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Education
B.S. Biochemistry, Fudan University (1996)
M.S. Computer Science, City College of New York, CUNY (2001)
Qikai Xu
Qikai Xu
Baylor College of Medicine
Department: Molecular & Human Genetics
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Phone: (713) 798-8308
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Honors

John J. Trentin Academic Excellence Award, 2003
Research Topic

Systematic Study of Gene Expression and Function Correlation in Dictyostelium
Research Description
 Gene expression profiling based on DNA microarray technology has been successfully applied in predicting functions for previously undefined genes. However, very poor predictions have also been observed. It has been suggested that expression profiling should be combined with other large-scale data sources such as interactomes and proteomes to make more reliable function predictions. Nevertheless, DNA microarray profiling is still the most convenient tool in the genome-scale study of gene functions.
In our ongoing functional genomic studies in Dictyostelium discoideum, it is critical to know the level of confidence associated with assigning functions to genes based on their expression patterns. We are therefore conducting a systematic study to find out the correlation between gene expression and gene functions. The strategy is to study the correlations in other relatively well annotated genomes like yeast, fruit fly and human, and find out some common rules. For example, we are trying to define which functional categories display consistent expression patterns and which categories do not. We will then apply and refine these rules in Dictyostelium. We have created a Gene Ontology tool, GOAT that can assign genes to hierarchical GO annotation groups. For each GO group, we estimated the homogeneity of gene expression patterns. After finishing the work in yeast, we will apply the method to other species. We will look for evolutionary conservation in groups with good correlation between gene expression and gene function. Finally, we will apply the method to the prediction of gene function in Dictyostelium.
Selected Publications
  • Mariko Katoh, Chad Shaw, Qikai Xu, Nancy Van Driessche, Takahiro Morio, Hidekazu Kuwayama, Shinji Obara, Hideko Urushihara, Yoshimasa Tanaka, and Gad Shaulsky (2004). An orderly retreat: Dedifferentiation is a regulated process. PNAS, 101:7005-7010.
  • Qikai Xu, Miroslava Ibarra, Dana Mahadeo, Chad Shaw, Eryong Huang, Adam Kuspa, David Cotter, and Gad Shaulsky (2004). Transcriptional transitions during Dictyostelium spore germination. Eukaryotic Cell, 3:1101-1110.
  • Tomaz Curk, Janez Demsar, Qikai Xu, Gregor Leban, Uros Petrovic, Ivan Bratko, Gad Shaulsky, and Blaz Zupan(2005). Microarray data mining with visual programming. Bioinformatics. 2005 Feb 1;21(3):396-8
  • Eichinger, L., J.A. Pachebat, G. Glöckner, M.-A. Rajandream, R. Sucgang (first five are co-first authors), M. Berriman, J. Song, R. Olsen, K. Szafranski, Q. Xu, B. Tunggal, S. Kummerfeld, M. Madera, B. A. Konfortov, P. Farbrother, A. T. Bankier, R. Lehmann, N. Hamlin, R. Davies, P. Gaudet, P. Fey, K. Pilcher, G. Chen, D. Saunders, E. Sodergren, P. Davis, A. Kerhornou, X. Nie, N. Hall, C. Anjard, L. Hemphill, N. Bason, F. Rivero, B. Desany, E. Just, T. Morio, R. Rost, C. Churcher, J. Cooper, S. Haydock, N. van Driessche, A. Cronin, I. Goodhead, D. Muzny, T. Mourier, A. Pain, M. Lu, D. Harper, R. Lindsay, H. Hauser, K. James, M. Quiles, M. B. Mohan, T. Saito, C. Buchrieser, A. Wardroper, M. Felder, M. Thangavelu, D. Johnson, A. Knights, H. Loulseged, K. Mungall, K. Oliver, C. Price, M.A. Quail, H. Urushihara, J. Hernandez, E. Rabbinowitsch, D. Steffen, M. Sanders, J. Ma, Y. Kohara, S. Sharp, M. Simmonds, S. Spiegler, A. Tivey, S. Sugano, B. White, D. Walker, J. Woodward, T. Winckler, Y. Tanaka, G. Shaulsky, M. Schleicher, G. Weinstock, A. Rosenthal, E.C. Cox, R. L. Chisholm, R. Gibbs, W. F. Loomis, M. Platzer, R. R. Kay, J. Williams, P. H. Dear, A. A. Noegel, B. Barrell and A. Kuspa. (2005). The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43-57
  • Qikai Xu and Gad Shaulsky (2005) GOAT: an R tool for Gene Ontology enrichment analysis. Applied Bioinformatics. 2005 4(4):281-3
  • Chubb,J.R., G. Bloomfield, Q. Xu, M. Kaller, A. Ivens, J. Skelton, B.M. Turner, W. Nellen, G. Shaulsky, R.R. Kay, W.A. Bickmore and R,H. Singer. (2006) Developmental Timing in Dictyostelium is Regulated by the Set1 Histone Methyltransferase. Developmental Biology, 2006 Feb 7; [Epub ahead of print]
  • J. Song, Q. Xu, R. Olsen, W. F. Loomis, G. Shaulsky, A. Kuspa1, and R. Sucgang.(2006) Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage. PLoS Computational Biology. 1(7), e71
  • M. Katoh, T.Curk, Q.Xu,B.Zupan, A.Kuspa and G.Shaulsky.(2006) Developmentally regulated DNA methylation in Dictyostelium. Eucaryotic Cell, 2006 Jan;5(1):18-25
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Last edited on: December 01, 2006

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