Liliana Florea

Liliana Photo

Assistant Professor
Department of Computer Science
George Washington University
E-mail: florea@gwu.edu
I am interested in applying computational techniques towards modeling and solving biological problems. In particular, my work revolves around designing methods and tools for: i) sequence and genome analysis; ii) alternative splicing identification and characterization; iii) comparative analyses of bacterial genomes, and iv) computational vaccine design.

Sequence and Genome Analysis

The sequencing of human and several other vertebrate genomes is creating opportunities like never before for comparative studies at the whole-genome scale. Such studies aim at identifying and characterizing commonalities and differences at either global or local scale, to predict functional sequence elements and to infer evolutionary relationships between species by exploring patterns of sequence re-arrangement and variation. We have developed and will continue to design and develop tools for comparing and annotating biological sequences that are fast, accurate and scalable, and thus capable of efficiently handling the wealth of new data.

Selected publications:

  • Zhou, L., J. Stanton, L. Florea (2008) --- "Universal seeds for cDNA-to-genome comparison", BMC Bioinform. 9(1):36. [Medline]
  • Zhou, L., L. Florea (2007) --- "Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment", J. Comput. Biol. 14(2), 113-130. [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.
  • 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]
  • 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]
Tools:
  • ESTmapper (high-throughput cDNA-to-genome alignment)
Alternative Splicing

Alternative splicing, the process by which a gene can create multiple mRNA and protein isoforms by selecting different combinations of exons, is a growing area of research with the promise to explain how a limited set of genes can produce the large repertoire of proteins in the cell. Alternatively spliced isoforms have also been associated with certain diseases. We have developed methods for annotating genomes with gene and alternative splicing information, and we will use them to further explore regulatory mechanisms that control splicing.

Selected publications:

  • Florea, L. (2006) --- "Bioinformatics of alternative splicing and its regulation", Brief Bioinform 7(1), 55-69. [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]
  • 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]

Tools:

  • Sim4 (cDNA-to-genomic sequence alignment)
  • AIR (gene and splice variant annotation)
Bacterial Genomics

The Enterix visualization suite consists of three web servers that display alignment information from 28 Enterobacterial genomes, together with annotations of genes and other functional or conserved elements. These sets of alignments and annotations have supported comparative genomics analyses to determine orthologous relationships and to validate the gene sets.

Selected publications:

  • 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]
  • McClelland, M., K.E. Sanderson, J. Spieth, S.W. Clifton, P. Latreille, L. Courtney, et al. (2001) --- “Complete genome sequence of Salmonella enterica serovar Typhimurium LT2”, Nature 413(6858), 852-856. [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]

Tools:

  • Enterix (bacterial genome alignments and annotations)
Computational Vaccine Design

Computational methods are reducing the time to biological discovery by directing wet lab experiments to selected areas of interest. This reduction in search space is particularly important when protein sequences are involved, where the size of the alphabet can lead to a very large set of candidates. Starting from a set of sequences of known epitopes and using the protein sets in the human genome and in the genomes of its pathogens, we developed algorithms to predict T-cell epitopes for Class I immunogenicity and studied their signatures in the target genome and across genomes.

Selected publications:

  • 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]
  • 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]


Page last modified: May 10th, 2007.