Liliana Florea, PhD

Assistant Professor, McKusick-Nathans Institute of Genetic Medicine and Department of Medicine
Contact | Education | Interests | Experience | Recognition | Publications |

Education:

Ph. D., Computer Science and Engineering (2000) The Pennsylvania State University
M.Sc., Computer Science and Engineering (1998) The Pennsylvania State University
B.S., Computer Science (1994) University of Bucharest, Romania

Interests:

Development of algorithms and tools for cDNA and genomic sequence alignment, comparative and evolutionary genomics, gene annotation, alternative splicing and its regulation, miRNA genomics and peptide-based vaccine design  

Experience:

• Assistant Professor   (July 2011 - present), Johns Hopkins University, Baltimore MD
  School of Medicine, McKusick-Nathans Institute for Genetic Medicine
• Assistant Research Scientist   (Sep 2008 - present), University of Maryland, College Park MD
  Center for Bioinformatics and Computational Biology, UMD Institute for Advanced Computer Studies
• Assistant Professor   (Jan 2005 - Aug 2008), George Washington University, Washington DC
  Department of Computer Science
• Assistant Professor   (Jan 2006 - Aug 2008, Adjunct: 2002-2006), George Washington University, Washington DC
  Department of Biochemistry and Molecular Biology
• Senior Staff Scientist   (Jul 2002 - Nov 2004), Celera /Applied Biosystems, Rockville MD
  Informatics Research Department, Advanced Research and Technology Division
• Computer Scientist (Oct 2000 - Jun 2002), Celera Genomics, Rockville MD
  Informatics Research Department

Recognition and Awards:

• Sloan Research Fellowship, Computational and Evolutionary Molecular Biology, 2006-2008
• GWU Selective Excellence Area: Systems Biology, 2007-2009
• GWU Dilthey Faculty Fellowship, 2006-2007
• Finalist, Microsoft New Faculty Fellowship 2005
• GWU Institute of Biomedical Engineering Interdisciplinary Research Fellowship, 2005

Selected Publications:

• Florea, L., A. Souvorov, T.S. Kalbfleisch, S.L. Salzberg (2011) --- "Genome assembly has a major impact on gene content: A comparison of annotation in two Bos taurus assemblies", PLoS ONE 6(6): e21400. [Medline].
• Walenz, B., L. Florea (2011) --- "Sim4db and leaff: Utilities for fast batch spliced alignment and sequence indexing", Bioinformatics 27(13):1869-70. [Medline]
• Banaudha, K., M. Kaliszewski, T. Korolnek, L. Florea, M.L. Yeung, K.T. Kuan, A. Kumar (2011) --- "MicroRNA silencing of tumor suppressor DLC-1 promotes efficient hepatitis C virus replication in primary human hepatocytes", Hepatology, 53(1):53-61. [Medline]
• Dalloul, R.A., J.A. Long, A.V. Zimin, L. Aslam, K. Beal, L.A. Bloomberg, et al. (2010) --- "Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis", PLoS Biology 8(9):e1000475. [Medline]
• Zhou, L., I. Mihai, L. Florea (2010) --- "Spaced seeds for cross-species cDNA-to-genome sequence alignment", Communications in Information & Systems 10(2):115-136. [Full text]
• Buckley, K.M., L.D. Florea, L.C. Smith (2009) --- "A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups", BMC Genomics 10(1):318. [Medline]
• Zhou, L., M. Pertea, A. Delcher, L. Florea (2009) --- "Sim4cc: A cross-species spliced alignment program", Nucleic Acids Res. 37(11):e80. [Medline]
• Zimin, A.V., A.L. Delcher, L. Florea, D.R. Kelley, M.C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, C.P. Van Tassell, T.S. Sonstegard, G. Marcais, M. Roberts, P. Subramanian, J.A. Yorke and S.L. Salzberg (2009) --- "A whole-genome assembly of the domestic cow, Bos taurus", Genome Biology 10(4):R42. [Medline]
• Heydarian, M., T. McCaffrey, L. Florea, Z. Yang, M.M. Ross, W. Zhou, S.E. Maynard (2009) --- "Novel splice variants of sFlt1 are upregulated in preeclampsia", Placenta 30(3), 250-255. [Medline]
• Zhou, L., I. Mihai, L. Florea (2008) --- "Effective cluster-based seed design for cross-species sequence comparisons", Bioinformatics 24(24), 2926-7. [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. [Full text]
• Zhou, L., J. Stanton, L. Florea (2008) --- "Universal seeds for cDNA-to-genome comparison", BMC Bioinformatics, 9:36. [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]
• 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]
• Porwollik, S., C.A. Santiviago, P. Cheng, L. Florea, M. McClelland (2005) --- "Differences in gene content between Salmonella enterica serovar Enteriditis isolates and comparison to closely related serovars Gallinarum and Dublin", J. Bacteriol. 187(18), 6545-6555. [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]
• 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, 54-66. [Medline]

Contact:

Liliana Florea, PhD

McKusick-Nathans Institute for Genetic Medicine
Johns Hopkins University School of Medicine
733 N Broadway, BRB 449
Baltimore, MD 21205
Phone: (443) 287-5624
E-mail: florea@jhu.edu