Publications

TargetRNA: a tool for predicting targets of small RNA action in bacteria. Brian Tjaden. Nucleic Acids Research, to appear, 2008. Software available.


Prediction of small, noncoding RNAs in bacteria using heterogeneous data. Brian Tjaden. Journal of Mathematical Biology, 56(1-2):183-200, 2008.


A novel Fur and iron-regulated small RNA, NrrF, is required for indirect Fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis. J.R. Mellin, Sulip Goswami, Susan Grogan, Brian Tjaden, and Caroline A. Genco. Journal of Bacteriology, 189(10):3686-3694, 2007.


A multidisciplinary course in computational biology. Brian Tjaden. Journal of Computing Sciences in Colleges, 22(6):80-87, 2007.


Target prediction for small, noncoding RNAs in bacteria. Brian Tjaden, Sarah S. Goodwin, Jason A. Opdyke, Maude Guillier, Daniel X. Fu, Susan Gottesman, and Gisela Storz. Nucleic Acids Research, 34(9):2791-2802, 2006. Software available.


An approach for clustering gene expression data with error information. Brian Tjaden. BMC Bioinformatics, 7:17, 2006. Supplemental data available.


A Survey of Computational Methods used in Microarray Data Interpretation. Brian Tjaden and Jacques Cohen. Applied Mycology and Biotechnology; Volume 6: Bioinformatics, Elsevier, 2006.


Training students to administer and defend computer networks and systesms. Brian Tjaden and Brett Tjaden. ACM SIGCSE Bulletin, 38(3):245-249, 2006.


Applications of Genomic Data: Microarrays, Expression Analysis, and Bacterial Genomes. Carsten Rosenow and Brian Tjaden. Microbial Genomes, Humana Press, 2004.


Global analysis of small RNA and mRNA targets of Hfq. Aixia Zhang, Karen M. Wassarman, Carsten Rosenow, Brian Tjaden, Gisela Storz, and Susan Gottesman. Molecular Microbiology, 50(4):1111-1124, 2003. Supplemental data available.


Coding in tongues: A bilingual programming perspective to data structures. Brian Tjaden and Hannah Tang. Journal of Computing Sciences in Colleges, 18(5):151-158, 2003.


Initial proteome analysis of model microorganism Haemophilus influenzae Rd strain KW20. Eugene Kolker, Samuel Purvine, Michael Y. Galperin, Serg Stolyar, David R. Goodlett, Alexey I. Nesvizhskii, Andrew Keller, Tao Xie, Jimmy K. Eng, Eugene Yi, Leroy Hood, Alex F. Picone, Tim Cherny, Brian C. Tjaden, Andrew F. Siegel, Thomas J. Reilly, Kira S. Makarova, Bernhard O. Palsson, and Arnold L. Smith. Journal of Bacteriology, 185(15):4593-4602, 2003.


Computational Methods for Transcription Analysis Using Oligonucleotide Microarrays. Brian Tjaden. Doctoral Dissertation, University of Washington, 2003.


Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Brian Tjaden, Rini Mukherjee Saxena, Sergey Stolyar, David R. Haynor, Eugene Kolker, and Carsten Rosenow. Nucleic Acids Research, 30(17):3732-3738, 2002. Supplemental data available.


Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. Brian Tjaden, David R. Haynor, Sergey Stolyar, Carsten Rosenow, and Eugene Kolker. Bioinformatics, 18: S337-S344, 2002. Supplemental data available.


Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data. Eugene Kolker, Brian C. Tjaden, Robert Hubley, Edward N. Trifonov, Andrew F. Siegel. Omics: A Journal of Integrative Biology, 6(1):123-130, 2002.


System and method for efficient and adaptive web accesses filtering. Sandeep R. Nair, Kingsum Chow, Ken T. Deeter, and Brian C. Tjaden. United States Patent Application 20020178169, filed May 23, 2001, published November 28, 2002.


Geographic location determination including inspection of network IP address. Kingsum Chow, Sumeet Dua, and Brian C. Tjaden. United States Patent Application 20020143991, filed March 16, 2001, published October 3, 2002.


The inverse nearest neighbor problem with astrophysical applications. Richard Anderson and Brian Tjaden. Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, 767-768, 2001.