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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.

51. Hong AM, Ferguson P, Dodds T, Jones D, Li M, Yang YH, Scolyer RA
Angela M Hong, Peter Ferguson, Tristan Dodds, Deanna Jones, Mengbo Li, Jean Yang, Richard A Scolyer: Significant association of PD-L1 expression with human papillomaviruspositivity and its prognostic impact in oropharyngeal cancer, Oral Oncology, 92 (2019), 33–39.

52. Lim SY, Lee JH, Gide TN, Menzies AM, Guminski A, Carlino MS, Breen EJ, Yang YH, Ghazanfar S, Kefford RF, Scolyer RA, Long GV, Rizos H
Su Y Lim, Jenny H Lee, Tuba N Gide, Alexander M Menzies, Alexander Guminski, Matteo S Carlino, Edmond J Breen, Jean Y H Yang, Shila Ghazanfar, Richard F Kefford, Richard A Scolyer, Georgina V Long and Helen Rizos: Circulating cytokines predict immune-related toxicity in melanoma patients receiving anti-PD-1–based immunotherapy, Clinical Cancer Research, 25 (2019), no. 5, 1557–1563.

53. da Silva IP, Wang KYX, Wilmott JS, Holst J, Carlino MS, Park JJ, Quek C, Wongchenko M, Yan Y, Mann G, Johnson DB, Quade JLM, Rai R, Kefford RF, Rizos H, Scolyer RA, Yang YH, Long GV, Menzies AM
Inês Pires da Silva, Kevin Y.X. Wang, James S. Wilmott, Jeff Holst, Matteo S. Carlino, John J. Park, Camelia Quek, Matthew Wongchenko, Yibing Yan, Graham Mann, Douglas B. Johnson, Jennifer L. McQuade, Rajat Rai, Richard F. Kefford, Helen Rizos, Richard A. Scolyer, Jean Y.H. Yang, Georgina V. Long and Alexander M. Menzies: Distinct molecular profiles and immunotherapy treatment outcomes of V600E and V600K BRAF-mutant melanoma, Clinical Cancer Research, 25 (2019), no. 4, 1272–1279.

54. Vernon ST, Hansen T, Knott KA, Yang YH, O'Sullivan JF, Figtree GA
Stephen T Vernon, Thomas Hansen, Katharine A. Knott, Jean Y. Yang, John F O'Sullivan and Gemma Figtree.: Utilizing state-of-the-art “omics” technology and bioinformatics to identify new biological mechanisms and biomarkers for coronary artery disease, Microcirculation, NA (2018), e12488.

55. 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.

56. Chaudhuri R, Krycer JR, Fazakerley DJ, Fisher-Wellman K, Su Z, Höhn KL, Yang YH, H JY, Kuncic Z, Vafaee F, James DE
R Chaudhuri, J. Krycer, D. Fazakerley, K. Fisher-Wellman, Z. Su, K.L. Höhn, J.Y.H. Yang, Z. Kuncic, F. Vafaee and D. E. James: The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes, Scientific Report, 8 (2018), no. 1, 1774.

57. Bisogni AJ, Ghazanfar S, Williams EO, Marsh HM, Yang YH, Lin DM
A.J. Bisogni and S. Ghazanfar and E. O. Williams and H.M. Marsh and J. Y. H. Yang and D.M. Lin: Tuning of delta-protocadherin adhesion through combinatorial diversity, Elife, 7 (2018), EPub.

58. Lim SY, Lee JH, Gide TN, Menzies AM, Guminski A, Carlino MS, Breen EJ, Yang YH, Ghazanfar S, Kefford RF, Scolyer RA, Long GV, Rizos H
Su Y Lim, Jenny H Lee, Tuba N Gide, Alexander M Menzies, Alexander Guminski, Matteo S Carlino, Edmond J Breen, Jean YH Yang, Shila Ghazanfar, Richard F Kefford, Richard A Scolyer, Georgina V Long, Helen Rizos: Circulating cytokines predict immune-related toxicity in melanoma patients receiving anti-PD-1-based immunotherapy, Clinical Cancer Research, 1 (2018), 2795.2018.

59. Sykes EK, McDonald CE, Ghazanfar S, Mactier S, Thompson JF, Scolyer RA, Yang YH, Mann GJ, Christopherson RI
Erin K Sykes, Cassandra E McDonald, Shila Ghazanfar, Swetlana Mactier, John F Thompson, Richard A Scolyer, Jean Y Yang, Graham J Mann, Richard I Christopherson: A 14-Protein Signature for Rapid Identification of Poor Prognosis Stage III Metastatic Melanoma, PROTEOMICS–Clinical Applications, 12 (2018), no. 3, 1700094.

60. Ghazanfar S, Strbenac D, Ormerod JT, Yang YH, Patrick E
Shila Ghazanfar, Dario Strbenac, John T Ormerod, Jean Y H Yang, Ellis Patrick: DCARS: differential correlation across ranked samples, Bioinformatics, 1 (2018), bty698.

61. 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.

62. Chaudhuri R, Krycer JR, Fazakerley DJ, Fisher-Wellman KH, Su Z, Hoehn KL, Yang YH, Kuncic Z, Vafaee F, James DE
Rima Chaudhuri, James R Krycer, Daniel J Fazakerley, Kelsey H Fisher-Wellman, Zhiduan Su, Kyle L Hoehn, Jean Yee Hwa Yang, Zdenka Kuncic, Fatemeh Vafaee & David E James: The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes, Scientific Reports, 8 (2018), no. 1, article 1774.

63. 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.

64. Wong G, Howell M, Patrick E, Yang YH
G. Wong, M. Howell, E. Patrick and J Yang: Taking Kidneys for Granted? Time to Reflect on the Choices We Make, Transplantation, 101 (2017), no. 12, 2812–2813.

65. 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.

66. Ghazanfar S, Vuocolo T, Morrison JL, Nicholas LM, Millen ICM, Yang YH, Buckley MJ, Tellam RL
Shila Ghazanfar, Tony Vuocolo, Janna L. Morrison, Lisa M. Nicholas, Isabella C. McMillen, Jean Y. H. Yang, Michael J. Buckley and Ross L. Tellam: Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis, PLOS ONE, 12 (2017), e0180378.

67. 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.

68. Chaudhuri R, Yang YH
Rima Chaudhuri and Jean Yee Hwa Yang: Cross-Species PTM Mapping from Phosphoproteomic Data, Protein Bioinformatics - From Protein Modifications and Networks to Proteomics, Methods in Molecular Biology - Springer Protocols, Humana Press, USA, (2017), 459–469. ISBN 978-1-4939-6783-4.

69. Patrick E, Schramm S-J, Ormerod JT, Scolyer RA, Mann GJ, Muller S, Yang YH
E Patrick, S-J Schramm, JT Ormerod, RA Scolyer, GJ Mann, S Mueller, YH Yang: A multi-step classifier addressing cohort heterogeneity improves performance of prognostic biomarkers in three cancer types, Oncotarget, 8 (2017), no. 2, 2807–2815.

70. Yang P, Patrick E, Humphrey SJ, Ghazanfar S, James DE, Jothi R, Yang YH
Pengyi Yang, Ellis Patrick, Sean J Humphrey, Shila Ghazanfar, David E James, Raja Jothi, Jean Yee Hwa Yang: KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis, Proteomics, 16 (2016), no. 13, 1868–1871.

71. Ghazanfar S, Yang YH
Shila Ghazanfar and Jean Yee Hwa Yang: Characterizing mutation–expression network relationships in multiple cancers, Computational Biology and Chemistry, 63 (2016), 73–82.

72. Ghazanfar S, Bisogni AJ, Ormerod JT, Lin DM, Yang YH
Shila Ghazanfar, Adam J. Bisogni, John T. Ormerod, David M. Lin, and Jean Y. H. Yang: Integrated single cell data analysis reveals cell specific networks and novel coactivation markers, BMC Systems Biology, 10 (2016), no. S5, 11–24.

73. Banihashemi N, Robillard R, Yang YH, Carpenter JS, Hermens DF, Naismith SL, Terpening Z, White D, Scott EM, Hickie IB
Nahid Banihashemi, Rébecca Robillard, Jean Yang, Joanne S Carpenter, Daniel F Hermens, Sharon L Naismith, Zoe Terpening, Django White, Elizabeth M Scott and Ian B Hickie: Quantifying the effect of body mass index, age, and depression severity on 24-h activity patterns in persons with a lifetime history of affective disorders, BMC Psychiatry, 16 (1) (2016), no. 317,

74. Madore J, Strbenac D, Vilain R, Menzies AM, Yang YH, Thompson JF, Long GV, Mann GJ, Scolyer RA, Wilmott JS
Jason Madore, Dario Strbenac, Ricardo Vilain, Alexander M Menzies, Jean Y H Yang, John F Thompson, Georgina V Long, Graham J Mann, Richard A Scolyer, and James SWilmott: PD-L1 Negative Status is Associated with Lower Mutation Burden, Differential Expression of Immune-Related Genes, and Worse Survival in Stage III Melanoma, Clinical Cancer Research, 22 (2016), no. 15, 3915–3923.

75. Strbenac D, Mann GJ, Yang YH, Ormerod JT
Dario Strbenac, Graham J Mann, Jean Y H Yang and John T Ormerod: Differential distribution improves gene selection stability and has competitive classification performance for patient survival, Nucleic Acids Research, 44 (2016), no. 13, e119.

76. Markus MA, Yang YH, Morris BJ
M Andrea Markus, Yee Hwa J Yang, Brian J Morris: Transcriptome-wide targets of alternative splicing by RBM4 and possible role in cancer, Genomics, 107 (2016), no. 4, 138–144.

77. Yang P, Patrick E, Humphrey SJ, Ghazanfar S, James DE, Jothi R, Yang YH
Pengyi Yang, Ellis Patrick, Sean J. Humphrey, Shila Ghazanfar, David E. James, Raja Jothi, Jean Yee Hwa Yang: KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis, Proteomics, 16 (2016), 1868 – 1871.

78. Jayawardana K, Schramm SJ, Tembe V, Muller S, Thompson JF, Scolyer RA, Mann GJ, Yang YH
K Jayawardana, S-J Schramm, V Tembe, S Mueller, JF Thompson, RA Scolyer, GJ Mann, J Yang: Identification, Review, and Systematic Cross-Validation of microRNA Prognostic Signatures in Metastatic Melanoma, Journal of Investigative Dermatology, 136 (2016), 245–254.

79. Strbenac D, Mann GJ, Ormerod JT, Yang YH
Dario Strbenac, Graham J Mann, John T Ormerod and Jean Y H Yang: ClassifyR: an R package for performance assessment of classification with applications to transcriptomics, Bioinformatics, 31 (2015), no. 11, 1851–1853.

80. Yang P, Zheng X, Jayaswal V, Hu G, Yang YH, Jothi R
Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi: Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data, PLoS Computational Biology, 11 (2015), no. 8, Art. e100440318 (18 pages).

81. Patrick E, Buckley MJ, Muller S, Lin DM, Yang YH
E Patrick, M Buckley, S Müller, DM Lin, YH Yang: Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from small sample miRNA-Seq and mRNA-Seq data, Bioinformatics, 31 (2015), no. 17, 2822–2828.

82. Chaudhuri R, Sadrieh A, Hoffman N, Parker B, Humphrey SJ, Stöckli J, Hill A, James DE, Yang YH
Rima Chaudhuri, Arash Sadrieh, Nolan Hoffman, Benjamin Parker, Sean Humphrey, Jacqueline Stöckli, Adam Hill, David James, Jean Yang: PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modification, BMC Genomics, 16 (2015), no. 1, Art. 617.

83. Jayawardana K, Schramm SJ, Haydu L, Thompson JF, Scolyer RA, Mann GJ, Muller S, Yang YH
Kaushala Jayawardana, Sarah-Jane Schramm, Lauren Haydu, John F Thompson, Richard A Scolyer, Graham J Mann, Samuel Müller and Jean Yee Hwa Yang: Determination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information, International Journal of Cancer, 136 (2015), no. 4, 863–874.

84. Mactier S, Kaufman KL, Wang P, Crossett B, Pupo GM, Kohnke PL, Thompson JF, Scolyer RA, Yang YH, Mann GJ, Christopherson RI
Swetlana Mactier, Kimberley L Kaufman, Penghao Wang, Ben Crossett, Gulietta M Pupo, Philippa L Kohnke, John F Thompson, Richard A Scolyer, Jean Y Yang, Graham J Mann and Richard I Christopherson: Protein signatures correspond to survival outcomes of AJCC stage III melanoma patients, Pigment Cell and Melanoma Research, 27 (2014), no. 6, 1106–1116.

85. Ma X, Yang P, Kaplan WH, Lee BH, Wu LE, Yang YH, Yasunaga M, Sato K, Chisholm DJ, James DE
Xiuquan Ma, Pengyi Yang, Warren H Kaplan, Bon Hyang Lee, Lindsay E Wu, Jean Yee-Hwa Yang, Mayu Yasunaga, Kenzo Sato, Donald J Chisholm, David E James: ISL1 Regulates Peroxisome Proliferator-Activated Receptor γ Activation and Early Adipogenesis via Bone Morphogenetic Protein 4-Dependent and -Independent Mechanisms, Molecular and Cellular Biology, 34 (2014), no. 29, 3607–3617.

86. Parnell GP, O'Connor KS, Patrick E, Ahlenstiel G, Suppiah V, van der Poorten D, Read SA, Leung R, Douglas MW, Yang YH, Stewart GJ, Liddle C, George J, Booth DR
O'Connor KS, Parnell G, Patrick E, Ahlenstiel G, Suppiah V, van der Poorten D, Read SA, Leung R, Douglas MW, Yang JY, Stewart GJ, Liddle C, George J and Booth DR: Hepatic metallothionein expression in chronic hepatitis C virus infection is IFNL3 genotype-dependent, Genes and Immunity, 15 (2014), no. 2, 88–94.

87. Yang P, Patrick E, Tan SX, Fazakerley DJ, Burchfield JG, Gribben C, Prior MJ, James DE, Yang YH
Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J Fazakerley, James Burchfield, Christopher Gribben, Matthew J Prior, David E James and Yee Hwa Yang: Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway, Bioinformatics, 30 (2014), no. 6, 808–814.

88. Tonks KT, Ng Y, Miller S, Coster AC, Samocha-Bonet D, Iseli TJ, Xu A, Patrick E, Yang YH, Junutula JR, Modrusan Z, Kolumam G, Stöckli J, Chisholm DJ, James DE, Greenfield JR
KT Tonks, Y Ng, S Miller, AC Coster, D Samocha-Bonet, TJ Iseli, A Xu, E Patrick, JY Yang, JR Junutula, Z Modrusan, G Kolumam, J Stöckli, DJ Chisholm, DE James, JR Greenfield: Impaired Akt phosphorylation in insulin-resistant human muscle is accompanied by selective and heterogeneous downstream defects., Diabetologia, 56 (2013), no. 4, 875–885.

89. Wang P, Yang YH, Raftery M, Zhong L, Wilson SR
Penghao Wang, Jean Yee Hwa Yang, Mark Raftery, Ling Zhong, Susan R Wilson: Latin Square Dataset for Evaluating the Accuracy of Mass Spectrometry-based Protein Identification and Quantification, Proceedings of the 2013 IEEE Conference on Bioinformatics and Biomedicine (BIBM), 2013, Guo-Zheng Li, Sunghoon Kim, Michael Hughes, Geoff McLachlan, Hongye Sun, Xiaohua Hu, Habtom Ressom, Baoyan Liu, Michel Liebman (eds.), IEEE Explore, IEEE, USA, (2013), 65–67.

90. Jayaswal V, Schramm SJ, Mann GJ, Wilkins MR, Yang YH
Vivek Jayaswal, Sarah-Jane Schramm, Graham J Mann, Marc R Wilkins and Yee Hwa Yang: VAN: an R package for identifying biologically perturbed networks via differential variability analysis, BMC Research Notes, 6 (2013), no. 430, Online.

91. Strbenac D, Armstrong NJ, Yang YH
Dario Strbenac, Nicola J Armstrong, Jean YH Yang: Detection and classification of peaks in 5' cap RNA sequencing data, BMC Genetics, 14 (2013), no. Sup. 5, 1–11.

92. Strbenac D, Armstrong NJ, Yang YH
Dario Strbenac, Nicola J Armstrong and Jean YH Yang: Correction: Detection and classification of peaks in 5' cap RNA sequencing data, BMC Genetics, 14 (2013), no. 1, Art. 767.

93. Patrick E, Buckley MJ, Lin DM, Yang YH
Ellis Patrick, Michael Buckley, David Ming Lin, Yee Hwa Yang: Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information, BMC Genomics, 14 (2013), no. Supplement 1, 1–9.

94. Jayawardana K, Muller S, Schramm SJ, Mann GJ, Yang YH
Kaushala Jayawardana, Samuel Müller, Sarah-Jane Schramm, Graham J Mann and Jean Yang: Vertical Data Integration for Melanoma Prognosis, Proceedings, 59th ISI World Statistics Congress, (2013), 1–6.

95. Yang YH, Markus MA, Mangs AH, Raitskin O, Sperling R, Morris BJ
Yee Hwa J Yang, M Andrea Markus, A Helena Mangs, Oleg Raitskin, Ruth Sperling, Brian J Morris: ZRANB2 localizes to supraspliceosomes and influences the alternative splicing of multiple genes in the transcriptome, Molecular Biology Reports, 40 (2013), no. 9, 5381–5395.

96. Schramm SJ, Li SS, Jayaswal V, Fung DCY, Campain AE, Pang CNI, Scolyer RA, Yang YH, Mann GJ, Wilkins MR
S J Schramm, S S Li, V Jayaswal, D C Y Fung, A E Campain, C N I Pang, R A Scolyer, Y H Yang, G J Mann, M R Wilkins: Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden, Pigment Cell and Melanoma Research, 26 (2013), no. 5, 708–722.

97. Humphrey SJ, Yang G, Yang P, Fazakerley DJ, Stöckli J, Yang YH, James DE
Sean J Humphrey, Guang Yang, Pengyi Yang, Daniel J Fazakerley, Jacqueline Stöckli, Jean Y Yang, and David E James: Dynamic adipocyte phosphoproteome reveals that akt directly regulates mTORC2, Cell Metabolism, 17 (2013), no. 6, 1009–1020.

98. Patrick E, Buckley MJ, Yang YH
Ellis Patrick, Michael Buckley and Yee Hwa Yang: Estimation of data-specific constitutive exons with RNA-Seq data, BMC Bioinformatics, 14 (2013), no. 31, 1–10.

99. Mann GJ, Pupo GM, Campain AE, Carter CD, Schramm SJ, Pianova S, Gerega SK, De Silva C, Lai K, Wilmott JS, Synnott M, Hersey P, Kefford RF, Thompson JF, Yang YH, Scolyer RA
Graham J Mann, Gulietta M Pupo, Anna E Campain, Candace D Carter, Sarah-Jane Schramm, Svetlana Pianova, Sebastien K Gerega, Chitra De Silva, Kenneth Lai, James S Wilmott, Maria Synnott, Peter Hersey, Richard F Kefford, John F Thompson, Yee Hwa Yang and Richard A Scolyer: BRAF Mutation, NRAS Mutation, and the Absence of an Immune-Related Expressed Gene Profile Predict Poor Outcome in Patients with Stage III Melanoma, Journal of Investigative Dermatology, 133 (2013), 509–517.

100. Chung SH, Shen W, Jayawardana K, Wang P, Yang YH, Shackel N, Gillies MC
S H Chung, W Shen, K Jayawardana, P Wang, J Yang, N Shackel, M C Gillies: Differential gene expression profiling after conditional müller-cell ablation in a novel transgenic model, Investigative Ophthalmology and Visual Science, 54 (2013), no. 3, 2142–2152.

101. Oates J, Casikar I, Campain AE, Muller S, Yang YH, Reid S, Condous G
Jennifer Oates, Ishwari Casikar, Anna Campain, Samuel Müller, Jean Yang, Shannon Reid, George Condous: A prediction model for viability at the end of the first trimester after a single early pregnancy evaluation, Australian and New Zealand Journal of Obstetrics and Gynaecology, 53 (2013), 51–57.

102. Yang P, Ma J, Wang P, Zhu Y, Zhou BB, Yang YH
Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing B. Zhou, and Yee Hwa (Jean) Yang: Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2012), no. 5, 1273–1280.

103. Wang P, Yang P, Yang YH
P Wang, P Yang and J Y H Yang: OCAP: An open comprehensive analysis pipeline for iTRAQ, Bioinformatics, 28 (2012), no. 10, 1404–1405.

104. Yang P, Humphrey SJ, Fazakerley DJ, Prior MJ, Yang G, James DE, Yang YH
Yang P, Humphrey SJ, Fazakerley DJ, Prior MJ, Yang G, James DE, Yang JYH: Re-Fraction: A Machine Learning Approach for Deterministic Identification of Protein Homologues and Splice Variants in Largescale MS-based Proteomics, Journal of Proteome Research, 11 (2012), no. 5, 3035–3045.

105. Schramm SJ, Campain AE, Scolyer RA, Yang YH, Mann GJ
Sarah-Jane Schramm, Anna E Campain, Richard A Scolyer, Yee Hwa Yang and Graham J Mann: Review and cross-validation of gene expression signatures and melanoma prognosis, Journal of Investigative Dermatology, 132 (2012), 274–283.

106. Jayaswal V, Lutherborrow MA, Yang YH
V Jayaswal, M Lutherborrow and Y H Yang: Measures of association for identifying microRNA-mRNA pairs of biological interest, PLoS ONE, 7 (2012), no. 1, art. no. e29612.

107. Marques FZ, Campain AE, Tomaszewski M, Zukowska-Szczechowska E, Yang YH, Charchar FJ, Morris BJ
Francine Z Marques, Anna E Campain, Maciej Tomaszewski, Ewa Zukowska-Szczechowska, Yee Hwa J Yang, Fadi J Charchar, Brian J Morris: Gene expression profiling reveals renin mRNA overexpression in human hypertensive kidneys and a role for microRNAs, Hypertension, 58 (2011), 1093–1098.

108. Marques FZ, Campain AE, Davern PJ, Yang YH, Head GA, Morris BJ
Francine Z Marques, Anna E Campain, Pamela J Davern, Yee Hwa J Yang, Geoffrey A Head,and Brian J Morris: Global identification of the genes and pathways differentially expressed in hypothalamus in early and established neurogenic hypertension, Physiological Genomics, 43 (2011), 766–771.

109. Peters T, Bulger DW, Loi TH, Yang YH, Ma C
Tim Peters, David W Bulger,To-Ha Loi, Jean Yee Hwa Yang and David Ma: Two-step cross -entropy feature selection for microarrays - power through complementarity, IEEE/ACM Transactions on computational biology and bioinformatics, 8 (2011), no. 4, 1148–1151.

110. Yang P, Ho JWK, Yang YH, Zhou BB
Pengyi Yang, Joshua WK Ho, Yee Hwa Yang, Bing B Zhou: Gene-gene interaction filtering with ensemble of filters, BMC Bioinformatics, 12, Supp 1 (2011), no. S10, 10 pages.

111. Wu JQ, Dwyer DE, Dyer WB, Yang YH, Wang B, Saksena NK
Jing Qin Wu, Dominic E Dwyer, Wayne B Dyer, Yee Hwa Yang, Bin Wang, Nitin K Saksena: Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease, Retrovirology, 8 (2011), no. 18, 1–21.

112. Loi TH, Campain AE, Bryant A, Molloy TJ, Lutherborrow MA, Turner J, Yang YH, Ma DDF
To Ha Loi, Anna Campain, Adam Bryant, Tim J Molloy, Mark Lutherborrow, Jennifer Turner, Yee Hwa Jean Yang and David DF Ma: Discriminating lymphomas and reactive lymphadenopathy in lymph node biopsies by gene expression profiling, BMC Medical Genomics, 4 (2011), no. 27, 10.

113. Marques FZ, Campain AE, Davern PJ, Yang YH, Head GA, Morris BJ
Francine Z Marques, Anna E Campain, Pamela J Davern, Yee Hwa J Yang, Geoffrey A Head, Brian J Morris: Genes Influencing Circadian Differences in Blood Pressure in Hypertensive Mice, PLoS ONE, 6 (2011), no. 4, 9 pages.

114. Collinson EJ, Wimmer-Kleikamp S, Gerega SK, Yang YH, Parish CR, Dawes IW, Stocker R
Emma J Collinson, Sabine Wimmer-Kleikamp, Sebastien K Gerega, Yee Hwa Yang, Christopher R Parish, Ian W Dawes and Roland Stocker: The yeast homolog of heme oxygenase-1 affords cellular antioxidant protection via the transcriptional regulation of known antioxidant genes, The Journal of Biological Chemistry, 286 (2011), no. 3, 2205–2214.

115. Jayaswal V, Lutherborrow MA, Ma DDF, Yang YH
Jayaswal V, Lutherborrow M, Ma DD, Yang YH: Identification of microRNA-mRNA Modules using Microarray Data, BMC Genomics, 12 (2011), 138.

116. Lutherborrow MA, Bryant A, Jayaswal V, Agapiou D, Palma CA, Yang YH, Ma DDF
Lutherborrow M, Bryant A, Jayaswal V, Agapiou D, Palma C, Yang YH, Ma DD: Expression profiling of cytogenetically normal acute myeloid leukemia identifies microRNAs that target genes involved in monocytic differentiation, American Journal of Hematology, 86 (2011), no. 1, 2–11.

117. Jensen SO, Apisiridej S, Kwong SM, Yang YH, Skurray RA, Firth N
Slade O Jensen, Sumalee Apisiridej, Stephen M Kwong, Yee Hwa Yang, Ronald A Skurray, Neville Firth: Analysis of the prototypical Staphysococcus aureus multiresistance plasmid pSK1, Plasmid, 64 (2010), 135–142.

118. Wang P, Yang P, Arthur J, Yang YH
Penghao Wang, Pengyi Yang, Jonathan Arthur and Jean Yee Hwa Yang: A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data, Bioinformatics, 26 (2010), no. 18, 2242–2249.

119. Karim RZ, Gerega SK, Yang YH, Spillane AJ, Carmalt H, Scolyer RA, Lee CS
Rooshdiya Z Karim, Sebastien K Gerega, Y H Yang, Andrew Spillane, Hugh Carmalt, Richard A Scolyer& C Soon Lee: p16 and pRb immunohistochemical expression increases with increasing tumour grade in mammary phyllodes tumours, Histopathology, 56 (2010), 868–875.

120. Campain AE, Yang YH
Anna Campain and Yee Hwa Yang: Comparison study of microarray meta-analysis, BMC Bioinformatics, 11 (2010), no. 48, 1–11.

121. Marques FZ, Campain AE, Yang YH, Morris BJ
Francine Z Marques, Anna E Campain, Yee Hwa J Yang and Brian J Morris: Meta-Analysis of genome-wide gene expression differences in onset and maintenance phases of genetic hypertension, Hypertension, 56 (2010), no. 2, 319. MR1669452

122. Jayaswal V, Lutherborrow MA, Ma DDF, Yang YH
Jayaswal V, Lutherborrow M, Ma DD, Yang YH: Idntification of microRNAs with regulatory potential using a matched microRNA -mRNA time-course data, Nucleic Acids Research, 37 (2009), no. 8, e60.

123. Karim RZ, Li W, Sanki A, Colman MH, Yang YH, Thompson JF, Scolyer RA
Karim RZ, Li W, Sanki A, Colman MH, Yang YH, Thompson JF, Scolyer RA: Reduced p16 and increased cyclin D1 and pRb expression are correlated with progression in cutaneous melanocytic tumors., International Journal of Surgical Pathology, 17 (2009), no. 5, 361–367.

124. Karim RZ, Gerega SK, Yang YH, Horvath LG, Spillane AJ, Carmalt H, Solyer RA, Lee CS
Karim RZ, Gerega SK, Yang YH, Horvath L, Spillane A, Carmalt H, Scolyer RA, Lee CS: Proteins from the Wnt pathway are involved in the pathogenesis and progression of mammary phyllodes tumours, Journal of Clinical Pathology, 62 (2009), no. 11, 1016–1020.

125. Karim RZ, Gerega SK, Yang YH, Spillane AJ, Carmalt H, Scolyer RA, Lee CS
Karim RZ, Gerega SK, Yang YH, Spillane A, Carmalt H, Scolyer RA, Lee CS: Phyllodes tumours of the breast: a clinicopathological analysis of 65 cases from a single institution., Breast, 18 (2009), no. 3, 165–170.

126. Wu JQ, Dwyer DE, Dyer WB, Yang YH, Wang B, Saksena NK
Wu JQ, Dwyer DE, Dyer WB, Yang YH, Wang B, Saksena NK: Transcriptional profiles in CD8+T cells from HIV plus progressors on HAART are characterized by coordinated up-regulation of oxidative phosphorylation enzymes and interferon responses, Virology, 380 (2008), no. 1, 124–135.

127. Kechris K, Yang YH, Yeh RF
Kechris K, Yang YH, Yeh RF: perdiction of alternatively skipped exons and splicing enhancers from exon junction arrays, BMC Genomics, 9 (2008), 551.

128. Lewis CC, Yang YH, Huang X, Banerjee SK, Blackburn MR, Baluk P, McDonald DM, Blackwell TS, Nagabhushanam V, Peters W, Voehringer D, Erle DJ
Lewis CC, Yang JY, Huang X, Banerjee SK, Blackburn MR, Baluk P, McDonald DM, Blackwell TS, Nagabhushanam V, Peters W, Voehringer D, Erle DJ.: Disease-specific gene expression profiling in multiple models of lung disease., American journal of respiratory and critical care medicine, 177 (2008), no. 4, 376–387.

129. Yang YH
Jean Yee Hwa Yang: Microarrays - Planning your experiment, Clinical Bioinformatics, Methods in Molecular Medicine, Humana Press, NJ USA, (2007), 71–85. ISBN 978-1-58829-791-4.

130. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH
Woodruff P.G., Boushey H.A., Dolganov G.M, Barker C.S., Yang Y.H.,: Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids, PNAS, 104 (2007), no. 40, 15858–15863.

131. Williams E, Xiao YY, Sickles H, Shafer P, Yona G, Yang YH, Lin F
E Williams, Y Xiao, H Sickles, P Shafer, G Yona, J Yang, D Lin: Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular, BMC Development Biology, 7 (2007), no. 48, 1.

132. Xiao YY, Segal MR, Yang YH, Yeh RF
Xiao, Y.Y., Segal, M., Yang, Y.H. and Yeh, R. F.: A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarray., Bioinformatics, 23 (2007), no. 12, 1459–1467.

133. Winn VD, Haimov-Kochman R, Paquet AC, Yang YH, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ
Winn, V.D., Haimov-Kochman, R., Paquet, A.C., Yang, Y.J., Madhusudhan, M.S.,Gormley, M., Feng, K.T., Bernlohr, D.A., McDonagh, S., Pereira, L., Sali, A. and Fisher,S.J.: Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term., Endocrinology, 148 (2007), no. 3, 1059–79.

134. Woodruff PG, Koth LL, Yang YH, Rodriguez MW, Favoreto S, Dolganov GM, Paquet AC, Erle DJ
Woodruff, P.G., Koth, L.L., Yang, Y.H., Rodriguez, M.W., Favoreto, S., Dolganov,G.M., Paquet, A.C. and Erle, D.J.: A distinctive alveolar macrophage activation state induced by cigarette smoking, Am J Respir Crit Care Med,, 172 (2005), 1383–1392.

135. Xiao YY, Yang YH, Burckin TA, Shiue L, Hartzog GA, Segal MR
Xiao, Y., Yang, Y. H., Burckin, T.A., Shiue, L., Hartzog, G.A., Segal, M.R..: analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing, PLoS Comput Biol., 1 (2005), no. 4, e39.

136. Kuperman DA, Lewis CC, Woodruff PG, Rodriguez MW, Yang YH, Dolganov GM, Fahy JV, Erle DJ
Kuperman, D.A., Lewis, C.C.,Woodruff, P.G., Rodriguez, M.W., Yang, Y.H., Dolganov,G.M., Fahy, J.V., Erle, D.J..: Dissecting asthma using focused transgenic modeling and functional genomics., J Allergy Clin Immunol., 116 (2005), no. 2, 305–311.

137. Barker CS, Griffin C, Dolganov GM, Hanspers K, Yang YH, Erle DJ
Barker, C., Griffin, C. Dolganov, G., Hanspers, K., Yang, J.and Erle, D.J.: Increase DNA hybridization specificity using sscDNA targets., BMC Genomics, 6 (2005), no. 1, 57.

138. Xiao YY, Segal MR, Yang YH
Xiao, Y. Y., Segal, M. and Yang, Y. H.: Stepwise Normalization of Two-Channel Spotted Microarrays., Statistical Applications in Genetics and Molecular Biolog,, 4 (2005), Article 4.

139. Gonzalez R, Yang YH, Griffin C, Allen L, Tigue Z, Dobbs L
Gonzalez, R., Yang, Y. H., Griffin, C., Allen, L., Tigue, Z. and Dobbs, L.: Freshly isolated Rat Alveolar Type I Cells, Type II Cells, and Cultured Type II Cells Have Distinct Molecular Phenotypes., Am J Physiol Lung Cell Mol Physiol., 288 (2005), no. 1, L179–89.

140. Yang YH, Xiao YY, Segal MR
Yang, Y. H., Xiao, Y. Y. and Segal, M.: Identifying differentially expressed genes from microarray experiments via statistic synthesis., Bioinformatics, 21 (2005), 1084–1093.

141. Lin DM, Yang YH, Scolnick J, Brunet L, Marsh M, Peng V, Okazaki Y
Lin D, Yang Y. H., Scolnick J., Brunet L., Marsh M., Peng V., Okazaki Y.,: Spatial patterns of gene expression in the olfactory bulb., PNAS,, 101 (2004), no. 34, 12718–12723.

142. Rodriguez MW, Paquet AC, Yang YH, Erle DJ
Rodriguez, M.W., Paquet, A.C., Yang, Y. H. and Erle, D.J.: Differential gene expression by integrin beta7+and beta7-memory T helper cells., BMC Immunology, NA (2004), 5–13.

143. Yang YH, Speed TP
Yang, Y. H. and Speed, T. P.: Design and Analysis of Comparative Microarray Experiments, Statistical Analysis of Gene Expression Microarray Data,, Chapman & Hall., New York, (2003), 35–92. ISBN 1-58488-327-8.

144. Erle DJ, Yang YH
Erle, D.J. and Yang, Y. H.: Asthma investigators begin to reap the fruits of genomics., Genome Biology,, 4 (2003), no. 11, 232. MR2311406

145. Diaz E, Yang YH, Loh KC, Tessier-Lavigne M, Speed TP, Ngai J
Diaz, E., Yang, Y. H., Loh, K. C., Tessier-Lavigne, M., Speed, T. P. and Ngai, J.: Molecular analysis of positional identity in the developing mouse retina., PNAS, 100 (2003), no. 9, 5491–5496.

146. Ball CA, Chen Y, Panavally S, Sherlock G, Speed TP, Spellman PT, Yang YH
C.A. Ball, Y. Chen, S. Panavally, G. Sherlock, T. Speed, P.T. Spellman, Y.H. Yang: Section7: An introduction to microarray bioinformatics., DNA Microarrays: A Molecular Cloning Manual., Cold Spring Harbor Press, Cold Spring Harbor, New York, (2002), 509–602. ISBN 0-87969-625-7.

147. Diaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P
Diaz, E., Ge, Y., Yang, Y. H., Loh, K.C., Serafini, T.A., Okazaki, Y., Hayashizaki, Y.,Speed. T.P., Ngai, J., and Scheiffele, P.: Molecular Analysis of Gene Expression in the Developing Pontocerebellar Projection System., Neuron, 36 (2002), no. 3, 417–434.

148. Yang YH, Speed TP
Yang, Y. H. and Speed, T. P.: Design issues for cDNA microarray experiments., Nature Review Genetics, 3 (2002), 579–558.

149. Speed TP, Yang YH
Speed, T. P. and Yang, Y. H.: Direct versus indirect designs for cDNA microarray experiments., Sankhya Series A,, 64 (2002), no. Series A, Pt 3, 706–720.

150. Yang YH, Buckley MJ, Dudoit S, Speed TP
Yang, Y. H., Buckley, M. J., Dudoit, S., and Speed, T. P.: Comparison of methods for image analysis on cDNA microarray data, Journal of Computational and Graphical Statistics, 11 (2002), 108–136. MR1963244

151. Yang YH, Dudoit S, Callow MJ, Speed TP
Yang, Y. H., Dudoit, S., Callow, M. J. and Speed, T. P.: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments., Statistica Sinica, 12 (2002), 111–139. MR1894191

152. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J and Speed TP: Normalization for cDNA microarray data: a composite method addressing local, global and multiple slide systematic variation., Nucleic Acid Research, 30 (2002), no. 4, E15.

153. Yang YH, Buckley MJ, Speed TP
Yang YH, Buckley MJ and Speed TP: Analysis of cDNA microarray images., Briefings in Bioinformatics,, 2 (2001), 341–349.

Number of matches: 153