zhang J, Chen K, Wu D, Cao W, Shang G, Yang YH, Wong-Lin K, Sun H, Zhang Z, Wang X, Chen W, Zou X
Jie Hao, Jiawei Zou, Jiaqiang Zhang, Ke Chen, Duojiao Wu, Wei Cao, Guoguo Shang, Jean Y H Yang, KongFatt Wong-Lin, Hourong Sun, Zhen Zhang, Xiangdong Wang, Wantao Chen, Xin Zou: scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data, Briefings in Bioinformatics, (2023), no. 24,

10. 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.

11. Lin Y, Loo L, Tran A, Lin DM, Moreno C, Hesselson D, Neely GG, Yang YH
Yingxin Lin,Lipin Loo,Andy Tran,David M. Lin,Cesar Moreno,Daniel Hesselson,G. Gregory Neely,Jean Y. H. Yang: Scalable workflow for characterization of cell-cell communication in COVID-19 patients, PLoS Computational Biology, 18 (2022), 10.

12. 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.

13. Lubomski M, Xu X, Holmes AJ, Yang YH, Sue CM, Davis RL
Michal Lubomski, Xiangnan Xu, Andrew J Holmes, Jean Y H Yang, Carolyn M Sue and Ryan L Davis: The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease, Journal of Neurology, 269 (2022), no. 2, 780–795.

14. Satgunaseelan L, Strbenac D, Tadi S, Nguyen K, Wykes J, Palme CE, Low THH, Yang YH, Clark JR, Gupta R
Laveniya Satgunaseelan, Dario Strbenac, Sahithi Tadi, Kevin Nguyen, James Wykes, Carsten E Palme, Tsu-Hui (Hubert) Low, Jean Y H Yang, Jonathan R Clark and Ruta Gupta: Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma, Cancers, 14 (2022), no. 21, Article 5213 (16 pages).

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. Wang KYX, Pupo GM, Tembe V, Patrick E, Strbenac D, Schramm SJ, Thompson JF, Scolyer RA, Muller S, Tarr G, Mann GJ, Yang YH
Kevin Y X Wang, Gulietta M Pupo, Varsha Tembe, Ellis Patrick, Dario Strbenac, Sarah-Jane Schramm, John F Thompson, Richard A Scolyer, Samuel Muller, Garth Tarr, Graham J Mann and Jean Y H Yang: Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine, npj Digital Medicine, 5 (open Access) (2022), no. 1, Article 85.

17. Satgunaseelan L, Strbenac D, Willet C, Chew T, Sadsad R, Wykes J, Low THH, Cooper WA, Lee CS, Palme C, Yang YH, Clark JR, Gupta R
Laveniya Satgunaseelan, Dario Strbenac, Cali Willet, Tracy Chew, Rosemarie Sadsad, James Wykes, Tsu-Hui (Hubert) Low, Wendy A Cooper, C Soon Lee, Carsten Palme, Jean Y H Yang, Jonathan R Clark, Ruta Gupta: Whole genome duplication in oral squamous cell carcinoma in patients younger than 50 years: implications for prognosis and adverse clinicopathological factors, Genes Chromosomes & Cancer, Open Access (2022), no. 2022, 11 pages.

18. Havula E, Ghazanfar S, Lamichane N, Francis D, Hasygar K, Liu Y, Alton LA, Johnstone J, Needham EJ, Pulpitel T, Clark T, Niranjan HN, Shang V, Tong V, Jiwnani N, Audia G, Alves AN, Sylow L, Mirth C, Neely GG, Yang YH, Hietakangas V, Simpson SJ, Senior AM
E Havula, S Ghazanfar, N Lamichane, D Francis , K Hasygar, Y Liu, L A Alton, J Johnstone, E J Needham, T Pulpitel, T Clark , H N Niranjan , V Shang, V Tong , N Jiwnani, G Audia, A N Alves, L Sylow, C Mirth, G G Neely, J Yang, V.Hietakangas, S J Simpson and A M Senior: Genetic variation of macronutrient tolerance in Drosophila melanogaster, Nature Communications, 13 (Open Access) (2022), no. 1, Art. 1637 (16 pages).

19. Vernon ST, Kott KA, Hansen T, Finemore M, Baumgart KW, Bhindi R, Yang YH, Hansen PS, Nicholls SJ, Celermajer DS, Ward MR, van Nunen SA, Grieve SM, Figtree GA
Stephen T Vernon, Katharine A Kott, Thomas Hansen, Meghan Finemore, Karl W Baumgart, Ravinay Bhindi, Jean Yang, Peter S Hansen, Stephen J Nicholls, David S Celermajer, Michael R Ward, Sheryl A van Nunen, Stuart M Grieve and Gemma A Figtree: Immunoglobulin E Sensitization to Mammalian Oligosaccharide Galactose-α-1,3 (α-Gal) Is Associated With Noncalcified Plaque, Obstructive Coronary Artery Disease, and ST-Segment–Elevated Myocardial Infarction, Arteriosclerosis, thrombosis, and vascular biology, 42 (2022), no. 3, 352–361.

20. 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).

21. Chan A, Jiang W, Blyth E, Yang YH, Patrick E
Adam Chan, Wei Jiang, Emily Blyth, Jean Yang and Ellis Patrick: treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data, Genome Biology, 22 (Open Access) (2021), no. 1, Article no. 324 (14 pages).

22. Francis D, Ghazanfar S, Havula E, Krycer JR, Strbenac D, Senior AM, Minard AY, Geddes T, Nelson ME, Weiss F, Stöckli J, Yang YH, James DE
Deanne Francis, Shila Ghazanfar, Essi Havula, James R Krycer, Dario Strbenac, Alistair Senior, Annabel Y Minard, Thomas Geddes, Marin E Nelson, Fiona Weiss, Jacqueline Stöckli, Jean Y H Yang, David E James: Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes, G3 Genes Genomes Genetics, 11 (2021), no. 10, jkab171, 14 pages.

23. Hu A, Stewart C, Craig JC, Wyburn K, Pleass H, Kanellis J, Lim WH, Yang YH, Wong G
Anne Hu, Cameron Stewart, Jonathan C Craig, Kate Wyburn, Henry Pleass, John Kanellis, Wai H Lim, Jean Yang and Germaine Wong: Jurisdictional inequalities in deceased donor kidney allocation in Australia, Kidney International, 100 (2021), 49–54.

24. Zhang Y, Wong G, Yang YH
Yunwei Zhang, Germaine Wong, Jean Yee Hwa Yang: Trash or Treasure: Rescuing Discard Kidneys, Transplantation, 105 (2021), no. 9, 1914–1915.

25. 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).

26. He J, Lin Y, Meng M, Li J, Yang YH, Wang H
Jian He, Yingxin Lin, Mei Meng, Jingquan Li, Jean YH. Yang, Hui Wang: Construction of a Human Cell Landscape of COVID-19 Infection at Single-cell Level, Aging and Disease, 12 (2021), no. 3, 705–709.

27. Schäfer S, Wang KYX, Sundling F, Yang YH, Liu A, Nanan R
Samuel Schäfer, Kevin Wang, Felicia Sundling, Jean Yang, Anthony Liu, Ralph Nanan: Modelling maternal and perinatal risk factors to predict poorly controlled childhood asthma, PLoS One, 16 (Open Access) (2021), no. Issue 5 May 2021, Article number e0252215.

28. Eastwood J, Wang A, Khanlari S, Yang YH
John Eastwood, Andy Wang, Sarah Khanlari, Alicia Montgomery & Jean Yee Hwa Yang: Psychosocial stratification of antenatal indicators to guide population-based programs in perinatal depression, BMC Pregnancy and Childbirth, 21 (2021), no. Open Access, Article number 277.

29. 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.

30. Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang YH
Shila Ghazanfar, Yingxin Lin, Xianbin Su, David M Lin, Ellis Patrick, Ze Guang Han, John C Marioni and Jean Yee Hwa Yang: Investigating higher-order interactions in single-cell data with scHOT, Nature Methods, 17 (2020), 799–806.

31. Xu X, Solon‑Biet SM, Senior AM, Raubenheimer D, Simpson SJ, Fontana L, Muller S, Yang YH
Xiangnan Xu, Samantha M Solon‑Biet, Alistair Senior, David Raubenheimer, Stephen J Simpson, Luigi Fontana, Samuel Mueller and Jean Y H Yang: LC-N2G: a local consistency approach for nutrigenomics data analysis, BMC Bioinformatics, 21 (2020), no. Open Access, Article 530.

32. Romanes SE, Omerod JT, Yang YH
Sarah E Romanes, John T Ormerod and Jean Y H Yang: Diagonal Discriminant Analysis With Feature Selection for High-Dimensional Data, Journal of Computational and Graphical Statistics, 29 (2020), no. 1, 114–127.

33. 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.

34. 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.

35. 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.

36. Hewavisenti R, Ferguson A, Wang KYX, Jones D, Gebhardt T, Edwards J, Zhang M, Britton W, Yang YH, Hong A, Palendira U
Rehana Hewavisenti, Angela Ferguson, Kevin Wang, Deanna Jones, Thomas Gebhardt, Jarem Edwards, Mei Zhang, Warwick Britton, Jean Yang, Angela Hong, Umaimainthan Palendira: CD103+ tumor-resident CD8+ T cell numbers underlie improved patient survival in oropharyngeal squamous cell carcinoma, Journal for immunotherapy of cancer, 8 (Open Access) (2020), no. 1, e000452 (8 pages).

37. 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.

38. 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.

39. 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.

40. Wang KYX, Tarr G, Yang YH, Muller S
Kevin YX Wang, Garth Tarr, Jean YH Yang and Samuel Mueller: Fast and approximate exhaustive variable selection for generalised linear models with APES, Australian and New Zealand Journal of Statistics, 61 (2019), no. 4, 445–465. MR4052183

41. 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.

42. Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang YH, Scruggs BS, Lavender CA, Rivals E, Jothi KAR
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 (2019), no. 1, Article number 3072 (12 pages).

43. 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).

44. 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.

45. 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.

46. 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.

47. Wang KYX, Menzies AM, Silva IP, Wilmott JS, Yan Y, Wongchenko M, Kefford RF, Scolyer RA, Long GV, Tarr G, Muller S, Yang YH
Kevin YX Wang, Alexander M Menzies, Ines P Silva, James S Wilmott, Yibing Yan, Matthew Wongchenko, Richard F Kefford, Richard A Scolyer, Georgina V Long, Garth Tarr, Samuel Mueller and Jean YH Yang: bcGST – an interactive bias-correction method to identify over-represented gene-sets in boutique arrays, Bioinformatics, 35 (2019), no. 8, 1350–1357.

48. Vernon ST, Hansen T, Kott KA, Yang YH, Sullivan JFO, Figtree GA
Stephen T Vernon,Thomas Hansen, Katharine A Kott, Jean Y Yang, John F. O'Sullivan, Gemma A Figtree: Utilizing state-of-the-art “omics” technology and bioinformatics to identify new biological mechanisms and biomarkers for coronary artery disease, Microcirculation, 26 (2019), no. 2, Article No. e12488.

49. 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.

50. Ghazanfar S, Strbenac D, Ormerod JT, Yang YH, Patrick E
Shila Ghazanfar, Dario Strbenac, John T Ormerod, Jean Y H Yang and Ellis Patrick: DCARS: Differential correlation across ranked samples, Bioinformatics, 35 (2019), no. 5, 823–829.

Number of matches: 153 (showing page 1 of 4) Select page: 1  2  3  4