Selected Publications 

  • 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.
  • 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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