Teaching Fields:

• BIOI 4860/8866 Bioinformatics Algorithms. 3 CR hrs. Every fall, since 2006. Co-teach with Dr. Ali in IS&T.

• BIOI 4960 Seminar (Colloquium) in Bioinformatics. 1 CR hr. Every fall, since 2006.

• BIOL 4050 Bioinformatics Programming. 3 CR hrs. Summer 2007.

• BIOI 3000 Applied Bioinformatics. 3 CR hrs. Every spring, since 2006.

• BIOI 1000 Introduction to Bioinformatics. 3 CR hrs. Fall 2005. Co-taught with Dr. Pauley in IS&T.

Research Interests:

We are interested in bioinformatics, with particular research interests in evolutionary bioinformatics and influenza viral genomics. My lab develops a variety of databases and computational tools to facilitate a broad spectrum of biological and medical research. Currently we have several ongoing projects as summrized below:

(1) Assembling the Euteleost Tree of Life (ETOL), funded by NSF. This collaborative research involves 9 PIs from 8 institutions. We are committed to developing infrastructure to facilitate research coordination and dissemination of study results. In addition, we take care of the development of nuclear gene markers for fish phylogeny analysis. See Phylomarker website for the progress of phylogenetic marker development and source code download. The ETOL project has its own website at http://www.fishtree.org.

(2) G-protein coupled receptor (GPCR) mining system, funded by NIH (sub-agreement with UNL, PI: Dr E. Moriyama). We are developing a hierarchical protein family prediction system for mining GPCRs from many genomes. My Lab is involved in the development of database and Web interface. To know what the system can do for you, check our website: http://bioinfolab.unl.edu/emlab/7tmr/.

(3) Influenza A virus genomics. In collaboration with Dr. Ruben Donis at CDC (http://www.cdc.gov/), we are developing an application for genotyping avian flu viruses. We expect to apply this tool for the study of virus evolution, specially the genome reassortment events. Plenty of functions are available in the project website, http://www.flugenome.org.

(4) World-wide genetic variations of Asian carps, funded by National Natural Science Foundation of China (NSFC), PI: Sifa Li, SHFU. Our involvement is to collect samples from the US and conduct bioinformatics analysis.

Selected Publications:

1. Gustsche, A., T. Heng-Moss, G. Sarath, P. Twigg, Y. Xia, G. Lu and D. Mornhinweg. 2008. Gene expression profiling of tolerant barley in response to Diuraphis noxia (Hemipetra: Aphididae) feeding. The Bulletin of entomological Research 10: 1-11. Link to Pubmed.
2. Wang, C., Q. Chen, G. Lu, J. Xu, Q. Yang and S. Li. 2008. Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96-101. Link to ScienceDirect.
3. Lu, G., T. Rowley, T. Davis, and R. Donis. 2008. A Web-based tool for the clade designation of highly pathogenic avian influenza H5N1 viruses in Options for the Control of Influenza VI. J.M. Katz (Eds.) International Medial Press, London, 397-399.
4. Zhang, S., X. Fang, T. Davis, R. Donis, G. Lu. 2008. Multidimensional scaling and model-based clustering analyses for the clade assignments of the HPAI H5N1 viruses in Options for the Control of Influenza VI. J.M. Katz (Eds.). International Medial Press, London, 279-281.
   
5. Lu, G. and J. Ni. 2008. Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07). BMC Bioinformatics 9 (Suppl 6): S1.
6. Lu, G., S. Zhang, and X. Fang, 2008. An improved string composition method for sequence comparison. BMC Bioinformatics 9 (Suppl 6): S15.
7. Saleh A, R. Alvarez-Venegas, M. Yilmaz , O. Le, G. Hou, M. Sadder, A. Al-Abdallat, Y. Xia, G. Lu, I. Ladunga, Z. Avramova. 2008. The highly similar arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical tunctions. Plant Cell 20:568-79.
   
8. Lu, G., K. Buyyani, N. Goty, D. Ruben, and Z. Chen. Influenza A virus informatics: genotype-centered database and genotype annotation. The IEEE Conference Proceedings of the Computations in Bioinformatics and Biosciences (SCBB|07). International Multi-Symposiums on Computer and Computational Sciences (IMSCCS), the University of Iowa, Iowa City, Iowa, USA. August 13-15, 2007.
9. Lu, G, T. Rowley, R. Garten, R. Donis. 2007. FluGenome: A web tool for genotyping influenza A virus. Nucleic Acids Research. doi:10.1093/nar/gkm365. [PDF]
   
10. Li C., G. Orti, G. Zhang, and G. Lu. 2007. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evolutionary Biology 7: 44. [PDF]
    
11. Lu, G., T. V. Nguyen, Y. Xiao, and M. Fromm. 2006. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data. BMC Bioinformatics 7(Suppl 4): S26. [PDF]
12. Lu, G., J. Laying, R. M. Koala, T.W. Rowley, L. Zhang, X. Chen, and E. N. Moriyama. 2006. Genome Blast: A Web Tool for Small Genome Comparison. BMC Bioinformatics 7(Suppl 4): S18. [PDF]
13. S. Lopez, G. Lu, and Z. Chen. 2006. XML modeling of miRNA. Workshop NETTAB 2006. Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics. Is Morus Relais, S. Margherita di Pula (CA) And POLARIS Science and Technology Park of Sardinia, Pula (CA). [PDF]
14. R. Alvarez-Venegas, Xia Y, G. Lu, Z. Avramova. 2006. Phosphoinositide 5-Phosphate and Phosphoinositide 4-Phosphate Trigger Distinct Specific Responses of Arabidopsis Genes; Genome-Wide Expression Analyses. Plant Signaling & Behavior 1(3):140-151.
15. Alvarez-Venegas, R, M. Sadder, A. Hlavacka, F. Baluska, Y. Xia, G. Lu, A. Firsov, G. Sarath, H. Moriyama, J. G. Dubrovsky, and Z. Avramova. 2006. The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes. PNAS 103: 6049-6054.
16. Scott, M., G. Lu, M. Hallett, and D. Thomas. 2004. The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics 20: 937-944.
17. De Cock, H. E. V., S. L. Marks, Stacy B. A., Zabka T., Burkitt J., G. Lu, D. J. Steffen and G.E. Duhamel. 2004. Ileocolitis Associated with Anaerobiospirillum in Cats. J. Clin. Microbiol. 42: 2752-2758.
18. G. Lu, and E. Moriyama. 2004.  Vector NTI, a balanced all-in-one sequence analysis suite. Briefings in Bioinformatics 5: 378-388.
19. Duhamel, G. E., C. J. Stryker, G. Lu, V. J. Wong, R. P. Tarara. 2003. Colonic Spiral Bacteriosis of Colony-Raised Rhesus Macaques Associated with Brachyspira and Helicobacter. Anaerobe 9:45-55.
20. Lu, G., M. Hallett, S. Pollock, and D. Thomas. 2003. DePIE: Designing Primers for Protein Interaction Experiments. Nucleic Acids Research 31:3755-3757.

Databases:

• Fugal genome database - genome sequence and annotation of model fungal organisms, with Moriyama and Harris at UNL

• Hera Database - human endoplasmic reticulum (ER) protein database, mainly developed by M Scott, hosted in McGill Center for Bioinformatics

• FluGenome - predicting genotypes of given genome sequences, collaboration with R. Donis in CDC.

Software:

• AffyMiner - microarray data mining. Developed at UNL and UNO.

• DePIE - designing primers for protein interaction experiments, with M. Hallett at McGill

• GenomeBLAST - small genome comparison, with people at UNL and UNO.

• Phylomarker - Mining phylogenetic markers for assembling the Treee of Life.

• Peptide Sorter - sorting de novo peptide lists for known or unknown proteins, with Ingrid Jordon-Thaden and The Nguyen at UNL.

Other Responsibilities:

• Facilitator, UNO Bioinformatics Research Triangle

• Steering committee member, DeepFin - a research coordination network of systematic ichthyologists and biologists

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