Bioinformatics

Publications

Yi L, S Lu, F Fotouhi, Y Deng, and SJ Brown (2004) Incremental Genetic K-means Algorithm and its Application in Gene Expression Data Analysis, Bioinformatics, 28:172.

Shen J, SI Chang, ES Lee, Y Deng and SJ Brown (2005) Determination of cluster number in clustering microarray data. Applied Mathematics and Computation, 169:1172-1185.

Boyko E, C. M. Smith, T. Vankatappa, J. Bruno, Y. Deng, S. R. Starkey, and D. Klaahsen. (2006) The molecular basis of plant gene expression during aphid invasion: wheat Pto- and Pti-likesequences modulate aphid-wheat interaction. J. Econ. Entomol. 99:1430-1445.

Deng Y, Y Dong, SJ Brown, C Zhang (2006). An Integrated Web-Based Model for Management, Analysis and Retrieval of EST Biological Information, LNCS 3842: 931 – 938.

Wang L, and SJBrown (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Research, 34:W243-W248 (including the cover figure of the Web Server issue).

Wang L and SJ Brown (2006) Prediction of DNA-binding residues from sequence features. Journal of Bioinformatics and Computational Biology, 4:1141-1158.

Wang L and SJ Brown (2006) A support vector machine approach for prediction of DNA-binding residues in protein sequences. In Intelligent engineering systems through artificial neural networks, vol. 16, eds. Dagli et al., pp. 293-298. ASME Press.

Paradesi M.S.R., L Wang, SJ Brown and WH Hsu (2006) Mining domain association rules from protein-protein interaction data. In Intelligent engineering systems through artificial neural networks, vol. 16, eds. Dagli et al., pp. 213-218.

Dearden PK, M Wilson, L Sablan, P Osborne, M Havler, E McNaughton, K Kimura, W Dunn, N Milshina, MHasselmann, T Gempe, M Schioett, J Willi, SJ Brown, C Elsik, P Holland, T Kadowakiand M Beye. (2006) Patterns of conservation and change in Honeybee developmental genes. Genome Research 16:1376-84.

The Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera Nature 443: p931-949.

Wang L, S Wang, Y Li and SJ Brown (2007) Beetlebase: a database for the Tribolium Genome Project NAR (database issue) D476-9.

The Tribolium Genome Sequencing Consortium. (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452:949-55.

Park Y, J Aikins, L Wang, RW Beeman, B Oppert, J Lord, SJ Brown, MD Lorenzen, S Richards, GM Weinstock and RA Gibbs. (2008) Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem. Mol Biol. 38:380-386.

Bolognesi R, A Beerman, L Farzana, N Wittkopp, R Lutz, G Balavoine, SJ Brown and R Schröder (2008) Tribolium Wnts: evidence for a larger repertoire in insects with overlapping expression patterns that suggest multiple redundant functions in embyrogenesis. Dev. Genes Evol. 281:193-202.

Shippy T, M Ronshaugen, J Cande, J He, R Beeman, M Levine, SJ Brown and RE Denell (2008) Analysis of the Tribolium Homeotic Complex: Insights into mechanisms constraining insect Hox Clusters. Dev. Genes Evol. 218:127-39.

Wang J, Y Du, S Wang, SJ Brown and Y Park (2008) Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum. Insect Biochem. Mol Biol. 38:490-498.

Wang S, MD Lorenzen, R Beeman and SJ Brown (2008) Analysis of Repetitve DNA distribution patterns in the Tribolium castaneum Genome. Genome Biology epub 9:R61.

Caragea C, D Caragea, A Silvescu and V Honavar (2010) Semi-supervised Prediction of Protein Subcellular Localization Using Abstraction Augmented Markov Models. In: BMC Bioinformatics, Special Issue on Machine Learning in Computational Biology(MLCB). pS6.

Kim HS, T Murphy, J Xia, D Caragea, Y Park, R Beeman, M Lorenzen, J Manak, S Butcher and SJ Brown (2010) BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Journal of Nucleic Acid Research, 2010, Vol. 38, Database issue D437-D442.

Nemoto N, CR Chingakham, T Udagawa, S Wang, E Thorson, Z Winter, T Ohira, M li, L Valasek, SJ Brown and K Asano (2010) Yeast 18s rRNA is Directly Involved in the Ribosomeal Response to Stringent AUG Selection during Translation Initiation. Journal of Biological Chemistry, 285: 322000-33212.

Steller M, S Kambhampati and D Caragea (2010) Comparative analysis of expressed sequence tags from three castes and two life stages of the termite Reticulitermes flavipes, BMC Genomics 2010, 11:463

Travers SE, Z Tang, D Caragea, KA Garrett, S H Hulbert, JE Leach, J Bai, A Saleh, AK Knapp, PA Fay, J Nippert, PS Schnable and MD Smith (2010) Spatial and temporal variation of big bluestem (Andropogon gerardii) transcription profiles with climate change. Journal of Ecology, 98:374-383. Selected as Editor's Choice for March 2010.

Xia J, D Caragea and SJ Brown (2010) Prediction of alternatively spliced exons using support vector machines. In: International Journal on Data Mining and Bioinformatics 4;411-430.

Merzendorfer, H., H.S. Kim, S.S. Chaudhari, M. Kumari, C.A. Specht, S. Butcher, S.J. Brown, J.R. Manak, R.W. Beeman, K.J. Kramer, et al. (2012). Genomic and proteomic studies on the effects of the insect growth regulator diflubenzuron in the model beetle species Tribolium castaneum. Insect Biochem Mol Biol 44: 264-276. PMID: 22212827

Shelton J., Coleman M. C., Herndon N., Lu N., Lam E.T., Anantharaman T. and Brown S.J. (2015). Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool. bioRxiv doi: http://dx.doi.org/ 10.1101/020966. (Accepted in press BMC Genomics).

Shelton J. and Brown S.J. (2015) Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files. bioRxiv doi: http://dx.doi.org/10.1101/024448. (In review BMC Genomics).

Books, Book Chapters and Conference Papers

Yi L, S Lu, F Fotouhi, Y Deng, and SJ Brown (2004) FGKA: A Fast Genetic K-means Algorithm", in (ACM: Proc. of the 19th ACM Symposium on Applied Computing, Nicosia, Cyprus, March, 2004). pp.162-163.

Wang Land SJ Brown (2006) Prediction of RNA-binding residues in protein sequences using support vector machines. In Proceedings of the 28th IEEE Engineering in Medicine and Biology Conference (EMBC 2006), pp. 5830-5833. IEEE Press.

Das S, D Caragea, WH Hsu and SM Welch (Eds.) Computational Methodologies in Gene Regulatory Networks, IGI Publishers, New York. Book chapters received and reviewed. To appear, 2009. (http://www.k-state.edu/cmgrn/).

Xia J, D Caragea and SJBrown (2008) Exploring Alternative Splicing Features using Support Vector Machines. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'08), Philadelphia, PA. [Acceptance rate: 24%]

Paradesi MSR, D Caragea and WH Hsu (2008). Incorporating Graph Features for Predicting Protein-Protein Interactions. Book Chapter. Biological Data Mining in Protein Interaction Networks.Eds.: X.-L. Li and S.-K. Ng. IGI Publishers.

Volkova S, D Caragea, WH Hsu, J Drouhard and L Fowles (2010) Boosting Biomedical Entity Extraction by using Syntactic Patterns for Semantic Relation Discovery. In: Proceedings of the 2010 IEEE/WIC/ACM International Conference on Web Intelligence (WI'10), Toronto, Canada.

Volkova S, D Caragea, WH Hsu, S Bujuru (2010) Animal Disease Event Recognition and Classification. In: Proceedings of the First International Workshop on Web Science and Information Exchange in the Medical Web (MedEx'10). Collocated with the 19th World Wide Web Conference WWW-2010, Raleigh, NC, USA.

Caragea C, A Silvescu, D Caragea, and V Honavar (2010) Semi-Supervised Sequence Classification Using Abstraction Augmented Markov Models. In: Proceedings of the ACM Conference on Bioinformatics and Computational Biology. p257.