Selected Publications 

  • Lee, C.J., Florea, L., Sears, C.L., Maruthur, N., Potter, J.J., Schweitzer, M., Magnuson, T., Clark, J.M. (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]
  • Kelley, D.Z., Flam, E.L., Guo, T., Danilova, L.V., Zamuner, F., Bohrson, C., Considine, M., Windsor, E.J., Bishop, J.A., Zhang, C., Koch, W.M., Sidransky, D., Westra, W.H., Chung, C.H., Califano, J.A., Wheelan, S., Favorov, A.V., Florea, L., Fertig, E.J., Gaykalova, D.A. (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, 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 34(11):1859-1867. [Medline]
  • Yang, G., L. Florea (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]
  • 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 [Full text]
  • 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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