Selected Publications 

  • Nidadavolu LS, Cosarderelioglu C, Gomez AM, Wu Y, Bopp T, Zhang C, Nguyen T, Marx Rattner R, Yang H, Antonescu C, Florea L, Talbot CC, Smith B, Foster DB, Fairman JE, Yenokyan G, Chung T, Le A, Walston JD, Abadir PM (2023). Interleukin-6 drives mitochondrial dysregulation and accelerates physical decline: insights from an inducible humanized IL-6 knock-in mouse model, J Gerontol 78(10):1740-1752. [Medline]
  • Gutierrez-Hoffmann M, Fan J, O'Meally RN, Cole RN, Florea L, Antonescu C, Talbot CC, Tiniakou E, Darrah E, Soloski MJ (2023). The Interaction of Borrelia burgdorferi with human dendritic cells: functional implications, J Immunol 211(4):612-625. [Medline]
  • Moyer AJ, Fernandez F-X, Li Y, Klinedinst DK, Florea LD, Kazuki Y, Oshimura M, Reeves RH (2023). Overexpression screen of chromosome 21 genes reveals modulators of Sonic hedgehog signaling relevant to Down syndrome, Dis Model Mech 16(4):dmm049712. [Medline]
  • Yang G, Sabunciyan S, Florea L (2022). Comprehensive and scalable quantification of splicing differences with MntJULiP, Genome Biol. 23(1):195. [Medline]
  • Shin E, Schwartz KB, Jones-Brando LV, Florea LD, Sabunciyan S, Delong Wood L, Yolken RH (2022). Expression of HLA and autoimmune pathway genes in liver biopsies of young subjects with Autoimmune Hepatitis Type 1, J Pediatr Gastroenterol Nutr 5(3):269-275. [Medline]
  • Florea L, Payer L, Antonescu C, Yang G, Burns K (2021). Detection of Alu exonization events in human frontal cortex from RNA-seq data, Frontiers Molecular Biosciences 8:727537. [Medline]
  • Wang Q, Hernández-Ochoa EO, Viswanathan MC, Blum ID, Do DC, Granger JM, Murphy KR, Wei A-C, Aja S, Liu N, Antonescu CM, Florea LD, Talbot CC, Mohr D, Wagner KR, Regot S, Lovering RM, Gao P, Bianchet MA, Wu MN, Cammarato A, Schneider MF, Bever GS, Anderson ME (2021). CaMKII oxidation is a critical performance/disease trade-off acquired at the dawn of vertebrate evolution, Nat Commun 12(1):3175. [Medline]
  • Yang G, Cope L, He Z, Florea L (2021). Jutils: A visualization toolkit for differential alternative splicing events, Bioinformatics 37(22):4272-4. [Medline]
  • Umapathi P, Mesubi OO, Banerjee PS, Abrol N, Wang Q, Luczak ED, Wu Y, Granger JM, Wei A-C, Reyes Gaido OE, Florea L, Talbot Jr CC, Hart GW, Zachara NE, Anderson ME (2021). Excessive O-GlcNAcylation causes heart failure and sudden death, Circulation 143(17):1687-1703. [Medline]
  • 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.[Medline].
  • Song L, Sabunciyan S, Yang G, and Florea L (2019). A multi-sample approach increases the accuracy of transcript assembly, Nature Commun 10(1):5000. [Medline]
  • 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 & Devel, 33(19-20):1381-1396. [Medline]
  • 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. 29(10):3239-3245. [Medline]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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 and Florea L (2015). Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads, GigaScience, 4:48. [Full text]
  • Wang Z, Ceniccola K, Florea L, Wang BD, Lee NH, and Kumar A (2015). Viral non-coding RNA inhibits HNF4α expression in HCV associated hepatocellular carcinoma, Infectious Agents and Cancer , 10(1):19. [Medline]
  • Song L, Florea L, and Langmead B (2014). Lighter: fast and memory-efficient error correction without counting, Genome Biology, 15:509. [Medline]
  • Bao W, Florea L, Wu N, Wang Z, Banaudha K, Qian J, Houzet L, Kumar R, and Kumar A (2014). Loss of nuclear PTEN in HCV-infected human hepatocytes, Infectious Agents and Cancer, 9:23. [Full text]
  • Florea L and Salzberg SL (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, Song L and Salzberg SL (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, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SAW, Polyak K, Florea LD, and Kumar R (2013). RNA sequencing of cancer reveals novel splicing alterations, Sci. Rep. 3:1689. [Medline]

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