L I L I A N A   D.   F L O R E A
Associate Professor
McKusick-Nathans Institute of Genetic Medicine and
Department of Medicine
Johns Hopkins University School of Medicine
1900 E. Monument, Welch 113 Baltimore, MD 21205
Ph: (443) 287-5624 (w)
E-mail: florea@jhu.edu

 
PROFILE
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.

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

HONORS 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

EXPERIENCE
  • Associate Professor   (Apr 2016 - present), Johns Hopkins University School of Medicine, Baltimore MD
    McKusick-Nathans Institute of Genetic Medicine, and Department of Medicine
  • Faculty Manager   (Jul 2014 - present), Computational Biology Consulting Core, Johns Hopkins School of Medicine
  • Assistant Professor   (Jul 2011 - Mar 2016), Johns Hopkins University School of Medicine, Baltimore MD
    McKusick-Nathans Institute of Genetic Medicine, and Department of Medicine
  • Adjunct Assistant Professor   (Jan 2013 - present), Johns Hopkins University, Baltimore MD
    Department of Computer Science
  • Assistant Research Scientist   (Sep 2008 - Jul 2011), University of Maryland, College Park MD
    Center for Bioinformatics and Computational Biology, and UMIACS
  • Assistant Professor   (Jan 2005 - Aug 2008), George Washington University, Washington DC
    Department of Computer Science, and 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
  • Graduate Research Assistant   (May 1995 - Aug 2000), Penn State University, University Park PA
    Computational Molecular Biology Group, Department of Computer Science and Engineering
  • Assistant Researcher   (Nov 1993 - May 1995)
    The Institute of World Economy, Bucharest, Romania

RESEARCH PORTFOLIO
 
Journal Publications
  • Song, L., D. Shankar, L. Florea (2016) -- "Rascaf: Improving genome assembly with RNA-seq data", The Plant Genome 9(3), doi: 10.3835/plantgenome2016.03.0027 [Full text]
  • Guerrero-Preston, R., B.L. Valle, A. Jedlicka, N. Turaga, O. Folawiyo, F. Pirini, F. Lawson, A. Vergura, M.J. Noordhuis, A. Dziedzic, G. Perez, M. Renehan, C. Guerrero-Diaz, E. De Jesus-Rodriguez, T. Díaz-Montes, J. Rodriguez-Orengo, K. Méndez, J. Romaguera, B.J. Trock, L. Florea and D. Sidransky (2016) --- "Molecular triage of premalignant lesions in liquid-based cervical cytology and circulating cell free DNA from urine, using methylated viral and host genes", Cancer Prevention Research, doi: 10.1158/1940-6207.CAPR-16-0138, In press. [Medline]
  • Song, L., S. Sabunciyan, L. Florea (2016) --- "CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads", Nucl. Acids Res. 44(10):e98. [Medline]
  • Canzar, S., L. Florea (2016) --- "Computational methods for transcript assembly from RNA-seq reads", In Computational Methods for Next Generation Sequencing Data Analysis 2016, Editors: Ion Mandoiu and Alexander Zelikovsky, Wiley-Interscience, John Wiley & Sons, Inc., Hoboken, NJ, 199-216.
  • Song, L., L. Florea (2015) --- "Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads", GigaScience, 4:48. [Full text]
  • Wang, Z., K. Ceniccola, L. Florea, B.D. Wang, N.H. Lee, A. Kumar (2015) --- "Viral non-coding RNA inhibits HNF4α expression in HCV associated hepatocellular carcinoma", Infectious Agents and Cancer, 10(1):19. [Medline]
  • Song, L., L. Florea, B. Langmead (2014) --- "Lighter: fast and memory-efficient error correction without counting", Genome Biology, 15:509. [Medline]
  • Bao, W., L. Florea, N. Wu, Z. Wang, K. Banaudha, J. Qian, L. Houzet, R. Kumar and A. Kumar (2014) -- "Loss of nuclear PTEN in HCV-infected human hepatocytes", Infectious Agents and Cancer, 9:23. [Full text]
  • Florea, L. and S.L. Salzberg (2013) --- "Genome-guided transcriptome assembly in the age of next generation sequencing", IEEE/ACM Trans. Computational Biology and Bioinformatics, 10(5):1234-40. [PubMed,Full text]
  • Florea, L., L. Song and S.L. Salzberg (2013) --- "Thousands of exon skipping events differentiate splicing patterns in sixteen human tissues", F1000Research 2013, 2:188 (doi: 10.12688/f1000research.2-188.v1). [PubMed,Open access]
  • Eswaran, J., A. Horvath, S. Godbole, S.D. Reddy, P. Mudvari, K. Ohshiro, D. Cyanam, S. Nair, S.A.W. Fuqua, K. Polyak, L.D. Florea, R. Kumar (2013) --- "RNA sequencing of cancer reveals novel splicing alterations", Sci. Rep. 3:1689. [PubMed]
  • Song, L., L. Florea (2013) --- "CLASS: Constrained transcript assembly of RNA-seq reads", Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing - RECOMB-SEQ 2013, BMC Bionformatics 14(Suppl 5):S14. [PubMed]
  • Eswaran, J., D. Cyanam, P. Mudvari, S.D.N. Reddy, S.B. Pakala, S.S. Nair, L. Florea, S.A.W. Fuqua, S. Godbole, R. Kumar (2012) --- "Transcriptomic landscape of breast cancers through mRNA sequencing", Sci. Rep. 2:264, doi:10.1038/srep00264. [PubMed]
  • 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. [PubMed].
  • Walenz, B., L. Florea (2011) --- "Sim4db and leaff: Utilities for fast batch spliced alignment and sequence indexing", Bioinformatics 27(13):1869-70. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • Zhou, L., M. Pertea, A. Delcher, L. Florea (2009) --- "Sim4cc: A cross-species spliced alignment program", Nucleic Acids Res. 37(11):e80. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • Zhou, L., I. Mihai, L. Florea (2008) --- "Effective cluster-based seed design for cross-species sequence comparisons", Bioinformatics 24(24), 2926-7. [PubMed]
  • 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. [PubMed].
  • 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. [PubMed]
  • 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. [PubMed]
  • Florea, L. (2006) --- "Bioinformatics of alternative splicing and its regulation", Brief Bioinform. 7(1), 55-69. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

Conference Participation
  • Yang, G., L. Florea (2016) --- "JULiP: An eficient model for accurate intron selection from multiple RNA-seq samples", 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2016), Atlanta, GA (talk).
  • Yang, G., L. Florea (2016) --- "JULiP: Efficient and accurate intron selection from multiple RNA-seq samples", CSHL-Wellcome Trust Genome Informatics Meeting 2016, Hinxton, Cambridge, UK (poster).
  • Song L., D. Shankar, L. Florea (2016) --- "Rascaf: Genome assembly scaffolding with RNA-seq data", Cold Spring Harbor Laboratory Meeting - The Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Song, L., B. Langmead, L. Florea (2016) --- "Lighter and Rcorrector: Tools for next generation sequencing error correction", Intln. Plant and Animal Genome Conference -- PAG XXIV, San Diego, CA (poster).
  • Song, L., L. Florea (2016) --- "Rascaf: Improving genome assembly with RNA-seq data", Intln. Plant and Animal Genome Conference -- PAG XXIV, San Diego, CA (poster).
  • Song, L., B. Langmead, and L. Florea (2015) --- "Lighter and Rcorrector: A suite for next generation sequencing error correction", Cold Spring Harbor Laboratory Meeting - The Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Song, L. and L. Florea (2015) --- "Improving the alternative splicing annotation of plant genomes - Rosaceae", Intln. Plant and Animal Genome Conference XXIII, San Diego, CA (poster).
  • Song, L., and L. Florea (2014) --- "Rcorrector: Error correction for Illumina RNA-seq reads", Cold Spring Harbor Laboratory Meeting - Biological Data Science, Cold Spring Harbor, NY (poster).
  • Song, L., and L. Florea (2013) --- "CLASS - A program for accurate reconstruction of genes and alternative splicing variations from RNA-seq data", Cold Spring Harbor Laboratory Meeting - Genome Informatics, Cold Spring Harbor, NY (poster).
  • Song, L. and L. Florea (2013) --- "CLASS and ASprofile: Resources for alternative splicing annotation from RNA-seq data", International Plant and Animal Genomes Meeting XXI, San Diego, CA (poster).
  • Guerrero-Preston, R., M. McClelland, D. Sidransky, L. Florea (2012) --- "Web-based tools for visualization of the Human Papilloma Virus genome dynamics: A computational approach to cancer prevention and control", AACR Eleventh Annual International Conference on Frontiers in Cancer Prevention Research, Anaheim, CA (poster).
  • Florea, L., S.L. Salzberg (2012) --- "Dynamic alternative splicing profiles from RNA-seq data in sixteen human tissues", Cold Spring Harbor Laboratory Meeting - Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Florea, L., S.L. Salzberg (2011) --- "Accurate detection of RNA-DNA differences in RNA-seq data with rddChecker", Cold Spring Harbor Laboratory Meeting - Genome Informatics, Cold Spring Harbor, NY (poster).
  • Florea, L., S.L. Salzberg (2011) --- "Genome-wide identification of RNA editing sites from RNA-seq data in 16 human tissues", Cold Spring Harbor Laboratory Meeting - The Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Florea, L., A. Souvorov, S.L. Salzberg (2010) --- "Genes and genomes, an imperfect world: Comparison of gene annotations of two Bos taurus draft assemblies", Beyond the Genome Conference, Boston, MA (poster).
  • Florea, L., C. Riemer, M. Pertea, S. Forsythe, S.L. Salzberg, M. McClelland (2009) --- "Enterix: Visualization of alignment and genome dynamics in Enteric bacteria", 17th Annual Microbial Genomics Conference, Rocky Gap State Park, MD (poster).
  • Zhou, L., M. Pertea, L. Florea (2009) --- "Detecting coding regions in sequence alignments with spaced seeds", Workshop in Algorithms for Bioinformatics - WABI 2009, Philadelphia, PA (poster).
  • Florea, L., J. Qian, W. Ahmad, A. Kumar (2009) --- "Identification of vmiRNAs in the HCV genome by comparative genomics", Cold Spring Harbor Laboratory Meeting - The Biology of Genomes, Cold Spring Harbor, NY.
  • Zimin, A., A. Delcher, L. Florea, F. Hahrahan, D. Kelley, G. Marcais, M. Roberts, M. Schatz, P. Subramanian, S. Salzberg, J. Yorke (2009) --- "Improved assembly of the Bos taurus genome", Plant & Animal Genomes XVII Conference, San Diego, CA.
  • Zhou, L., A. Delcher, M. Pertea, L. Florea (2008) --- "Universal spaced seeds: Improving the accuracy of cross-species cDNA-to-genome alignment", 16th Annual Intln. Conference on Intelligent Systems for Molecular Biology - ISMB2008, Toronto, Canada (poster).
  • Zhou, L., L. Florea (2008) --- "Sensitive and specific cross-species cDNA-to-genome alignment with spaced seeds", 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, CO.
  • Zhou, L., A. Delcher, M. Pertea, L. Florea (2007) --- "Universal spaced seeds: Improving the accuracy of cross-species cDNA-to-genome alignment", Cold Spring Harbor Meeting - Genome Informatics, 122.
  • Zhou, L., L. Florea (2007) --- "Good spaced seeds for cross-species mRNA-to-genome alignment", IEEE 7th International Conference on BioInformatics and BioEngineering - BIBE 2007, Harvard University Medical School, Boston, MA.
  • Guven, E., L. Florea (2007) --- "Sequence signatures of exon dynamics in the evolution of alternative splicing", Cold Spring Harbor Meeting - The Biology of Genomes, 129.
  • Zhou, L., L. Florea (2006) --- "Designing spaced seeds for accurate cross-species cDNA-to-genome alignment with varying evolutionary distances", SMBE 2006 - Genomes, Evolution and Bioinformatics, Arizona State University, Tempe, AZ.
  • Florea, L., X. Zhao (2005) --- "Sequence conservation and mutation in alternative splicing in relation to evolutionary change", 24th Summer Symposium in Molecular Biology - Comparative and Functional Genomics, Penn State University, University Park, PA.
  • Florea, L., Y. Zhang, X. Zhao, W. Miller, L. Elnitski (2004) --- "Evolutionary conservation of exonic splicing enhancers and alternative splicing patterns in whole genome human-mouse-rat alignments", Pacific Symposium on Biocomputing Extended Workshop on Alternative Splicing, Hawaii HI.
  • Florea, L., V. Di Francesco, J. Miller, R. Turner, B. Walenz, C. Mobarry, I. Dew, R. Charlab, M. Harris, G. Merkulov, A. Yao, P. Li, G. Sutton (2003) --- "AIR: A computational framework for the Celera rat genome annotation", Cold Spring Harbor Meeting on Rat Genomics & Models, Abstracts, 72-72.
  • Di Francesco, V., L. Florea, A. Yao, M. Harris, J. Miller, R. Turner, C. Mobarry, C. Xiao, J. Hoover, G. Merkulov, R. Charlab, B. Walenz, G. Sutton, P.W. Li (2003) --- "Analysis of the Celera rat genome annotation", Cold Spring Harbor Meeting on Rat Genomics & Models, Abstracts, 8-8.
  • Florea, L., C. Riemer, S. Schwartz, M. McClelland, W. Miller (2000) --- "Web-based visualization tools for bacterial genome alignments", TIGR - Fourth Annual Conference on Microbial Genomes, Chantilly VA.
  • Zhang, J., K.M. Chao, L. Florea, W. Miller (1997) --- "Alignment requirements for NCBI's Genomes division", RECOMB 97 - First International Conference on Research in Computational Molecular Biology, Santa Fe NM.
Patent Applications
  • Hoffman, S., S. Istrail, L. Florea, B. Halldorsson, O. Kohlbacher, R. Schwartz (2004) --- "Methods for peptide-protein binding prediction". [Full text]
  • Xiao, C., V. Di Francesco, B.P. Walenz, P.W. Li, M.J. Campbell, L. Florea (2005) --- "Methods and systems for identifying genes, splice variants, and transcripts using an evidence mapping approach". [Full text]

INVITED TALKS
  • "Assessing the Alternative Splicing Landscape in Normal and Cancer Cells with RNA-seq Data", April 2017, First Symposium on Translational Precision Oncology in Romania (STOP CANCER), Bucharest, Romania.
  • "Discovering Alternative Splicing Variation from Large Numbers of RNA-seq Samples", October 2016, 2nd Annual Next Generation Sequencing USA Congress & Single Cell Genomics and Transcriptomics USA Congress, Boston, MA.
  • "Going Deep: Ultra-sensitive Computational Detection of Splicing Variation from a Single and from Multiple RNA-seq Samples", September 2016, SPLICING2016, Lisbon, Portugal.
  • "Detecting Variation in the Transcriptome with RNA-seq data", November 2015, National Institutes of Aging NIA/NIH, Baltimore, MD.
  • "Discovering Alternative Splicing Variation from RNA-seq Data", October 2015, Next Generation Sequencing USA Congress & Single Cell Genomics and Transcriptomics USA Congress, Boston, MA.
  • "Bits to Biology: Designing Computational Methods for Next Generation Sequencing Data Analysis", March 2015, Grand Rounds, Department of Medicine, General Internal Medicine, Johns Hopkins School of Medicine, Baltimore, MD.
  • "SpliceBox: Methods for Transcriptome and Alternative Splicing Analysis", May 2014, 2nd Annual Next Generation Sequencing Data Congress, London, UK.
  • "Decoding the Genes and their Alternative Splicing Variations with Splice Graphs", October 2013, Department of Computer Science, Johns Hopkins University, Baltimore MD.
  • "Computational Methods and Tools for Alternative Splicing Annotation from RNA-seq Data", June 2013, Next Generation Sequencing Data Congress, London, UK.
  • "Genome Assembly Consequences for Gene Annotation", January 2013, International Plant and Animal Genomes Meeting XXI, San Diego CA.
  • "Dynamic Alternative Splicing Profiles from RNA-seq Data in Sixteen Human Tissues", October 2012, Young Genomics Investigator Symposium, Johns Hopkins University, Baltimore MD.
  • "Written in the Genome: Assembly Consequences for Genome Annotation", August 2012, Cambridge Healthtech Institutes's Next Generation Sequencing Data Analysis, Providence RI.
  • "Novel Splice Variant Discovery from RNA-seq Sequence Data in 16 Human Tissues", May 2011, Genome Assembly Special Forces Workshop, Brown University, Providence RI.
  • "The (R)evolving Genome Annotation Problem", April 2011, George Washington University, Washington DC.
  • "Comparative Methods for Gene and Alternative Splicing Annotation", August 2007, National Human Genome Research Institute (NHGRI), Bethesda MD.
  • "Spaced Seeds for Cross-Species cDNA-to-Genome Alignment", December 2006, Advances in Genomic Tool Construction (AGTC) Workshop, Brown University, Providence RI.
  • "Designing Tools for cDNA-to-Genome Alignment", October 2006, University of Maryland, Center for Bioinformatics and Computational Biology, College Park MD.
  • "A Computational Framework for Alternative Splicing Annotation", October 2003, George Washington University, Department of Biochemistry and Molecular Biology, Washington DC.
  • "Outstanding Issues in Genomics in the Post-Genome Era", March 2003, Georgetown University, Computer Science Department, Washington DC.
  • "Four Issues that Face Genomics in the Post-Genome Era", March 2003, 3rd IEEE Symposium on Bioinformatics and Bioengineering BIBE2003, Bethesda MD.
  • "Web-based Visualization Tools for Bacterial Genome Alignments", January 2001, ASM and TIGR Conference on Microbial Genomes, Monterey CA.
  • "Harvesting the Information from the Human Genome", August 2001, SIAC 2001 - Bioinformatics and Data Mining, Dayton OH.

OTHER PROFESSIONAL ACTIVITIES
 
Editorial board, Journal of Computational Biology
Editorial Board, Scientific Reports
Associate Editor, International Journal of Computational Bioscience
ALCoB 2014 Program Committee
ACM BCB 2013 Program Committee; Organizing Committee; Local Co-Chair
BIOINFORMATICS 2011-2017 Program Committee
IEEE ICCABS 2011-2016 Program Committee
WABI 2007, 2009, 2010, 2011, 2012, 2013 Program Committee
ISBRA 2008, 2009 Program Committee
BIOT 2008, 2009, 2010 Program Committee
BIBM 2007, 2008 Program Committee; 2015 Local Co-Chair
GWU University Committee on Research, 2006-2008
RECOMB 2003, 2004 Program Committee
RECOMB 2002 Conference Organizing Committee/Posters Chair
Editor, Currents in Computational Molecular Biology, Poster Abstracts at RECOMB 2002
NIH NCI-I Study Section 2016 (ad-hoc) NIH NHGRI GSP Special Emphasis Panel 2015 (ad-hoc) NIH NHGRI ENCODE-SEP (M2) Study Section 2012
NIH IMST-E Study Section 2009-present
NIH GCAT Study section 2010 (ad-hoc)
NIH GGG-J Study Section, 2006-2008
NSF Panel reviewer (IOS), 2014
NSF panel reviewer (CISE), 2005, 2013, 2016
Referee, Genome Biology
Referee, Genome Research
Referee, Biology Direct
Referee, Journal of Computational Biology
Referee, Nucleic Acids Research Journal
Referee, Journal of Bioinformatics
Referee, BMC Bioinformatics
Referee, BMC Genomics
Phi Kappa Phi Honor Society