Yi Xing, Ph.D.
Phone: (310)-904-2162, E-mail: yi-xing@uiowa.edu
7/2006-present Assistant Professor
Department of Internal Medicine
Roy J. and Lucille A. Carver College of Medicine, University of Iowa
4/2006-present Visiting Scholar
Department of Statistics, Stanford University, Prof. Wing Wong.
Department of Developmental Biology, Stanford University, Prof. Matthew Scott.
9/2001-4/2006 Graduate Research Assistant
Molecular Biology Institute, University of California Los Angeles, Prof. Christopher Lee.
1/2000-7/2001 Undergraduate Research Assistant
School of Life Sciences, University of Science and Technology of China, Prof. Jing Liu.
2001-2006- Ph.D. Molecular Biology, University of California Los Angeles
1996-2001- B.S. Molecular and Cell Biology; B.E. Computer Science and Technology
University of Science and Technology of China
2006 Finalist, Walter M. Fitch Prize, Society for Molecular Biology and Evolution
2005 UCLA MBI Amgen Dissertation Award
2005 UCLA Dissertation Year Fellowship (2005-2006)
2005 RNA Society Student Fellow Award (Travel Fellowship to ISMB2005)
2003 Outstanding Poster Award, 25th UCLA MBI Arrowhead Research Conference
- Pre-mRNA Splicing and Alternative Splicing
- Comparative and Evolutionary Genomics
- Microarray Data Analysis
2007
22. Xing, Y.*, Ouyang, Z., Kapur, K., Scott, MP., Wong, WH*. (2007) Molecular Biology and Evolution, Accepted. (* joint corresponding authors)
21. Parker, DS., Hsiao, RL., Xing, Y., Resch, A., Lee, C. (2007) Solving the problem of trans-genomic query with alignment tables. IEEE Transactions on Computational Biology and Bioinformatics. In press.
20. Xing,Y., Lee,C. (2007) Relating alternative splicing to proteome complexity and genome evolution. Book chapter, Alternative splicing in the postgenomic era, Eurekah Biosciences Series. In press.
19. Xing,Y. (2007) Genomic analysis of alternative splicing in cancers. Frontiers in Bioscience, In press.
18. Lee , JA., Xing, Y., Nguyen, D., Xie, J., Lee, C., Black, DL. (2007) Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements. PLoS Biology. 5(2):e40.
2006
17. Xing, Y., Kapur, K., Wong, WH. (2006) Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE, 1(1):e88.
16. Xing, Y., Lee, C. (2006) Alternative splicing and RNA selection pressure: evolutionary consequences for eukaryotic genomes. Nature Reviews Genetics, 7:499-509.
15. Xing,Y., Wang, Q., Lee,C. (2006) Evolutionary divergence of exon flanks: A dissection of mutability and selection. Genetics, 173(3):1787-91.
14. Xing,Y. *#,Yu,T. *, Wu, Y., Roy, M., Kim, J., Lee,C.# (2006) An expectation-maximization algorithm for probabilistic reconstruction of full-length isoforms from splice graphs. Nucleic Acids Research, 34:3150-3160 (# joint corresponding authors; * joint first authors)
13. Xing,Y.,Lee,C. (2006) Can RNA selection pressure distort the measurement of Ka/Ks? Gene, 370:1-5
2005
12. Xing,Y.,Lee,C. (2005) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics, 21: 3701-3703.
11. Xing,Y.,Lee,C. (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl. Acad. Sci. U.S.A., 102:13526-13531.
10. Xing,Y.,Lee,C. (2005) Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. PLoS Genetics, 1(3):e34
2004
9. Xing,Y.,Lee,C. (2004) Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends in Genetics. 20:472-5
8. Resch,A., Xing, Y., Alekseyenko, A., Modrek, B., Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res. 32:1261-9
7. Xing,Y.,Resch,A.,Lee,C. (2004) The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures, Genome Research. 14(3):426-41
6. Resch,A., Xing,Y., Modrek,B.,Gorlick,M., Riley,R., Lee, C. (2004) Assessing the impact of alternative splicing on domain interactions in the human proteome, Journal of Proteome Research. 3:76-83
5. Grasso,C.,Modrek,B.,Xing,Y.,Lee,C. (2004) Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pac. Symp. Biocomputing. World Scientific: Singapore 29-41
2003
4. Xing,Y., Xu, Q, Lee,C. (2003) Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains, FEBS Letters 555(3):572-8
3. Zewail,A.*, Xie, M.W.*, Xing, Y., Lin, L., Zhang, P.F., Zou, W., Saxe, J.P., and Huang, J. (2003) Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc. Natl. Acad. Sci. U.S.A. 100: 3345-3350.
2. Lee C, Atanelov L, Modrek B, Xing Y. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res. 31(1):101-5.
2002
1. Cheng, LS., Xing, Y.,Liu J. (2002) Antibody humanization design by computer modeling. Journal of University of Science and Technology of China 32(5):591-601.
2006.5 - Alternative splicing and RNA selection pressure: a new force in genome evolution, Invited Talk, Walter M. Fitch Symposium, Society of Molecular Biology and Evolution 2006 Annual Conference, Tempe, AZ, USA
2006.1 - Evidence of functional selection pressure for tissue-specific alternative splicing events, Poster, UCLA-IPAM Workshop on Sequence Analysis toward Systems Biology
2006.1 - A genomic view of alternative splicing: How alternative splicing helped build the genomes and proteomes. Invited Talk, Stanford University, Palo Alto, CA
2005.9 - Alternative splicing and genome evolution. Invited Talk, Fudan University, Shanghai, China
2005.8 - RNA alternative splicing as an evolutionary strategy. Invited Talk, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
2005.6 - Solving the isoform problem: a key connection between raw alternative splicing data and protein functions. Invited Talk, Alternative Splicing SIG, ISMB2005, Detroit, MI
2005.4 - From genome-wide discoveries of alternative splicing to understanding its impact on the entire proteome. Invited Talk, Experimental Biology 2005, San Diego, CA
2004.10 - Alternative splicing opens neutral paths for evolution, Poster, 2004 NAS Sackler Colloquia on Bioinformatics , Irvine, CA
2004.5 - Alternative splicing and human proteome diversity, Invited Talk, 2004, IPAM Proteomics Symposium, Los Angeles, CA
2004.2 - Inferring full-length transcript and protein isoforms from fragmentary sequence data, Poster, 2004 Gordon Research Conference on Structural , Functional and Evolutionary Genomics, Ventura, CA
2004.1 - Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains, Poster, 2004 Pacific Symposium of Biocomputing, Big Island, HI
2003.10 - Reconstructing human transcriptome by multi-assembly of human expressed sequences, Poster, 25th UCLA MBI Arrowhead Research Conference, Lake Arrowhead, CA
Societies
Member of the International Society for Computational Biology
Member of the RNA Society
Member of the Sigma Xi Society
Member of the Society for Molecular Biology and Evolution
Academic Service
Reviewer for: Nucleic Acids Research, Molecular Biology and Evolution, BMC Genomics, Genome Biology, PNAS, Bioinformatics, PLoS Computational Biology, PLoS Biology