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M. Gruell, L. Peña-Castillo, M.E. Mulligan, and A.S. Lang. Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA. RNA Biology 2017. O. Meruvia-Pastor, P. Patra, K. Andres, C. Twomey, and L. Peña-Castillo. OMARC: An online multimedia application for training health care providers in the assessment of respiratory conditions. International Journal of Medical Informatics 2016. (pdf) N. L. Ferguson, L. Peña-Castillo, M.A. Moore, D.R.D. Bignell, and K. Tahlan. Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus. Journal of Industrial Microbiology & Biotechnology 2016. L. Peña-Castillo, M. Gruell, M.E. Mulligan, and A.S. Lang. Detection of bacterial small transcripts from RNA-Seq data: a comparative assessment. In the proceedings of the Pacific Symposium on Biocomputing (PSB) 2016; 21:456-467. L. Peña-Castillo and Gwenael Badis. Systematic determination of transcription factor DNA-binding specificities in Yeast. Protocol. Methods in Molecular Biology 2016; 1361:203-225. P. Patra, T. Izawa, and L. Peña-Castillo. REPA: Applying pathway analysis to genome-wide transcription factor binding data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, July 2015. (pdf) L. Peña-Castillo, R. G. Mercer, A. Gurinovich, S. J. Callister, A. T. Wright, A. B. Westbye, J. T. Betty and A. S. Lang. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics, 15(1):730, August 2014. D. Ray, H. Kazan, E.T. Chan, L. Peña-Castillo, S. Chaudhry, S. Talukder, B.J. Blencowe, Q. Morris, and T.R. Hughes. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotechnology, 27(7):667-670, July 2009. T. M. Alleyne, L. Peña-Castillo, G. Badis, S. Talukder, M. F. Berger, A. R. Gehrke, A. A. Philippakis, M. L. Bulyk, Q. D. Morris, and T. R. Hughes. Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics, 25(8):1012-1018, April 15, 2009. L.Peña-Castillo, M. Tasan, C.L. Myers, H. Lee, T. Joshi, C. Zhang, Y. Guan, M. Leone, A. Pagnani, W.K. Kim, C. Krumpelman, W. Tian, G. Obozinski, Y. Qi, S. Mostafavi, G.N. Lin, G.F. Berriz, F.D. Gibbons, G. Lanckriet, J. Qiu, C. Grant, Z. Barutcuoglu, D.P. Hill, D. Warde-Farley, C. Grouios, D. Ray, J.A. Blake, M. Deng, M.I. Jordan, W.S. Noble, Q. Morris, J. Klein-Seetharaman, Z. Bar-Joseph, T. Chen, F. Sun, O.G. Troyanskaya, E.M. Marcotte, D. Xu, T.R. Hughes, and F.P. Roth. A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology, 9(Suppl1):S2:1-19, June 27, 2008. M.F. Berger*, G. Badis*, A.R. Gehrke*, S. Talukder*, A.A. Philippakis, L. Peña Castillo, T.M. Alleyne, S. Mnaimneh, O.B. Botvinnik, E.T. Chan, F. Khalid, W. Zhang, D. Newburger, S. Jaeger, Q.D. Morris, M.L. Bulyk and T.R. Hughes. Variation in homeodomain DNA-binding revealed by high-resolution analysis of sequence preferences. Cell, 133(7):1266-1276, June 27, 2008 (* Co-first authors). L. Peña Castillo and T. R. Hughes. Why are there still over 1,000 uncharacterized yeast genes? Genetics, 176(1):7-14, May 2007. (Evaluated by F1000 Biology) F.E. Lovergrove*, L. Peña Castillo*, N. Mohammad, W.C. Liles, T.R Hughes, and K.C. Kain. Simultaneous Host and Parasite Expression Profiling Identifies Tissue-Specific Transcriptional Program Associated with Susceptibility or Resistance to Experimental Cerebral Malaria. BMC Genomics, 7:295, Nov 2006 (* These authors contributed equally). L. Peña Castillo and Stefan Wrobel. A comparative study on methods for reducing myopia of hill-climbing search in multirelational learning. Proceedings of the 21st International Conference on Machine Learning (ICML 2004), Banff Alberta, Canada, July 4-8, 2004. L. Peña Castillo and Stefan Wrobel. Learning Minesweeper with Multirelational Learning. Proceedings of the 18th International Joint Conference on Artificial Intelligence (IJCAI 2003), Acapulco, Mexico, August 9-15, 2003.