[ 2024202320222021202020192018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | <2000]


  • Florea L (2024). Predicting Alu exonization in the human genome with a deep learning model, 6th World Aging and Rejuvenation Conference (ARC2024), Paris, France (talk).
  • He Z, Chen O, Phillips N, Pasquesi GIM, Sabunciyan S, Florea L (2024). Predicting Alu exonization in the human genome with a deep learning model, bioRxiv 2024.01.03.574099. (doi: 10.1101/2024.01.03.574099)
  • Lui WW, Yang G, Florea L (2024). MntJULiP and Jutils: Differential splicing analysis of RNA-seq data with covariates, bioRxiv 2024.01.01.573825. (doi: 10.1101/2024.01.01.573825)


  • Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB (2023). Regulation of human interferon signaling by transposon exonization, bioRxiv 2023.09.11.557241 (doi: 10.1101/2023.09.11.557241)
  • Lui WW, Yang G, He Z, Sabunciyan S, Florea L (2023). MntJULiP and Jutils: Tools for differential splicing detection and visualization from complex RNA-seq data sets, Annual Meeting of the American Society for Human Genetics (ASHG2023), Washington, DC (poster).
  • Florea L (2023). Unravelling the combinatorial design of genes: Splice graph-based transcript reconstruction from RNA sequencing reads, SorinFest: Phase Transitions in Computer Science and Computational Biology Conference, Brown University, MA (YouTube).
  • Florea L (2023). Methods for differential splicing detection, 5th International SPLICING Conference (SPLICING2023), Caparica, Portugal (talk).
  • He Z, Florea L (2023). Predicting Alu exonization in the human genome with a Deep Learning model, Workshop on Emerging Methods for Sequence Analysis (WEMSA2023), State College, PA (talk).
  • 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]
  • Debeljak M, Cho S, Downs B, Considine M, Avin-McKelvey B, Wang Y, Perez PN, Grizzle WE, Hoadley KA, Lynch CF, Hernandez BY, van Diest PJ, Cozen W, Hamilton AS, Hawes D, Gabrielson E, Cimino-Mathews A, Florea LD, Cope L, Umbricht CB (2023). Multimodal genome-wide survey of Progressing and Non-progressing DCIS, American Association for Cancer Research (AACR) Annual Meeting, Orlando, FL (poster). 
  • Osborne LM, Payne JL, Florea L, Sabunciyan S (2023). Splicing of Extracellular Vesicle messenger RNAs during pregnancy is altered prior to the onset of postpartum depression, Society of Biological Psychiatry (SOBP) Annual Meeting, San Diego, CA (poster).
  • 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]


  • He Z, Florea L (2022). A Deep Learning model for predicting Alu exonization events, Cold Spring Harbor Laboratory Meeting – Biological Data Science, Cold Spring Harbor, NY (poster).
  • He Z, Sabunciyan S, Florea L (2022). Estimating the extent of Alu exonization in the human genome with a Deep Learning model, Cold Spring Harbor Laboratory Meeting – Transposable Elements, Cold Spring Harbor, NY (poster).
  • 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, 75(3):269-275. [Medline]
  • He Z, Florea L (2022). Prediction of Alu exonization events with a Deep Learning model, Cold Spring Harbor Laboratory Meeting – The Biology of Genomes, Cold Spring Harbor, NY (poster).


  • Yang G, He Z, Florea L (2021). Predicting alternative splicing regulation and the effects of sequence variation with a Probabilistic Deep Learning model, Cold Spring Harbor Laboratory (Virtual) Meeting – Genome Informatics, Cold Spring Harbor, NY (poster).
  • 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]
  • Schratz K, Gaysinskaya V, Cosner ZL, DeBoy EA, Xiang Z, Kasch-Semenza L, Florea L, Shah PD, Armanios M (2021). Somatic reversion impacts evolution of myelodysplastic syndromes and acute myeloid leukemia in the short telomere disorders, J Clin Invest. 131(18):e147598. [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 . [Medline]
  • Shin E, Jones-Brando LV, Florea LD, Schwartz KB, Yolken RH (2021). Development of methods to extract RNA from archived pediatric needle liver biopsies to produce sequencing data, J of Pediatr Gastroenterol 72(3):436-441. [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]
  • Paik JJ, Casciola-Rosen L, Shin JY, Albayda J, Tiniakou E, Leung DG, Gutierrez-Alamillo L, Perin J, Florea L, Antonescu C, Leung SG, Purwin G, Koenig A, Christopher-Stine L (2021). Study of Tofacitinib in refractory dermatomyositis: An open-label pilot study of ten patients, Arthritis Rheumatol 73(5):858-865. [Medline]


  • Yang G, Sabunciyan S, Florea L (2020). Comprehensive and scalable quantification of splicing differences with MntJULiP, bioRxiv doi:10.1101/2020.10.26.355941.
  • Florea, L (2020). High performance tools for analysis of large collections of RNA-seq data, SPLICING 2020, Lisbon, Portugal (virtual) (Talk). 
  • Yang G, Florea L (2020). Comprehensive identification of differential splicing events with MntJULiP, Cold Spring Harbor Laboratory (Virtual) Meeting - The Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Florea L, Payer L, Yang G, Antonescu C, Burns K (2020). Detection of Alu exonization events in human frontal cortex from RNA-seq data, Cold Spring Harbor Laboratory (Virtual) Meeting - The Biology of Genomes, Cold Spring Harbor, NY (poster).
  • Thompson KG, Rainer BM, Antonescu C, Florea L, Mongodin EF, Kang S, and Chien AL (2020). Minocycline and its impact on microbial dysbiosis in the skin and gastrointestinal tract of acne patients, Annals Dermatol 32(1):21-30. [PDF]
  • Thompson KG, Rainer BM, Antonescu C, Florea L, Mongodin EF, Kang S, and Chien AL (2020). Comparison of the skin microbiota in acne and rosacea, Exp Dermatol, doi: 10.1111/exd.14098. [Medline]
  • Guo T, Zambo KDA, Zamuner F, Ou T, Hopkins C, Kelley DZ, Wulf H, Winkler E, Erbe R, Danilova L, Considine M, Sidransky D, Favorov A, Florea L, Fertig EJ, Gaykalova DA (2020). Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma, Epigenetics, 15(9):959-971. [Medline]
  • Thompson KG, Shuster M, Ly BC, Antonescu C, Florea L, Chien AL, Kang S. Variability in skin microbiota between smokers, former smokers, and non-smokers, JAAD 83(3):942-944. [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 Communications 10(1):5000. [Medline]
  • Florea L, Song L, and Yang G (2019). Simultaneous multi-sample analysis sigificantly improves the accuracy of RNA-seq analysis, The 69th Annual Meeting of The American Society of Human Genetics (ASHG 2019), Oct 18, Houston, TX. (poster)
  • 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]
  • 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: A case-control study, Amer. Journal of Clinical Dermatology, 21(1):139-147. [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]
  • 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, 131:204-210. [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]


  • 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).


  • Song L, Shankar D, and Florea L (2016). Rascaf: Improving genome assembly with RNA-seq data, The Plant Genome, 9(3). [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).


  • 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., 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).


  • 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 Cancer, 9:23. [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).


  • 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).


  • 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).


  • 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).


  • 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).


  • 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.


  • 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.


  • 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.


  • 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.


  • 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.


  • 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.


  • 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.


  • 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]


  • 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]


  • 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.