Yuk Yee Leung

Publications

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Also see my Google Scholar page.

* denotes co-first authorship.

Peer Reviewed Publications

1. Kuksa P.P., Leung Y.Y., Vandivier L.E., Anderson Z., Gregory B.D. and Wang L.-S. (2017) "In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR. ", Methods in Molecular Biology - RNA methylation protocol 1562, 211-229. Link (PMID: 28349463)  

2. Torres C., Crowe E.P., Tuzer F., Gregory B.D., Donahue G., Gosai S.J., Cohen J., Leung Y.Y., Yetkin E., Nativio R., Wang L.-S., Sell C., Bonini N.M., Berger S.L. and Johnson F.B. (2016) "Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence. ", Front Aging Neurosci. 2016; 8: 208. Link (PMID: 27630559)  

3. Kuzma A., Valladares O., Cweibel R., Greenfest-Allen E., Childress D.M., Malamon J., Gangadharan P., Zhao Y., Qu L., Leung Y.Y., Naj A.C., Stoeckert C.J., Schellenberg G.D., and Wang L.-S. (2016) "NIAGADS: The NIA Genetics of Alzheimer's Disease Data Storage Site. ", Alzheimer's & Dementia 12 (11), 1200-1203 Link (PMID: na)  

4. Leung Y.Y.*, Kuksa P.P.*, Amlie-Wolf A., Valladares O., Ungar L.H., Kannan S., Gregory B.D. and Wang L.-S. (2016) "DASHR - Database of small human noncoding RNA. ", Nucleic acids research 44 (D1), D216-D222. Link (PMID: 26553799)  

5. Leung Y.Y., Toledo J.B, Nefedov A., Polikar R., Raghavan N., Xie S.X., Farnum M., Schultz T., Baek Y., Deerlin V., Hu W.T., Holtzman D.M., Fagan A.M., Perrin R.J., Grossman M., Soares H.D., Kling M.A., Mailman M., Arnold S.E., Narayan V.A., Lee V.M.-Y., Shaw L.M., Baker D., Wittenberg G.M., Trojanowski J.Q., Wang L.S., for the Alzheimer's Disease Neuroimaging Initiative. (2015) "Identifying amyloid-pathology related CSF biomarkers for Alzheimer's disease in a multi-cohort study. ", Alzheimer's & Dementia: Diagnosis, Assessment and Disease Monitoring 1(3):339-348. Link  

6. Ryvkin P.*, Leung Y.Y.*, Unger L.H., Gregory B.D. and Wang L.S. (2013) "Using machine learning and high-throughput RNA sequencing to characterize small non-coding RNAs. ", Methods , 67:28-35. Link (PMID: 24145223)  

7. Ryvkin P.*, Leung Y.Y.*, Silverman I.M.*, Childress M., Valladares O., Dragomir I., Gregory B.D. and Wang L.S. (2013) "HAMR: High throughput Annotation of Modified Ribonucleotides. ", RNA , 19(12):1684-92. Link (PMID: 24149843)  

8. Leung Y.Y.*, Ryvkin P.*, Gregory B. and Wang L.S. (2013) "CoRAL: Predicting non-coding RNAs from small RNA-sequencing data. ", Nucleic Acids Research , 41(14):e137. Link (PMID: 23700308)  

9. Leung Y.Y., Chang C.Q. and Hung Y.S. (2012) "An Integrated Approach for Identifying Wrongly Labeled Samples When Performing Classification in Microarray Data. ", PLoS ONE , 7(10): e46700. doi:10.1371/journal.pone.0046700. Link (PMID: 23082127)  

10. Wang L.S., Leung Y.Y., Chang S.K., Leight S., Knapik-Czajka M., Baek Y., Shaw L.M., Lee V.M., Trojanowski J.Q. and Clark C.M. (2012) "Comparison of xMAP and ELISA assays for detecting cerebrospinal fluid biomarkers of Alzheimer's disease. ", Journal of Alzheimer's disease , 31(2):439-445. Link (PMID: 22571982)  

11.Arnold S.E., Xie S.X., Leung Y.Y., Wang L.S., Kling M.A., Han X., Kim E., Wolk D.A., Bennett D.A., Chen-Plotkin A., Grossman M., Hu W., Lee V.M.-Y., Mackin S., Trojanowski J.Q., Wilson R.S., Shaw L.M. and Alzheimer's Disease Neuroimaging Initiative. (2012) "Plasma Biomarkers of Depressive Symptoms in Older Adults. ", Translational Psychiatry , 2, e65; doi:10.1038/tp.2011.63. Link (PMID: 22832727)  

12.Arnold S.E., Xie S.X., Leung Y.Y., Kim E., Kling M.A., Wilson R., Bennett D., Hu W., Mackin S., Grossman M., Chen-Plotkin A., Wolk D., Lee V.M.-Y., Trojanowski J.Q., and Shaw L.M. (2011) "Biochemical Biomarkers of Depressive Symptoms in ADNI. ", Alzheimer's & Dementia: The Journal of the Alzheimer's Association , 7(4), Supplement, S312. Link  

13. Leung Y.Y., and Wang L.S. (2011) "Multi-class classification using covariance among binary classifiers and its application to the analysis of tumor microarrays. ", Proceeding of 6th IASTED International Conference on Computational Intelligence and Bioinformatics (CiB) , DOI: 10.2316/P.2011.753-043. Link  

14. Leung Y.Y., and Hung Y.S. (2010) "A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification. ", IEEE/ACM Transactions on Computational Biology and Bioinformatics , 7(1), 108-117. Link (PMID: 20150673)  

15. Leung Y.Y., and Hung Y.S. (2009) "An Integrated Approach to Feature Selection and Classification for Microarray Data with Outlier Detection. ", Proceeding of 8th Annual International Conference on Computational Systems Bioinformatics (CSB). Link   

16. Leung Y.Y., Chang C.Q., Hung Y.S. and Fung P.C.W. (2006) "Gene Selection for Brain Cancer Classification. ", Proceeding of IEEE 28th International Conference of the Engineering in Medicine and Biology Society (EMBC) , 1, 5846-5849. Link (PMID: 17947170)  

17. Leung Y.Y., Chang C.Q., Hung Y.S. and Fung P.C.W. (2006) "Gene Selection in Microarray Data Analysis For Brain Cancer Classification. ", Proceeding of IEEE 4th International Workshop on Genomic Signal Processing and Statistics (GENSIPS) , 99-100. DOI:10.1109/GENSIPS.2006.353175. Link  

Conference posters

1.Leung Y.Y., Kuksa P.P., Amlie-Wolf A., and Wang L.-S. "The landscape of short RNAs in human cell types and tissues. ", *Reviewers' Choice Abstracts The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

2. Kuksa P.P., Leung Y.Y., Amlie-Wolf A., and Wang L.-S. "DASHR 2.0: Database of small non-coding RNAs in normal human tissues and cell types. ", The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

3. Chou Y.-F., Leung Y.Y., Valladares O., Kuzma A.B., Cantwell L., Qu L., Lin H.-J., Gangadharan P., Zhao Y., Malamon J., ADSP, Naj A., Salerno W.J., Schellenberg G.D., Wang. L.-S. "The GCAD workflow for processing 5000 whole genomes and 11,000 whole exomes from the Alzheimer's Disease Sequencing Project using Amazon cloud. ", The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

4. Greenfest-Allen E., Gangadharan P., Kuzma A., Qu L., Valladares O., Leung Y.Y., Naj A., Schellenberg G.D., Stoeckert Jr. C.J., Wang. L.-S. "NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) Genomics Database. ", The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

5. Lin H., Valladares O., Kuzma A., Greenfest-Allen E., Gangadharan P., Childress D., Cweibel R., Zhong C., Zhao Y., Qu L., Leung Y.Y., Naj A., Stoeckert Jr. C., Schellenberg G., Wang L.-S. "NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS): Update 2017. ", The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

6. Zhao Y., Kuzma A.B., Faber K.M., Salerno W.J., Leung Y.Y., Cantwell L.B., Feolo M., Stine A., Gupta N., Fulton R., Valladares O., Cweibel R., Applebaum E., Choi S.H., Hamilton-Nelson K.L., Lin H.-J., Muzny D., Qu L., Reyes D., Waligorski J., Farrell J., Naj A.C., Bis J.C., DeStefano A.L., Seshadri S., Boerwinkle E., Schellenberg G.D., Foroud T.M., Wang L.-S., Alzheimer's Disease Sequencing Project Data Flow Work Group. "The Alzheimer's Disease Sequencing Project (ADSP) data update 2017. ", The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.

7. Leung Y.Y., Kuksa P.P., Amlie-Wolf A., and Wang L.-S. "The landscape of regulatory post-transcriptionally derived small noncoding RNAs in the human transcriptome. ", The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.

8. Amlie-Wolf A., Tang M., Kuksa P.P., Leung Y.Y., Slaff B., King J., Dombroski B., Schellenberg G.D., and Wang L.-S. "INFERNO INFERring the molecular mechanisms of NOncoding genetic variants. ", The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.

9. Partch A., Valladares O., Cweibel R., Greenfest-Allen E., Childress M., Malamon J., Gangadharan P., Zhao Y., Qu L., Leung Y.Y., Naj A.C., Stoeckert, Jr. C.J., Schellenberg G.D. and Wang L.-S. "NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS). ", The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.

10. Leung Y.Y.*, Kuksa P.P*. Amlie-Wolf A., Valladares O., Gregory B.D. and Wang L.S. "DASHR - Database of small human noncoding RNA. ", The 65th Annual Meeting of the American Society of Human Genetics, Oct 6-10 2015, Baltimore, USA.

11. Kuksa P.P.*, Leung Y.Y.*, Amlie-Wolf A., Gregory B.D. and Wang L.S. "SPARS - Sequencing-based pipeline for annotating novel small non-coding RNAs. ", The 65th Annual Meeting of the American Society of Human Genetics, Oct 6-10 2015, Baltimore, USA.

12. Leung Y.Y., Unger L.H., Gregory B.D. and Wang L.S. "Genome-wide discovery of tissue specific properties of human small non-coding RNAs. ", The 64th Annual Meeting of the American Society of Human Genetics, Oct 18-22 2014, San Diego, CA, USA.

13. Ryvkin P.*, Leung Y.Y.*, Dragomir I., Greene R., Schuck T., Schellenberg G., Arnold S., Chen-Plotkin A., Unger L.H. , Deerlin V., Trojanowski J.Q., Gregory B.D. and Wang L.S. "Characterizing the Alzheimer's Disease prefrontal cortex transcriptome by multiple RNA-seq. ", Alzheimer's Association International Conference (AAIC), July 13-18 2013, Boston, MA, USA. Link  

14. Farnum M., Baek Y., Schultz T., Nefedov A., Xie S.X., Leung Y.Y., Toledo J., Raghavan N., Chen-Plotkin A., Wolk D., Polikar R., DiBernardo A., Siderowf A., Davatzikos C., Deerlin V., Shaw L., Elman L., Grossman M., Hurtig H., Lobanov V., Arnold S., Narayan V., Lee V.M.-Y., Trojanowski J.Q., Wittenberg G. and Wang L.S. "An Integrated Approach to the Development of Biomarkers for Alzheimer's Disease Using Hospital Population Data. ", Alzheimer's Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada. Link  

15. Nefedov A., Toledo J., Leung Y.Y., Raghavan N., Xie S.X., Polikar R., Farnum M., Schultz T., Baek Y., Lobanov V., DiBernardo A., Narayan V., Lee V.M.-Y., Arnold S., Trojanowski J.Q., Wang L.S. and Wittenberg G. "Neuropathological Subtypes Among Subjects with Alzheimer's disease.", Alzheimer's Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada. Link  

16. Leung Y.Y., Wang L.S., Hu W.T., Kling M.A., Wolk D.A., Trojanowski J.Q., Lee V.M.-Y., Shaw L.M. and Arnold S.E. "Cerebrospinal fluid biochemical biomarkers of depressive symptoms in older adults. ", Alzheimer's Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada. Link  

17. Leung Y.Y. and Wang L.S. "A Multi-Class Framework for Microarray Data Analysis.", 13th International MGED Meeting, focusing on translational genomics and high throughput sequencing, July 13 - 15 2010, Boston, MA, USA.

18. Leung Y.Y. and Hung Y.S. "Finding Stable Gene Sets for Microarray Data using Support Vector Machine.", World Congress on Bioengineering (WACBE), July 26-29 2009, Hong Kong.

Contact Information

3700 Hamilton Walk
D101 Richards Medical Research Laboratories
Perelman School of Medicine
University of Pennsylvania
Philadelphia PA 19104