Bioinformatics Publications by FBRCF Members

Aleman MJ, DeYoung MP, Tress M, Keating P, Perry GW, Narayanan R.
Inhibition of Single Minded 2 gene expression mediates tumor-selective apoptosis and differentiation in human colon cancer cells. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12765-70. Epub 2005 Aug 29.

Cai X.,"Exact Stochastic Simulation of Coupled Chemical Reactions with Delays," Journal of Chemical Physics, vol. 126, no. 12, article no. 124108, March 28, 2007. Also in Virtual Journal of Biological Physics Research, April 1, 2007.

Cai X. and Xu Z., "K-Leap Method for Accelerating Stochastic Simulations of Coupled Chemical Reactions," Journal of Chemical Physics, vol. 126, no.7, article no. 074102, February 21, 2007.

Cai X. and Wang X., "Stochastic Modeling and Simulation of Gene Networks," IEEE Signal Processing Magazine, vol. 24, no. 1, pp. 27-36, Jan. 2007.

Cai X. and Giannakis G.B., "Identifying Differentially Expressed Genes in Microarray Experiments with Model-Based Variance Estimation," IEEE Transactions on Signal Processing, vol. 54, no. 6, pp. 2418-2426, June 2006.

DeYoung MP, Tress M, Narayanan R., "Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors". Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4760-5. Epub 2003 Apr 3.

De Young MP, Damania H, Scheurle D, Zylberberg C, Narayanan R.,"Bioinformatics-based discovery of a novel factor with apparent specificity to colon cancer. In Vivo. 2002 Jul-Aug;16(4):239-48.

Guina T, Radulovic D, Bahrami AJ, Bolton DL, Rohmer L, Jones-Isaac KA, Chen J, Gallagher LA, Gallis B, Ryu S, Taylor GK, Brittnacher MJ, Manoil C, Goodlett DR. MglA Regulates Francisella tularensis subsp. novicida Response to Starvation and Oxidative Stress. J. Bacteriol. 2007 Jul 20; [Epub ahead of print]

Foss EJ, Radulovic R, Shaffer SA, Ruderfer, DM, Bedalov A, Goodlett DR & Kruglyak. Genetic basis of proteome variation in yeast. Nature genetics 39: 1369-1375, 2007.

Ramakrishnan S, Sharma HW, Farris AD, Kaufman KM, Harley JB, Collins K, Pruijn GJ, van Venrooij WJ, Martin ML, Narayanan R. Characterization of human telomerase complex. Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10075-9.

Ratan RR. Mining genome databases for therapeutic gold: SIM2 is a novel target for treatment of solid tumors. Trends Pharmacol Sci. 2003 Oct;24(10):508-10.

Scheurle D, DeYoung MP, Binninger DM, Page H, Jahanzeb M, Narayanan R. Cancer gene discovery using digital differential display. Cancer Res. 2000 Aug 1;60(15):4037-43.

Touchette N. Mouse to mice revelation: Genome yields cancer drug target. Genome news network, April 18, 2003.

Zhongwei Li, Xin Gong, Vedang H. Jochi Muxin Li. Co-evolution of tRNA 3' trailer sequences with 3' processing enzymes in bacteria RNA (2005), 11:567-577

Narayanan R., Bioinformatics approaches to cancer gene discovery. Methods Mol Biol. 2007;360:13-31. Review.

Patricia Buendia and Giri Narasimhan, Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach, Bioinformatics, 2007 (in press).

Gudmundsson J., Narasimhan G., Smid M., Distance-preserving Approximations of Polygonal Paths,
Computational Geometry -- Theory and Applications, 36:183-196, 2007.

Patricia Buendia, and Giri Narasimhan, Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network, Bioinformatics, 22(18):2313-2314, 2006.

Yang C., Mills D., Mathee K., Wang Y., Jayachandran K., Sikaroodi M., Gillevet P., Entry J., Narasimhan G.,
An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA, Journal of Microbiological Methods, 65(1):49-62, 2006.

Yang C., Zeng E., Li T., Narasimhan G., Clustering genes using gene expression and text literature data,
Proceedings of CSB'05 Stanford, CA, p329-340, August 2005.

Patricia Buendia and Giri Narasimhan, Sliding "MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach", Bioinformatics, 2007 (in press).

Gudmundsson J., Narasimhan G., Smid M., "Distance-preserving Approximations of Polygonal Paths", Computational Geometry -- Theory and Applications , 36:183-196, 2007.

Patricia Buendia, and Giri Narasimhan, "Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network", Bioinformatics, 22(18):2313-2314, 2006.

Yang C., Mills D., Mathee K., Wang Y., Jayachandran K., Sikaroodi M., Gillevet P., Entry J., Narasimhan G., "An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA", Journal of Microbiological Methods, 65(1):49-62, 2006.

Yang C., Zeng E., Li T., Narasimhan G.,"Clustering genes using gene expression and text literature data", Proceedings of CSB'05, Stanford, CA, p329-340, August 2005.

Shehadeh LA, Liebovitch LS, Jirsa VK, Relationship between global structures of genetic networks and mRNA levels measured by cDNA microarrays.Physica A 364 :297-314 (2006)

Liebovitch LS, Tsinoremas N, Pandya A.Devloping combinatorial multi-component therapies (CMCT) of drugs that are more specific and have fewer side effects than traditional one drug therapies Nonlinear Biomedical Physics (2007) in press.

He D., Wu X., and Zhu X., "SAIL-APPROX: An Efficient On-line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints", Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'07), San Jose, CA, November, 2007.

He Y., Wu X., Zhu X., and Arslan AN, "Mining Frequent Patterns with Wildcards from Biological Sequences", Proceedings of the 2007 IEEE International Conference on Information Reuse and Integration (IRI-07), Las Vegas, USA, pp.329-334, August, 2007.

FBRCF patents and inventions:
For details contact FAU Office of Technology Transfer

Methods of detecting a colon cancer cell- US patent (6,677,119) approved Jan 04
Abstract: Nucleic acids and polypeptides correlated with cancer are disclosed. Also disclosed are methods of detecting cancer in a biological sample by determining expression of a colon carcinoma related gene (CCRG) or protein in that sample.

Association of SIM2 with cancer- US patent (6,780,642) approved Aug 04
Abstract: Disclosed are methods of detecting cancer in a biological sample by detecting SIM2 nucleic acid or protein in the sample. Also disclosed are methods for treating cancer and identifying compounds that modulate SIM2 expression.