Yi Xing, Ph.D.

Assistant Professor Internal Medicine and Biomedical Engineering University of Iowa Iowa City, IA 52242 Ph. (319) 384 3099 yi-xing@uiowa.edu

Detailed Personal webpage
Research @ UIBME

• Pre-mRNA Splicing and Alternative Splicing
• Comparative and Evolutionary Genomics
• Microarray Data Analysis

• 2006: Doctor of Philosophy in Molecular Biology, University of California Los Angeles
• 2001: Bachelor of Science in Molecular and Cell Biology; Bachelor of Engineering in Computer Science and Technology, University of Science and Technology, China.

• 10/2007-present: Assistant Professor, Department of Internal Medicine and Biomedical Engineering, University of Iowa
• 4/2006-9/2007: Postdoc, Department of Statistics and Department of Developmental Biology, Stanford University

• 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.
• 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. To appear.
• Xing, Y. (2007) Genomic analysis of alternative splicing in cancers. Frontiers in Biosciences. 12:4034-4041.
• Kapur, K., Xing, Y., Ouyang, Z., Wong, WH. (2007) Exon arrays provide accurate assessments of gene expression. Genome Biology. 8:R82.
• Xing, Y. *, Ouyang, Z., Kapur, K., Scott, MP., Wong, WH*. (2007) Assessing the conservation of mammalian gene expression using high-density Exon Arrays. Molecular Biology and Evolution. 24(6):1-3. (* joint corresponding authors).
• Calarco, JA.*, Xing, Y.*, Caceres, M.*, Calarco, JP., Xiao, X., Pan, Q., Lee, C.,, Preuss, T. and Blencowe, B. (2007) Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Development. To appear. (* joint first authors).
• Xing, Y. (2007) Genomic analysis of alternative splicing in cancers.
  Frontiers in Biosciences. In press.
• 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.
• 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.
• Xing, Y., Kapur, K., Wong, WH. (2006) Probe selection and expression index
  computation of Affymetrix Exon Arrays. PLoS ONE. 1(1):e88.
• 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)
• Xing,Y., Wang, Q., Lee,C. (2006) Evolutionary divergence of exon flanks: A
  dissection of mutability and selection. Genetics. 173(3):1787-91.
• Xing, Y., Lee, C. (2006) Alternative splicing and RNA selection pressure:
  evolutionary consequences for eukaryotic genomes. Nature Reviews Genetics.
  7:499-509.
• Xing,Y.,Lee,C. (2006) Can RNA selection pressure distort the measurement of
  Ka/Ks? Gene. 370:1-5
• Xing,Y.,Lee,C. (2005) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics, 21: 3701-3703.
• 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.
• 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
• 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
• 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
• Xing,Y.,Resch,A.,Lee,C. (2004) The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures, Genome Research. 14(3):426-41
• 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
• 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
• 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
• 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.
• Lee C, Atanelov L, Modrek B, Xing Y. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res. 31(1):101-5.
• 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.