Liliana Florea's List of Publications

• Zhou, L., I. Mihai, L. Florea (2008) --- "Effective cluster-based seed design for cross-species sequence comparisons", Bioinformatics, in press.
• Zhou, L., J. Stanton, L. Florea (2008) --- "Universal seeds for cDNA-to-genome comparison", BMC Bioinformatics, 9:36. [Medline]
• Florea, L. (2008) --- "Alternative splicing in the human genome and its evolutionary consequences", In Encyclopedia of Life Sciences: Handbook of Human Molecular Evolution, D.N. Cooper & H. Kehrer-Sawatzki Eds., John Wiley & Sons Ltd., Chichester, UK, in press.
• Zhou, L., L. Florea (2007) --- "Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment", J. Comput. Biol. 2(14), 113-130. [Medline]
• Tanner, S., Z. Shen, J. Ng, L. Florea, R. Guigo, S.P. Briggs, V. Bafna (2007) --- "Improving gene annotation using peptide mass spectrometry", Genome Res. 17(2), 231-239. [Medline]
• Florea, L. (2006) --- “Bioinformatics of alternative splicing and its regulation”, Brief. Bioinform. 7(1), 55-69. [Medline]
• Cahan, P., A.M. Ahmad, H. Burke, S. Fu, Y. Lai, L. Florea, N. Dharker, T. Kobrinski, P. Kale, T.A. McCaffrey (2005) --- “List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists”, Gene 360(1), 78-82. [Medline]
• Lippert, R.A., X. Zhao, L. Florea, C. Mobarry, S. Istrail (2005) --- “Finding anchors for genomic sequence comparison”, J. Comput Biol. 12(6), 762-776. [Medline]
• Porwollik, S., A.C. Santiviago, P. Cheng, L. Florea, S. Jackson, M. McClelland (2005) --- “Differences in gene content between Salmonella enterica serovar Enteriditis isolates and comparison to closely related serovars Gallinarum and Dublin”, J. Bacter. 187(18), 6545-6555. [Medline]
• Florea, L., V. Di Francesco, J. Miller, R. Turner, C. Mobarry, A. Yao, M. Harris, B. Walenz, I. Dew, G. Merkulov, R. Charlab, Z. Deng, S. Istrail, P. Li, G. Sutton (2005) --- “Gene and alternative splicing annotation with AIR”, Genome Res. 15(1), 54-66. [Medline]
• Istrail, S., L. Florea, B.V. Halldorsson, O. Kohlbacher, R.S. Schwartz, V.B. Yap, J.W. Yewdell, S.L. Hoffman (2004) --- “Comparative immunopeptidomics of humans and their pathogens”, Proc. Natl. Acad. Sci. USA 101(36), 13268-13272. [Medline]
• Porwollik S., E.F. Boyd, C. Choy, P. Cheng, L. Florea, E. Proctor, M. McClelland (2004) --- “Characterization of Salmonella enterica subspecies I genovars by use of microarrays”, J. Bacteriol. 186(17), 5883-5898. [Medline]
• Istrail, S., G.G. Sutton, L. Florea, A. Halpern, C.M. Mobarry, R. Lippert et al. (2004) --- “Whole-genome shotgun assembly and comparison of human genome assemblies”, Proc. Natl. Acad. Sci. USA 101(7), 1916-1921. [Medline]
• Lippert, R.A., X. Zhao, L. Florea, C. Mobarry, S. Istrail (2004) --- “Finding anchors for genomic sequence comparison”, Proc. 8th Intln. Conf. on Research in Computational Biology - RECOMB 2004, 233-241. [Abstract]
• Florea, L., B. Halldorsson, O. Kohlbacher, R. Schwartz, S. Hoffman, S. Istrail (2003) --- “Epitope prediction algorithms for peptide-based vaccine design”, Proc. 2nd IEEE Computer Society Bioinformatics Conference, 17-26. [Abstract]
• Florea, L., M. McClelland, C. Riemer, S. Schwartz, W. Miller (2003) --- “EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae”, Nucleic Acids Res. 31(13), 3527-3532. [Medline]
• Porwollik, S., J. Frye, L.D. Florea, F. Blackmer, M. McClelland (2003) --- “A non-redundant microarray of genes for two related bacteria”, Nucleic Acids Res. 31(7), 1869-1876. [Medline]
• Elnitski, L., C. Riemer, H. Petrykowska, L. Florea, S. Schwartz, W. Miller, R. Hardison (2002) --- “PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences”, Genomics 80(6), 681-690. [Medline]
• McClelland, M., K.E. Sanderson, J. Spieth, S.W. Clifton, P. Latreille, L. Courtney, S. S. Porwollik, J. Ali, M. Dante, F. Du, S. Hou, D. Layman, S. Leonard, C Nguyen, K. Scott, A. Holmes, N. Grewal, E. Mulvaney, E. Ryan, H. Sun, L. Florea, W. Miller, T. Stoneking, M. Nhan, R. Waterston, R.K. Wilson (2001) --- “Complete genome sequence of Salmonella enterica serovar Typhimurium LT2”, Nature 413(6858), 852-856. [Medline]
• Venter J.C., M.D. Adams, G. Myers, P.W. Li, R. Mural, G.G. Sutton et al. (2001) --- “The sequence of the human genome”, Science 291(5507), 1304-1351. [Medline]
• Florea, L., C. Riemer, S. Schwartz, Z. Zhang, N. Stojanovic, W. Miller, M. McClelland (2000) --- “Web-based visualization tools for bacterial genome alignments’’, Nucleic Acids Res. 28(18), 3486-3496. [Medline]
• McClelland, M., L. Florea, K. Sanderson, S. Clifton, R. Wilson, W. Miller (2000) --- “Comparison of the E. coli K12 genome to sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica”, Nucleic Acids Res. 28(24), 4974-4986. [Medline]
• Florea, L., M. Li, C. Riemer, B. Giardine, W. Miller, R. Hardison (2000) --- “Validating computer programs for functional genomics in gene regulatory regions”, Current Genomics 1(1), 11-27. [Full text]
• Stojanovic, N., L. Florea, C. Riemer, D. Gumucio, J. Slightom, M. Goodman, W. Miller, R. Hardison (1999) --- “Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions”, Nucleic Acids Res. 27(19), 3899-3910. [Medline]
• Florea, L., G. Hartzell, Z. Zhang, G.M. Rubin, W. Miller (1998) --- “A computer program for aligning a cDNA sequence with a genomic DNA sequence”, Genome Res. 8(9), 967-974. [Medline]