{"id":11,"date":"2021-10-13T17:14:29","date_gmt":"2021-10-13T17:14:29","guid":{"rendered":"https:\/\/www.lisanwanglab.org\/yyee\/?page_id=11"},"modified":"2022-01-04T16:18:21","modified_gmt":"2022-01-04T21:18:21","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.lisanwanglab.org\/yyee\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

Google Scholar<\/h2>\n\n\n\n

Also see my Google Scholar<\/a> page.<\/p>\n\n\n\n

* denotes co-first authorship.<\/p>\n\n\n\n

Peer Reviewed Publications<\/h2>\n\n\n\n

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1. Kuksa P.P., Liu C.-L., Fu W., Qu L., Zhao Y., Katanic Z., Kuzma A.B., Ho P.-C., Tzeng K.-T., Valladares O., Chou S.-Y, Naj A.C, Schellenberg G.D., Wang L.-S., Leung Y.Y<\/span> (2021) “Alzheimer’s disease variant portal (ADVP): a catalog of genetic findings for Alzheimer’s disease<\/strong>“. In Press: Journal of Alzheimer’s disease<\/em>. doi: https:\/\/doi.org\/10.1101\/2020.09.29.20203950 Link (PMID: NA)<\/a> <\/p>\n\n\n\n

2. Lee W.-P., Tucci A.A., Conery M., Leung Y.Y.<\/span>, Kuzma A.B., Valladares O., Chou Y.-F., Lu W., Wang L.-S., Schellenberg G.D., Tzeng J.-Y. (2021) “Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project<\/strong>“. Front Genet<\/em>; doi: 10.3389\/fgene.2021.752390. Link (PMID: 34804120)<\/a><\/p>\n\n\n\n

3. Jin B., Capra J.A., Benchek P., Wheeler N., Naj A.C., …, Leung Y.Y.<\/span>, …, Haines J.L., Crawford D.C., Bush W.S. (2021) “An Association Test of the Spatial Distribution of Rare Missense Variants within Protein Structures Improves Statistical Power of Sequencing Studies<\/strong>“. BioRxiv<\/em>; doi: https:\/\/doi.org\/10.1101\/2021.08.09.455695 <\/p>\n\n\n\n

4. Naj A.C., Leonenko G., Jian X., Grenier-Boley B., Dalmasso M.C., Bellenguez ., …, Leung Y.Y.<\/span>, …, Williams J., Lambert J.-C., Schellenberg G.D. (2021) “Genome-Wide Meta-Analysis of Late-Onset Alzheimer\u2019s Disease Using Rare Variant Imputation in 65,602 Subjects Identifies Novel Rare Variant Locus NCK2: The International Genomics of Alzheimer\u2019s Project (IGAP)<\/strong>“. medRxiv<\/em>; doi: https:\/\/doi.org\/10.1101\/2021.03.14.21253553<\/p>\n\n\n\n

5. Kuksa P.P, Gangadharan P., Katanic Z., Kleidermacher L., Amlie-Wolf A., Lee C.-Y., Qu L., Greenfest-Allen E., Valladares O., Leung Y.Y.<\/span>, Wang L.-S. (2021) “FILER: a framework for harmonizing and querying large-scale functional genomics knowledge<\/strong>“. In press: NAR Genomics and Bioinformatics<\/em>. doi: https:\/\/doi.org\/10.1101\/2021.01.22.427681 Link (PMID: NA)<\/a><\/p>\n\n\n\n

6. Amlie-Wolf A., Kuksa P.P., Lee C.-Y., Mlynarski E.E., Leung Y.Y.<\/span>, Wang L.-S. (2021) “Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations<\/strong>“. Methods Mol Biol<\/em>.; doi: 10.1007\/978-1-0716-1158-6_6. Link (PMID: 33326071)<\/a><\/p>\n\n\n\n

7. Kunkle B.W., Schmidt M., Klein H.-U., Naj A.C., Hamilton-Nelson K.L., Larson E.B., …, Leung Y.Y.<\/u>, …, Schellenberg, G.D., Mayeux R., Pericak-Vance, M.A., Reitz, C. and the Writing Group for the Alzheimer\u2019s Disease Genetics Consortium (ADGC) (2021) “Novel Alzheimer disease risk loci and pathways in African American individuals using the African genome resources panel: a meta-analysis<\/strong>“. JAMA Neurol.<\/em>; doi: 10.1001\/jamaneurol.2020.3536 Link (PMID: 33074286)<\/a><\/p>\n\n\n\n

8. Greenfest-Allen E., Klamann C., Gangadharan P., Kuzma A., Leung Y.Y.<\/u>, Valladares O., Schellenberg G., Stoeckert C.J., Wang L.-S.. (2021) “NIAGADS Alzheimer\u2019s GenomicsDB: A resource for exploring Alzheimer\u2019s Disease genetic and genomic knowledge.<\/strong>“, BioRxiv<\/em>; doi: https:\/\/doi.org\/10.1101\/2020.09.23.310276 <\/p>\n\n\n\n

9. Kling M.A., Goodenowe D.B., Senanayake V., M. Siamak, Arnold M., Massaro T.J., Baillie R., Han X., Leung Y.Y.<\/u>, Nho K., Kueider-Paisley A., Tenenbaum J.D., Wang L.-S., Shaw L.M., Trojanowski J.Q., Kaddurah-Daouk R.F., for the Alzheimer’s Disease Metabolomics Consortium (ADMC) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI)*(2020) “Circulating ethanolamine plasmalogen indices in Alzheimer’s disease: Relation to diagnosis, cognition, and CSF tau.”<\/b>, Alzheimers Dement.<\/em>; doi: https:\/\/doi.org\/10.1002\/alz.12110 Link (PMID: 32715599)<\/a>   <\/p>\n\n\n\n

10. Kuksa P.P., Li F., Kannan S., Gregory B.D., Leung Y.Y.<\/u>, Wang L-S. (2020) “HiPR: High-throughput Probabilistic RNA structure inference.”<\/b>, Computational and Structural Biotechnology<\/em>; doi: 10.1016\/j.csbj.2020.06.004 Link (PMID: 32637050)<\/a>   <\/p>\n\n\n\n

11. Kuksa P.P., Lee C.-Y., Amlie-Wolf A., Gangadharan P., Mlynarski E.E., Chou Y.-F., Lin H.-J., Issen H., Greenfest-Allen E., Valladares O., Leung Y.Y.<\/u>, Wang L-S. (2020) “SparkINFERNO: A scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.”<\/b>, Bioinformatics<\/em>; doi: 10.1093\/bioinformatics\/btaa246 Link (PMID: 32330239) <\/a>   <\/p>\n\n\n\n

12. Amlie-Wolf A., Tang M., Way J., Dombroski B., Jiang M., Vrettos N., Chou Y.-F., Zhao Y., Kuzma A., Mlynarski E.E., Leung Y.Y.<\/u>, Brown C.D., Wang L.-S., G.D. Schellenberg (2019) “Inferring the molecular mechanisms of noncoding Alzheimer’s disease-associated genetic variants.”<\/b>, Journal of Alzheimer’s Disease<\/em>; doi: 10.3233\/JAD-190568 Link (PMID: 31561366)<\/a>   <\/p>\n\n\n\n

13. Leung Y.Y.<\/u>, Valladares O., Chou Y.-F., Lin H.-J., Kuzma A., Cantwell L., Qu L., Gangadharan P., Alzheimers Disease Sequencing Project (ADSP), Salerno W.J., Schellenberg G.D., Wang L.-S.(2018) “VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project.”<\/b>, Bioinformatics<\/em>; doi: 10.1093\/bioinformatics\/bty894 Link (PMID: 31004159)<\/a>   <\/p>\n\n\n\n

14. Kuksa P.P., Amlie-Wolf A., Katanic Z., Valladares O., Wang L.-S., Leung Y.Y.<\/u> (2018) “DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.”<\/b>, Bioinformatics<\/em>; doi: 10.1093\/bioinformatics\/bty709 Link (PMID: 30668832)<\/a>   <\/p>\n\n\n\n

15. Kuksa P.P., Amlie-Wolf A., Katanic Z., Valladares O., Wang L.-S., Leung Y.Y.<\/u> (2018) “SPAR: Small RNA-seq Portal for Analysis of sequencing expeRiments.”<\/b>, Nucleic Acids Res<\/em>, doi: 10.1093\/nar\/gky330 Link (PMID: 29733404)<\/a>   <\/p>\n\n\n\n

16. Butkiewicz M., Blue E., Leung Y.Y.<\/u>, Jian X., Marcora E., Renton A., Kuzma A., Wang L.-S., Koboldt D., Haines J.L., Bush W.S. (2018) “Functional Annotation of genomic variants in studies of Late-Onset Alzheimer’s Disease. “<\/b>, Bioinformatics<\/em>, doi: 10.1093\/bioinformatics\/bty177 Link (PMID: 29590295)<\/a>   <\/p>\n\n\n\n

17. Kuksa P.P., Leung Y.Y.<\/u>, 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. “<\/b>, Methods in Molecular Biology – RNA methylation protocol<\/em>, doi: 10.1007\/978-1-4939-6807-7_14 Link (PMID: 28349463)<\/a>   <\/p>\n\n\n\n

18. Kuzma A., Valladares O., Cweibel R., Greenfest-Allen E., Childress D.M., Malamon J., Gangadharan P., Zhao Y., Qu L., Leung Y.Y.<\/u>, 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. “<\/b>, Alzheimer’s & Dementia<\/em>, doi: https:\/\/doi.org\/10.1016\/j.jalz.2016.08.018 Link (PMID: NA)<\/a>   <\/p>\n\n\n\n

19. Torres C., Crowe E.P., Tuzer F., Gregory B.D., Donahue G., Gosai S.J., Cohen J., Leung Y.Y.<\/u>, 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. “<\/b>, Front Aging Neurosci<\/em>, doi: 10.3389\/fnagi.2016.00208 Link (PMID: 27630559)<\/a>   <\/p>\n\n\n\n

20. Leung Y.Y.*<\/u>, 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. “<\/b>, Nucleic acids research<\/em>, doc: https:\/\/doi.org\/10.1093\/nar\/gkv1188 Link (PMID: 26553799)<\/a>   <\/p>\n\n\n\n

21. Leung Y.Y.<\/u>, 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. “<\/b>, Alzheimer’s & Dementia: Diagnosis, Assessment and Disease Monitoring<\/em>, doi: 10.1016\/j.dadm.2015.06.008 Link (PMID: 26693175)<\/a>   <\/p>\n\n\n\n

22. Ryvkin P.*, Leung Y.Y.*<\/u>, 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. “<\/b>, Methods<\/em>, doi: https:\/\/doi.org\/10.1016\/j.ymeth.2013.10.002 Link (PMID: 24145223)<\/a>   <\/p>\n\n\n\n

23. Ryvkin P.*, Leung Y.Y.<\/u>*, Silverman I.M.*, Childress M., Valladares O., Dragomir I., Gregory B.D. and Wang L.S. (2013) “HAMR: High throughput Annotation of Modified Ribonucleotides. “<\/b>, RNA<\/em>, doi: doi:10.1261\/rna.036806.112 Link (PMID: 24149843)<\/a>   <\/p>\n\n\n\n

24. Leung Y.Y.*<\/u>, Ryvkin P.*, Gregory B. and Wang L.S. (2013) “CoRAL: Predicting non-coding RNAs from small RNA-sequencing data. “<\/b>, Nucleic Acids Research<\/em>, doi: DOI: 10.1093\/nar\/gkt426 Link (PMID: 23700308)<\/a>   <\/p>\n\n\n\n

25. Leung Y.Y.<\/u>, Chang C.Q. and Hung Y.S. (2012) “An Integrated Approach for Identifying Wrongly Labeled Samples When Performing Classification in Microarray Data. “<\/b>, PLoS ONE<\/em>, doi: https:\/\/doi.org\/10.1371\/journal.pone.0046700 Link (PMID: 23082127)<\/a>   <\/p>\n\n\n\n

26. Wang L.S., Leung Y.Y.<\/u>, 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.”<\/b>, Journal of Alzheimer’s disease<\/em>, doi: doi: 10.3233\/JAD-2012-120082 Link (PMID: 22571982)<\/a>   <\/p>\n\n\n\n

27. Schott J.M., … Leung Y.Y.<\/u>, … ADNI Investigators.(2012) “Using CSF biomarkers to replicate genetic associations in Alzheimer’s disease.”<\/b>, Neurobiol Aging.<\/em>, doi: DOI: 10.1016\/j.neurobiolaging.2011.02.008 Link (PMID: 21459483)<\/a>   <\/p>\n\n\n\n

28. Arnold S.E., Xie S.X., Leung Y.Y.<\/u>, 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. “<\/b>, Translational Psychiatry<\/em>, doi: doi:10.1038\/tp.2011.63. Link (PMID: 22832727)<\/a>   <\/p>\n\n\n\n

29. Arnold S.E., Xie S.X., Leung Y.Y.<\/u>, 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. “<\/b>, Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association<\/em>, doi: https:\/\/doi.org\/10.1016\/j.jalz.2011.05.907 Link (PMID: NA)<\/a>    <\/p>\n\n\n\n

30. Leung Y.Y.<\/u>, and Wang L.S. (2011) “Multi-class classification using covariance among binary classifiers and its application to the analysis of tumor microarrays. “<\/b>, Proceeding of 6th IASTED International Conference on Computational Intelligence and Bioinformatics (CiB)<\/em>, doi: DOI: 10.2316\/P.2011.753-043. Link (PMID: NA)<\/a>    <\/p>\n\n\n\n

31. Leung Y.Y.<\/u>, and Hung Y.S. (2010) “A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification. “<\/b>, IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>, doi: DOI:10.1109\/TCBB.2008.46 Link (PMID: 20150673)<\/a>   <\/p>\n\n\n\n

32. Leung Y.Y.<\/u>, and Hung Y.S. (2009) “An Integrated Approach to Feature Selection and Classification for Microarray Data with Outlier Detection. “<\/b>, Proceeding of 8th Annual International Conference on Computational Systems Bioinformatics (CSB)<\/em>. Link (PMID: NA) <\/a>   <\/p>\n\n\n\n

33. Leung Y.Y.<\/u>, Chang C.Q., Hung Y.S. and Fung P.C.W. (2006) “Gene Selection for Brain Cancer Classification. “<\/b>, Proceeding of IEEE 28th International Conference of the Engineering in Medicine and Biology Society (EMBC)<\/em>, doi: DOI: 10.1109\/IEMBS.2006.260197 Link (PMID: 17947170)<\/a>   <\/p>\n\n\n\n

34. Leung Y.Y.<\/u>, Chang C.Q., Hung Y.S. and Fung P.C.W. (2006) “Gene Selection in Microarray Data Analysis For Brain Cancer Classification. “<\/b>, Proceeding of IEEE 4th International Workshop on Genomic Signal Processing and Statistics (GENSIPS)<\/em>, doi: DOI: 10.1109\/GENSIPS.2006.353175 Link (PMID: NA)<\/a>    <\/p>\n\n\n\n

Conference posters<\/h2>\n\n\n\n

1. Ionita M., Kuksa P.P., Chen C., Leung Y.Y<\/u>, Wang L.-S. “Dissecting multiple-signal GWAS loci and their regulatory roles in Alzheimer\u2019s Disease.<\/strong>“, Virtual Annual Meeting of the American Society of Human Genetics (ASHG), Oct 18-22, 2021. <\/em> <\/p>\n\n\n\n

2. Chung J., Sun X., Schmidt M., Song Y., \u2026, Leung Y.Y<\/u>, \u2026, Kunkle B.W., Martin E.R. “Exome Sequencing Identifies Variants on the X-Chromosome Associated with Alzheimer\u2019s Disease (AD) in the Alzheimer\u2019s Disease Sequencing Project (ADSP)<\/strong>.” Virtual Annual Meeting of the American Society of Human Genetics (ASHG), Oct 18-22, 2021. <\/em> <\/p>\n\n\n\n

3. Leung Y.<\/u>, Kuksa P.P., Chou Y.F., Liu C.-L., Fu W., …, Naj A.C., Schellenberg G.D., Wang L.-S. “Characterization of regulatory roles of genetics signals curated from >200 GWA studies in Alzheimer\u2019s Disease Variant Portal (ADVP).<\/strong>” Virtual Alzheimer’s Association International Conference (AAIC), July 26-30 2021. <\/em> <\/p>\n\n\n\n

4. Lee W.P., Conery M., Valladares O., Chou Y.-F., Leung Y.Y<\/u>, …, Schellenberg G.D., Wang L.-S., Tzeng J.-Y. “Copy Number Variation (CNV) Identification and Association Study on 3,928 Alzheimer\u2019s Disease Whole Genome Sequencing Data from Alzheimer\u2019s Disease Sequencing Project (ADSP).<\/strong>“, Virtual Alzheimer’s Association International Conference (AAIC), July 26-30 2021. <\/em> <\/p>\n\n\n\n

5. Issen H., Kuzma A.B., Valladares O., Greenfest-Allen E., …, Leung Y.Y.<\/u>, …, Naj A.C., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer\u2019s Disease Data Storage Site (NIAGADS): 2021 Update.<\/strong>“, Virtual Alzheimer’s Association International Conference (AAIC), July 26-30 2021. <\/em> <\/p>\n\n\n\n

6. Greenfest-Allen E., Klamann C., Mlynarski E.E., Kuksa P.P., Gangadharan P., Kuzma A.B., Valladares O., Leung Y.Y.<\/u>, Stoeckert C.J., Wang L.-S. “Introducing the NIAGADS Alzheimer\u2019s GenomicsDB API: a toolkit for remote exploration of Alzheimer\u2019s disease genetics.”<\/b>, Virtual Alzheimer’s Association International Conference (AAIC), July 26-30 2021. <\/em> <\/p>\n\n\n\n

7. Leung Y.Y.<\/u>, Kuksa P., Qu L., Zhao Y., Katanic Z., Kuzma A.B., Fu W., Liu C.-L., Ho P.-C., Tzeng K.-T., Valladares O., Chou S.-Y., Naj A.C. Schellenberg G.D., Wang L.-S. “Alzheimer’s disease variant portal (ADVP): harmonized genetics data and evidence collection for Alzheimer’s disease.”<\/b>, Virtual Alzheimer’s Association International Conference (AAIC), July 27-31 2020. <\/em> <\/p>\n\n\n\n

8. Kleidermacher L., Kuksa K., Lee C.-Y., Amlie-Wolf A., Schellenberg G.D., Wang L.-S, Leung Y.Y.<\/u>. “Genome-wide profiling of the noncoding regulatory mechanisms in Alzheimer’s Disease.”<\/b>, Virtual Alzheimer’s Association International Conference (AAIC), July 27-31 2020. <\/em> <\/p>\n\n\n\n

9. Vogel B., Kuzma A., Valladares O., Greenfest-Allen E., Klamann C., Issen H., Gangadharan P., Katanic Z., Zhao Y., Qu L., Lin H.-J., Moon M.K., Leung Y.Y.<\/u>, Naj A.C., Stoeckert Jr. C.J., Schellenberg G.D., Wang L.-S “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Update 2020.”<\/b>, Virtual Alzheimer’s Association International Conference (AAIC), July 27-31 2020. <\/em> <\/p>\n\n\n\n

10. Leung Y.Y.<\/u>, Kuksa P.P., Lee C.-Y., Chou Y.-F., Amlie-Wolf A., Schellenberg G.D., Wang L.-S. “Non-coding regulatory landscape of Alzheimer’s Disease variants using GWAS of 63,926 individuals. “<\/b>, 69th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 14-19, 2019, Houston, Texas. <\/em> <\/p>\n\n\n\n

11. Kuksa P.P., Gangadharan P., Lee C.-Y., Chou Y.-F., Greenfest-Allen E., Lin H.-J., Katani\u0107 Z., Valladares O., Leung Y.Y.<\/u>, Wang L.-S. “GADB: Large-scale, curated Functional Genomics Annotation Database. “<\/b>, 69th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 14-19, 2019, Houston, Texas. <\/em> <\/p>\n\n\n\n

12. Lee C.-Y., Kuksa P.P., Amlie-Wolf A., Mlynarski E.E., Chou Y.-F., Lin H.-J., Greenfest-Allen E., Katanic Z., Valladares O., Kuzma A., Naj A., Schellenberg G.D., Leung Y.Y.<\/u>, Wang L.-S., Alzheimer’s Disease Sequencing Project “INFERNO2: Scalable Spark-based framework for inferring dysregulated enhancer and noncoding RNAs for WGS and GWAS data. “<\/b>, 69th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 14-19, 2019, Houston, Texas. <\/em> <\/p>\n\n\n\n

13. Leung Y.Y.<\/u>, Amlie-Wolf A., Schellenberg G.D., Wang L.-S. “Inferring the Noncoding Regulatory Mechanisms Underlying Genetic Susceptibility Contributed By Different CSF Endophenotypes in AD.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14\u201318 2019, Los Angeles, California. <\/em> <\/p>\n\n\n\n

14. Wang L.-S., Leung Y.Y.<\/u>, Valladares O., Chou Y.-F., Kuzma A.B., Gangadharan P., Cantwell L., Qu L., Lin H.-J., Malamon J., Zhao Y., ADSP, Martin E., Naj A., Schellenberg G.D. “Genome Center for Alzheimer’s Disease whole exome (WES) and whole genome sequencing (WGS) data update.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14\u201318 2019, Los Angeles, California. <\/em> <\/p>\n\n\n\n

15. Greenfest-Allen E., Gangadharan P., Kuzma A.B., Leung Y.Y.<\/u>, Qu L., Klamann C., Valladares O., Stoeckert C.J., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Alzheimer’s GenomicsDB – 2019 Update.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14\u201318 2019, Los Angeles, California. <\/em> <\/p>\n\n\n\n

16. Vogel B., Kuzma A.B., Valladares O., Greenfest-Allen E., Gangadharan P., Zhao Y., Katanic Z., Qu L., Lin H.-J., Moon M.K., Leung Y.Y.<\/u>, Issen H., Klamann C., Naj N., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Update 2019.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14\u201318 2019, Los Angeles, California. <\/em> <\/p>\n\n\n\n

17. Badri, Leung Y.Y.<\/u>, Naj N., Schellenberg G.D., Wang L.-S. “Rare Variants in Familial Late-Onset Alzheimer’s Disease Identified from Large Scale Whole Genome Sequencing.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14\u201318 2019, Los Angeles, California. <\/em> <\/p>\n\n\n\n

18. Chou Y.-F., Leung Y.Y.<\/u>, Valladares O., Lin H.-J., Kuzma A., Cantwell L., Qu L., Gangadharan, P., ADSP, Salerno W.J., Schellenberg G.D., Wang L.-S. “VCPA: Genomic variant calling pipeline and data management tool for Alzheimer’s disease sequencing project. “<\/b>, 68th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 15-20, 2018, San Diego, California. <\/em> <\/p>\n\n\n\n

19. Valladares O., Kuzma A., Greenfest-Allen E., Gangadharan, P., Vogel B., Zhong C., Katanic Z., Qu L., Moon M.K., Leung Y.Y.<\/u>, Naj N., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Update 2018. “<\/b>, 68th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 15-20, 2018, San Diego, California. <\/em> <\/p>\n\n\n\n

20. Greenfest-Allen E., Gangadharan, P., Kuzma A., Qu L., O. Valladares; Leung Y.Y.<\/u>, Bush W., Naj N., Schellenberg G.D., Stoeckert C.J., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) Alzheimer’s genomics database: 2018 update. “<\/b>, 68th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 15-20, 2018, San Diego, California. <\/em> <\/p>\n\n\n\n

21. Greenfest-Allen E., Gangadharan, P., Kuzma A., Qu L., O. Valladares; Leung Y.Y.<\/u>, Bush W., Naj N., Schellenberg G.D., Stoeckert C.J., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) Alzheimer’s genomics database: 2018 update. “<\/b>, 68th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 15-20, 2018, San Diego, California. <\/em> <\/p>\n\n\n\n

22. Amlie-Wolf A., Qu L., Mlynarski E.E., Kuksa P.P., Leung Y.Y.<\/u>, Brown C.D., Schellenberg G.D., Wang L.-S. “Inferring enhancer and noncoding RNA dysregulation underlying 2,419 UK Biobank phenotypes. “<\/b>, *Selected platform talk, 68th Annual Meeting of the American Society of Human Genetics (ASHG), Oct 15-20, 2018, San Diego, California. <\/em> <\/p>\n\n\n\n

23. Xiaoling Zhang, … Leung Y.Y.<\/u>, … Lindsay A Farrer “A rare missense variant of CASP7 is associated with familial late-onset Alzheimer’s disease. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

24. Leung Y.Y.<\/u>, Chou Y., Arnold S.E., Trojanowski J.Q., Schellenberg G.D., Wang L.-S. “CSF Small RNA Biomarkers FOR Alzheimer’S Disease. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

25. Gangadharan P., Leung Y.Y.<\/u>, Valladares O., Chou Y., Kuzma A.B., Cantwell L.B., Qu L., Lin H., Zhao Y., Malamon J.S., Naj A.C., Salerno W.J., Schellenberg G.D., Wang L.-S. “The GCAD Cloud-based Workflow for processing whole exome and whole genome data from the Alzheimer’s Disease Sequencing Project. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

26. Greenfest-Allen E., Gangadharan P., Kuzma A.B., Leung Y.Y.<\/u>, Qu L., Valladares O., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Alzheimer’S Genomics Database. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

27. Vogel B., Kuzma A.B., Valladares O., Greenfest-Allen E., Gangadharan P., Zhao Y., Zhong C., Katanic Z., Qu L., H. Lin, Leung Y.Y.<\/u>, Naj A.C., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): Update 2018. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

28. Kuzma A.B., Faber K.M., Salerno W.J., Leung Y.Y.<\/u>, Cantwell L.B., Gupta N., Fulton R., Valladares O., Vogel B., Applebaum E., Choi S.H., Hamilton-Nelson K.L., Zhao Y., 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. “The Alzheimer’s Disease Sequencing Project (ADSP) data update 2018. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 22\u201326 2018, Chicago, Illinois.<\/em> <\/p>\n\n\n\n

29. Leung Y.Y.<\/u>, Kuksa P.P., Amlie-Wolf A., and Wang L.-S. “The landscape of short RNAs in human cell types and tissues. “<\/b>, *Reviewers’ Choice Abstracts, The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.<\/em> <\/p>\n\n\n\n

30. Chou Y.-F., Leung Y.Y.<\/u>, 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. “<\/b>, The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.<\/em> <\/p>\n\n\n\n

31. Zhao Y., Kuzma A.B., Faber K.M., Salerno W.J., Leung Y.Y.<\/u>, 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. “<\/b>, The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.<\/em> <\/p>\n\n\n\n

32. Kuksa P.P., Leung Y.Y.<\/u>, Amlie-Wolf A., and Wang L.-S. “DASHR 2.0: Database of small non-coding RNAs in normal human tissues and cell types. “<\/b>, The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.<\/em> <\/p>\n\n\n\n

33. Greenfest-Allen E., Gangadharan P., Kuzma A., Qu L., Valladares O., Leung Y.Y.<\/u>, Naj A., Schellenberg G.D., Stoeckert Jr. C.J., Wang. L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) Genomics Database. “<\/b>, The 67th Annual Meeting of the American Society of Human Genetics, Oct 17-21, Orlando, USA.<\/em> <\/p>\n\n\n\n

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

35. Kuzma A., Faber K., Salerno W., Leung Y.Y.<\/u>, Cantwell L.B., Feolo M., Stine A., Gupta N., Fulton R., Valladares O., Cweibel R., Appelbaum E., Choi S.-E., Hamilton-Nelson K.-L., Lin H.-J., Muzny D., Qu L., Reyes-Dumeyer D., Waligorski J., Farrell J., Naj A.C., Bis J.C., Destefano A.L., Seshadri S., Boerwinkle E., Schellenberg G.D., Foroud T.M., L.-S. Wang “THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP) DATA UPDATE 2017. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 16-20 2017, London, UK.<\/em> <\/p>\n\n\n\n

36. Valladares O., Kuzma A., Greenfest-Allen E., Childress D.M., Cweibel R., Gangadharan P., Lin H., Qu L., Leung Y.Y.<\/u>, Naj A.C., Stoeckert C.J., Schellenberg G.D., Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS): 2017. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 16-20 2017, London, UK.<\/em> <\/p>\n\n\n\n

37. Partch A., Valladares O., Cweibel R., Greenfest-Allen E., Childress M., Malamon J., Gangadharan P., Zhao Y., Qu L., Leung Y.Y.<\/u>, Naj A.C., Stoeckert, Jr. C.J., Schellenberg G.D. and Wang L.-S. “NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS). “<\/b>, The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.<\/em> <\/p>\n\n\n\n

38. Leung Y.Y.<\/u>, Kuksa P.P., Amlie-Wolf A., and Wang L.-S. “The landscape of regulatory post-transcriptionally derived small noncoding RNAs in the human transcriptome. “<\/b>, The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.<\/em> <\/p>\n\n\n\n

39. Amlie-Wolf A., Tang M., Kuksa P.P., Leung Y.Y.<\/u>, Slaff B., King J., Dombroski B., Schellenberg G.D., and Wang L.-S. “INFERNO – INFERring the molecular mechanisms of NOncoding genetic variants. “<\/b>, The 66th Annual Meeting of the American Society of Human Genetics, Oct 18-22, Vancouver, Canada.<\/em> <\/p>\n\n\n\n

40. Leung Y.Y.<\/u>*, Kuksa P.P*. Amlie-Wolf A., Valladares O., Gregory B.D. and Wang L.S. “DASHR – Database of small human noncoding RNA. “<\/b>, The 65th Annual Meeting of the American Society of Human Genetics, Oct 6-10 2015, Baltimore, USA.<\/em> <\/p>\n\n\n\n

41. Kuksa P.P.*, Leung Y.Y.*<\/u>, Amlie-Wolf A., Gregory B.D. and Wang L.S. “SPARS – Sequencing-based pipeline for annotating novel small non-coding RNAs. “<\/b>, The 65th Annual Meeting of the American Society of Human Genetics, Oct 6-10 2015, Baltimore, USA.<\/em> <\/p>\n\n\n\n

42. Leung Y.Y.<\/u>, Unger L.H., Gregory B.D. and Wang L.S. “Genome-wide discovery of tissue specific properties of human small non-coding RNAs. “<\/b>, The 64th Annual Meeting of the American Society of Human Genetics, Oct 18-22 2014, San Diego, CA, USA. <\/em> <\/p>\n\n\n\n

43. Ryvkin P.*, Leung Y.Y.<\/u>*, 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. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 13-18 2013, Boston, MA, USA. <\/em> Link<\/a>   <\/p>\n\n\n\n

44. Farnum M., Baek Y., Schultz T., Nefedov A., Xie S.X., Leung Y.Y.<\/u>, 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. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada.<\/em> Link<\/a>   <\/p>\n\n\n\n

45. Nefedov A., Toledo J., Leung Y.Y.<\/u>, 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.”<\/b>, Alzheimer’s Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada. <\/em> Link<\/a>   <\/p>\n\n\n\n

46. Leung Y.Y.<\/u>, 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. “<\/b>, Alzheimer’s Association International Conference (AAIC), July 14-19 2012, Vancouver, British Columbia, Canada. <\/em> Link<\/a>   <\/p>\n\n\n\n

47. Leung Y.Y.<\/u> and Wang L.S. “A Multi-Class Framework for Microarray Data Analysis.”<\/b>, 13th International MGED Meeting, focusing on translational genomics and high throughput sequencing, July 13 – 15 2010, Boston, MA, USA. <\/em> <!–Link (PMID: 24145223)<\/a>  –> <\/p>\n\n\n\n

48. Leung Y.Y.<\/u> and Wang L.S. “An Integrated Approach to Feature Selection and Classification for Microarray Data with Outlier Detection.”<\/b>, 8th Annual International Conference on Computational Systems Bioinformatics (CSB 2009), Stanford University, California. Aug 2009 <\/em> Link<\/a>   <\/p>\n\n\n\n

49. Leung Y.Y.<\/u> and Hung Y.S. “Finding Stable Gene Sets for Microarray Data using Support Vector Machine.”<\/b>, World Congress on Bioengineering (WACBE), July 26-29 2009, Hong Kong. <\/em> <!–Link (PMID: 24145223)<\/a>  –> <\/p>\n\n\n\n

50. Leung Y.Y.<\/u>, Chang C.Q., Hung Y.S. and Fung P.C.W. “Gene Selection for Brain Cancer Classification.”<\/b>, IEEE 28th International Conference of the Engineering in Medicine and Biology Society, New York City, New York, USA Aug\/Sep 2006. <\/em> Link<\/a>   <\/p>\n\n\n\n

51. Leung Y.Y.<\/u>, Chang C.Q., Hung Y.S. and Fung P.C.W. “Gene Selection in Microarray Data Analysis For Brain Cancer Classification.”<\/b>, IEEE 4th International Workshop on Genomic Signal Processing and Statistics (GENSIPS), College Station, Texas, USA May 2006. <\/em> Link<\/a>   <\/p>\n\n\n\n

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CONTACT INFORMATION<\/h2>\n\n\n\n

3700 Hamilton Walk
D101 Richards Medical Research Laboratories
Perelman School of Medicine
University of Pennsylvania
Philadelphia PA 19104<\/p>\n<\/div>\n\n\n\n

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View On Map<\/a>
(215) 573-3729<\/span>
yyee@pennmedicine.upenn.edu<\/a><\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Google Scholar Also see my Google Scholar page. * denotes co-first authorship. Peer Reviewed Publications 1. Kuksa P.P., Liu C.-L., Fu W., Qu L., Zhao Y., Katanic Z., Kuzma A.B., Ho P.-C., Tzeng K.-T., Valladares O., Chou S.-Y, Naj A.C, Schellenberg G.D., Wang L.-S., Leung Y.Y (2021) “Alzheimer’s disease variant portal (ADVP): a catalog of […]<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-11","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/pages\/11","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/comments?post=11"}],"version-history":[{"count":26,"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/pages\/11\/revisions"}],"predecessor-version":[{"id":93,"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/pages\/11\/revisions\/93"}],"wp:attachment":[{"href":"https:\/\/www.lisanwanglab.org\/yyee\/wp-json\/wp\/v2\/media?parent=11"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}