[ 20192018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | <2000]

2019

  • Gable D, Gaysinkaya V, Atik C, Talbot C, Kang B-H, Stanley S, Pugh E, Amat-Codina N, Schenk K, Arcasoy M, Brayton C, Florea L, and Armanios M (2019). The nuclear exosome targeting component ZCCHC8 is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation, Genes & Development, Accepted.
  • Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S, and Chien AL (2019). Characterization and analysis of the skin microbiota in rosacea, Amer. Journal of Clinical Dermatology, Accepted.
  • Lee CJ, Florea L, Sears CL, Maruthur N, Potter JJ, Schweitzer M, Magnuson T, and Clark JM (2019). Changes in gut microbiome after bariatric surgery versus medical weight loss in a pilot randomized trial, Obes Surg. doi: 10.1007/s11695-019-03976-4. [Medline]
  • Kassiri B, Shrestha E, Kasprenski M, Antonescu C, Florea LD, Sfanos KS, and Wang MH (2019). A prospective study of the urinary and gastrointestinal microbiome in prepubertal males, Urology. doi: 10.1016/j.urology.2019.05.031. [Medline]

2018

  • Kelley DZ, Flam EL, Guo T, Danilova LV, Zamuner F, Bohrson C, Considine M, Windsor EJ, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra WH, Chung CH, Califano JA, Wheelan S, Favorov AV, Florea L, Fertig EJ, and Gaykalova DA (2018). Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma, Transl Res. pii: S1931-5244(18): 30108-7. [Medline]
  • ​Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo K, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, and Fertig EJ (2018). Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer, Bioinformatics 34(11):1859-1867. [Medline]

2017

  • Parry EM, Gable DL, Stanley SE, Khalil SE, Antonescu V, Florea L, and Armanios M (2017). Germline mutations in DNA repair genes in lung adenocarcinoma, J. Thorac. Oncol. 12(11):1673-1678. [Medline]
  • Yang G, and Florea L (2017). JULiP: An efficient model for accurate intron selection from multiple RNA-seq samples, IEEEXplore - 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 1-15. doi: 10.1109/ICCABS.2016.7802769 [Free text]
  • Yang G, and Florea L (2017). JULiP++: Fast and ultra-sensitive identification of differential splicing events from large RNA-seq data collections, Cold Spring Harbor Laboratory Meeting - Genome Informatics, Cold Spring Harbor, NY (poster).
  • Song L, and Florea L (2017). CLASSX: Scalable simultaneous transcript assembly of multiple RNA-seq data sets, Cold Spring Harbor Laboratory Meeting - Genome Informatics, Cold Spring Harbor, NY (poster).

2016

  • Song L, Shankar D, and Florea L (2016). Rascaf: Improving genome assembly with RNA-seq data, The Plant Genome 9(3), doi: 10.3835/plantgenome2016.03.0027. [Medline]
  • Song L, Sabunciyan S, and Florea L (2016). CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads, Nucl. Acids Res. 44(10):e98. [Medline]
  • Guerrero-Preston R, Valle BL, Jedlicka A, Turaga N, Folawiyo O, Pirini F, Lawson F, Vergura A, Noordhuis MJ, Dziedzic A, Perez G, Renehan M, Guerrero-Diaz C, De Jesus-Rodriguez E, Díaz-Montes T, Rodriguez-Orengo J, Méndez K, Romaguera J, Trock BJ, Florea L, and Sidransky D (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 9(12):915-924[Medline]
  • Canzar S, and Florea L (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, Langmead B, and Florea L (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, Shankar D, and Florea L (2016). Rascaf: Improving genome assembly with RNA-seq data, Intln. Plant and Animal Genome Conference -- PAG XXIV, San Diego, CA (poster).
  • Song L, Shankar D, and Florea L (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, and Florea L (2016). JULiP: Efficient and accurate intron selection from multiple RNA-seq samples, CSHL/Wellcome Trust Genome Informatics Meeting 2016, Hinxton, Cambridge, UK (poster).

2015

  • Song, L., L. Florea (2015) --- "Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads", GigaScience4:48. [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 Cancer10(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).

2014

  • Song, L., L. Florea, B. Langmead (2014) --- "Lighter: fast and memory-efficient error correction without counting", Genome Biology15:509. [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 Cancer9:23. [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).

2013

  • 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 2013BMC 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).

2012

  • 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).

2011

  • 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", Hepatology53(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).

2010

  • 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).

2009

  • 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.

2008

  • 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.

2007

  • 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.

2006

  • 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.

2005

  • 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.

2004

  • 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.

2003

  • 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.

2002

  • 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]

2001

  • 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]

2000

  • 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.

< 2000

  • 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.