Liliana Florea

Summary

Affiliation: George Washington University
Country: USA

Publications

  1. pmc EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae
    Liliana Florea
    Informatics Research, Celera Applied Biosystems, 45 W Gude Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:3527-32. 2003
  2. ncbi request reprint Bioinformatics of alternative splicing and its regulation
    Liliana Florea
    Department of Computer Science, George Washington University, Academic Center Rm 714, Washington DC 20052, USA
    Brief Bioinform 7:55-69. 2006
  3. pmc Gene and alternative splicing annotation with AIR
    Liliana Florea
    Informatics Research, Applied Biosystems, Rockville, Maryland 20850, USA
    Genome Res 15:54-66. 2005
  4. ncbi request reprint Finding anchors for genomic sequence comparison
    Ross A Lippert
    Informatics Research, Celera Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    J Comput Biol 12:762-76. 2005
  5. pmc Sim4cc: a cross-species spliced alignment program
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    Nucleic Acids Res 37:e80. 2009
  6. pmc Universal seeds for cDNA-to-genome comparison
    Leming Zhou
    Department of Computer Science, George Washington University, Washington DC, 20052, USA
    BMC Bioinformatics 9:36. 2008
  7. pmc Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
    Brian Walenz
    The J Craig Venter Institute, Rockville, MD 20850, USA
    Bioinformatics 27:1869-70. 2011
  8. ncbi request reprint Effective cluster-based seed design for cross-species sequence comparisons
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    Bioinformatics 24:2926-7. 2008
  9. ncbi request reprint Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    J Comput Biol 14:113-30. 2007
  10. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004

Detail Information

Publications16

  1. pmc EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae
    Liliana Florea
    Informatics Research, Celera Applied Biosystems, 45 W Gude Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:3527-32. 2003
    ..The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments...
  2. ncbi request reprint Bioinformatics of alternative splicing and its regulation
    Liliana Florea
    Department of Computer Science, George Washington University, Academic Center Rm 714, Washington DC 20052, USA
    Brief Bioinform 7:55-69. 2006
    ..Bioinformatics efforts tackling these two questions are just at the beginning. This article is a survey of these methods...
  3. pmc Gene and alternative splicing annotation with AIR
    Liliana Florea
    Informatics Research, Applied Biosystems, Rockville, Maryland 20850, USA
    Genome Res 15:54-66. 2005
    ....
  4. ncbi request reprint Finding anchors for genomic sequence comparison
    Ross A Lippert
    Informatics Research, Celera Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    J Comput Biol 12:762-76. 2005
    ..genome.ucsc.edu), and show that a significant portion of the two genomes can be found in selected exact matches, with very limited amount of sequence duplication...
  5. pmc Sim4cc: a cross-species spliced alignment program
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    Nucleic Acids Res 37:e80. 2009
    ....
  6. pmc Universal seeds for cDNA-to-genome comparison
    Leming Zhou
    Department of Computer Science, George Washington University, Washington DC, 20052, USA
    BMC Bioinformatics 9:36. 2008
    ..As the number and variety of genomes increases, it becomes desirable to identify a small set of universal seeds that perform optimally or near-optimally on a large range of comparisons...
  7. pmc Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
    Brian Walenz
    The J Craig Venter Institute, Rockville, MD 20850, USA
    Bioinformatics 27:1869-70. 2011
    ..The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses...
  8. ncbi request reprint Effective cluster-based seed design for cross-species sequence comparisons
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    Bioinformatics 24:2926-7. 2008
    ..Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed...
  9. ncbi request reprint Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment
    Leming Zhou
    Department of Computer Science, George Washington University, Washington, DC 20052, USA
    J Comput Biol 14:113-30. 2007
    ..We illustrate our methods with the alignment of chicken coding sequences against the human genome assembly version HG17...
  10. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
    ..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats...
  11. pmc Comparative immunopeptidomics of humans and their pathogens
    Sorin Istrail
    Celera Genomics, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:13268-72. 2004
    ....
  12. ncbi request reprint List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists
    Patrick Cahan
    The George Washington University Medical Center, Department of Biochemistry and Molecular Biology, 2300 I Street NW Ross Hall 541, Washington, D C 20037, United States
    Gene 360:78-82. 2005
    ..Its application to the fields of stem cell, cancer, and aging research is demonstrated by comparing published papers...
  13. pmc Improving gene annotation using peptide mass spectrometry
    Stephen Tanner
    Bioinformatics Program, University of California, San Diego, La Jolla, California 92093 0419, USA
    Genome Res 17:231-9. 2007
    ..Our results demonstrate that proteomic profiling should play a role in any genome sequencing project...
  14. ncbi request reprint Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid
    Michael McClelland
    Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
    Nat Genet 36:1268-74. 2004
    ..Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae)...
  15. ncbi request reprint Epitope prediction algorithms for peptide-based vaccine design
    Liliana Florea
    Celera Applied Biosystems
    Proc IEEE Comput Soc Bioinform Conf 2:17-26. 2003
    ..The third class of methods uses sequence profiles obtained by clustering known epitopes to score candidate peptides. By integrating these methods, using a simple voting heuristic, we achieve improved accuracy over the state of the art...
  16. ncbi request reprint PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences
    Laura Elnitski
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Genomics 80:681-90. 2002
    ....