Liliana Florea - Publications

• Song, L., D. Shankar, L. Florea (2016) -- "Rascaf: Improving genome assembly with RNA-seq data", The Plant Genome, doi: 10.3835/plantgenome2016.03.0027, In press [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., 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., D. Shankar, 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., 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).
• 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., 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., 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., 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., 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]
• Song, L., L. Florea (2014) --- "Rcorrector: Error correction for Illumina RNA-seq reads", Cold Spring Harbor Laboratory Meeting - Biological Data Science, Cold Spring Harbor, NY (poster).

• 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. [Medline]
• 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. [Medline]
• 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).
• 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).

• 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. [Medline]
• 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).
• 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", Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research, Anaheim, CA (poster).

• 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. Jeang, 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]
• Bao, W., L. Houzet, J. Qian, K. Banaudha, L. Florea, K.-T. Jeang, A. Kumar (2011) --- "Hepatitis C virus derived microRNA, vmiR-11, targets PTEN tumor suppressor", 18th Intln. Symposium on Hepatitis C Virus and Related Viruses - HCV2011, Seattle, WA (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).

• 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]
• 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).

• 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]
• 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., I. Mihai, L. Florea (2008) --- "Effective cluster-based seed design for cross-species sequence comparisons", Bioinformatics 24(24), 2926-7. [Medline]
• 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. [Full text]
• 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., 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]
• 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.

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

• 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]
• 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.

• 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., 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., 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]
• 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.

• 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]
• 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.

• 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]
• 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.