Selected Publications 

  • Kazuki Y, Gao FJ, Li Y, Moyer AJ, Devenney B, Hiramatsu K, Miyagawa-Tomita S, Abe S, Kazuki K, Kajitani N, Uno N, Takehara S, Takiguchi M, Yamakawa M, Hasegawa A, Shimizu R, Matsukura S, Noda N, Ogonuki N, Inoue K, Matoba S, Ogura A, Florea LD, Savonenko A, Xiao M, Wu D, Batista DA, Yang J, Qiu Z, Singh N, Richtsmeier JT, Takeuchi T, Oshimura M, Reeves RH (2020) --- "A non-mosaic transchromosomic mouse model of Down syndrome carrying the long arm of human chromosome 21", eLife 9:e56223. doi: 10.7554/eLife.56223. [Medline].
  • Song, L., S. Sabunciyan, G. Yang, and L. Florea (2019) --- "A multi-sample approach increases the accuracy of transcript assembly", Nature Communications 10:5000doi:10.1038/s41467-019-12990-0. [Medline]
  • G., Afsari, B., Guo, T., Considine, M., Florea, L., Kagohara, L.T., Stein-O'Brien, G.L., Kelley, D., Flam, E., Zambo, K., Ha, P.K., Geman, D., Ochs, M.F., Califano, J.A., Gaykalova, D.A., Favorov, A.V., Fertig, E.J. (2018) --- "Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer", Bioinformatics doi: 10.1093/bioinformatics/bty004 (Advanced access). [Medline]
  • Parry, E.M., D.L. Gable, S.E. Stanley, S.E. Khalil, V. Antonescu, L. Florea, M. Armanios (2017) -- "Germline mutations in DNA repair genes in lung adenocarcinoma", J. Thorac. Oncol. 12(11):1673-1678. [Medline]
  • 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. [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", 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 Cancer 10(1):19. [Medline]
  • 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]
  • 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]

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