Liliana D Florea

Associate Professor

19982019
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Research Output 1998 2019

2019

A multi-sample approach increases the accuracy of transcript assembly

Song, L., Sabunciyan, S., Yang, G. & Florea, L., Dec 1 2019, In : Nature communications. 10, 1, 5000.

Research output: Contribution to journalArticle

Open Access
assembly
RNA
Pectinidae
Statistical Models
Politics

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males

Kassiri, B., Shrestha, E., Kasprenski, M., Antonescu, C., Florea, L. D., Sfanos, K. S. & Wang, M. H., Jan 1 2019, In : Urology.

Research output: Contribution to journalArticle

Microbiota
Prospective Studies
Urine
Anti-Bacterial Agents
Ribosomal DNA
Bariatric Surgery
Weight Loss
Obesity
Gastric Bypass
Metabolic Diseases

Characterization and Analysis of the Skin Microbiota in Rosacea: A Case–Control Study

Rainer, B. M., Thompson, K. G., Antonescu, C., Florea, L., Mongodin, E. F., Bui, J., Fischer, A. H., Pasieka, H. B., Garza, L. A., Kang, S. & Chien, A. L., Jan 1 2019, (Accepted/In press) In : American Journal of Clinical Dermatology.

Research output: Contribution to journalArticle

Rosacea
Microbiota
Skin
Nose
Cheek

ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation

Gable, D. L., Gaysinskaya, V., Atik, C. C., Conover Talbot, C., Kang, B., Stanley, S. E., Pugh, E. W., Amat-Codina, N., Schenk, K. M., Arcasoy, M. O., Brayton, C., Florea, L. D. & Armanios, M., Oct 1 2019, In : Genes and Development. 33, 19-20, p. 1381-1396 16 p.

Research output: Contribution to journalArticle

Open Access
Exosomes
Pulmonary Fibrosis
Telomere
Transcriptome
Histones
2018

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

Kelley, D. Z., Flam, E. L., Guo, T., Danilova, L. V., Zamuner, F. T., 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., Florea, L. D., Fertig, E. & Gaykalova, D., Jan 1 2018, (Accepted/In press) In : Translational Research.

Research output: Contribution to journalArticle

Alternative Splicing
Protein Isoforms
Tumors
Neoplasms
Cell proliferation

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer

Afsari, B., Guo, T., Considine, M., Florea, L. D., Tsukamoto Kagohara, L., Stein-O'Brien, G. L., Kelley, D., Flam, E., Zambo, K. D., Ha, P. K., Geman, D., Ochs, M. F., Califano, J. A., Gaykalova, D., Favorov, A. & Fertig, E., Jun 1 2018, In : Bioinformatics. 34, 11, p. 1859-1867 9 p.

Research output: Contribution to journalArticle

Tumors
Tumor
Cancer
Protein Isoforms
Genes
2017

Germline Mutations in DNA Repair Genes in Lung Adenocarcinoma

Parry, E. M., Gable, D. L., Stanley, S. E., Khalil, S. E., Antonescu, V., Florea, L. D. & Armanios, M., Nov 1 2017, In : Journal of Thoracic Oncology. 12, 11, p. 1673-1678 6 p.

Research output: Contribution to journalArticle

Germ-Line Mutation
DNA Repair
BRCA2 Gene
Genes
Neoplasms
2016

CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads

Song, L., Sabunciyan, S. & Florea, L. D., Jun 2 2016, In : Nucleic Acids Research. 44, 10, e98.

Research output: Contribution to journalArticle

RNA
RNA Sequence Analysis
Ribosomal RNA
Alternative Splicing
Computational Biology

Computational Methods for Transcript Assembly from RNA-SEQ Reads

Canzar, S. & Florea, L. D., Sep 6 2016, Computational Methods for Next Generation Sequencing Data Analysis. wiley, p. 245-268 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational methods
RNA
Genes
Bioinformatics
Merging

JULiP: An efficient model for accurate intron selection from multiple RNA-seq samples

Yang, G. & Florea, L. D., Dec 30 2016, 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2016. Institute of Electrical and Electronics Engineers Inc., 7802769

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA
Introns
introns
Alternative Splicing
alternative splicing

Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes

Guerrero-Preston, R., Valle, B. L., Jedlicka, A. E., Turaga, N., Folawiyo, O., Pirini, F., Lawson, F., Vergura, A., Noordhuis, M., Dziedzic, A., Perez, G., Renehan, M., Guerrero-Diaz, C., Jesus Rodríguez, E. D., Diaz-Montes, T., Orengo, J. R., Mendez, K., Romaguera, J., Trock, B., Florea, L. D. & 1 others, Sidransky, D., Dec 1 2016, In : Cancer Prevention Research. 9, 12, p. 915-924 10 p.

Research output: Contribution to journalArticle

Papillomaviridae
Triage
Cell Biology
Area Under Curve
Urine

Rascaf: Improving genome assembly with RNA sequencing data

Song, L., Shankar, D. S. & Florea, L. D., Nov 1 2016, In : Plant Genome. 9, 3

Research output: Contribution to journalArticle

RNA Sequence Analysis
genome assembly
Molecular Sequence Annotation
sequence analysis
Genome
2015

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

Song, L. & Florea, L. D., 2015, In : GigaScience. 4, p. 48 1 p.

Research output: Contribution to journalArticle

Error correction
RNA
Genome
RNA Sequence Analysis
Genes

Viral non-coding RNA inhibits HNF4α expression in HCV associated hepatocellular carcinoma

Wang, Z., Ceniccola, K., Florea, L. D., Wang, B. D., Lee, N. H. & Kumar, A., Jul 8 2015, In : Infectious Agents and Cancer. 10, 1, 19.

Research output: Contribution to journalArticle

Hepatocyte Nuclear Factor 4
Untranslated RNA
Viral RNA
Hepacivirus
Hepatocellular Carcinoma
2014

Lighter: fast and memory-efficient sequencing error correction without counting

Song, L., Florea, L. D. & Langmead, B., 2014, In : Genome Biology. 15, 11, p. 509 1 p.

Research output: Contribution to journalArticle

error correction
algal bloom
filter
sampling

Loss of nuclear PTEN in HCV-infected human hepatocytes

Bao, W., Florea, L. D., Wu, N., Wang, Z., Banaudha, K., Qian, J., Houzet, L., Kumar, R. & Kumar, A., Jul 18 2014, In : Infectious Agents and Cancer. 9, 1, 23.

Research output: Contribution to journalArticle

Hepacivirus
Hepatocytes
Karyopherins
Untranslated RNA
Viral RNA
2013

CLASS: Constrained transcript assembly of RNA-seq reads

Song, L. & Florea, L. D., Apr 10 2013, In : BMC Bioinformatics. 14, SUPPL.5, S14.

Research output: Contribution to journalArticle

RNA
Genes
Contiguity
Gene
Program assemblers
Transcriptome
Sequencing
Genome
Genes
Gene

RNA sequencing of cancer reveals novel splicing alterations

Eswaran, J., Horvath, A., Godbole, S., Reddy, S. D., Mudvari, P., Ohshiro, K., Cyanam, D., Nair, S., Fuqua, S. A. W., Polyak, K., Florea, L. D. & Kumar, R., 2013, In : Scientific Reports. 3, 1689.

Research output: Contribution to journalArticle

RNA Sequence Analysis
Breast Neoplasms
Transcriptome
Neoplasms
Protein Isoforms

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues

Florea, L. D., Song, L. & Salzberg, S. L., Nov 21 2013, In : F1000Research. 2, 188.v2.

Research output: Contribution to journalArticle

Exons
Tissue
Alternative Splicing
Genes
Software
2012

Transcriptomic landscape of breast cancers through mRNA sequencing

Eswaran, J., Cyanam, D., Mudvari, P., Reddy, S. D. N., Pakala, S. B., Nair, S. S., Florea, L. D., Fuqua, S. A. W., Godbole, S. & Kumar, R., 2012, In : Scientific Reports. 2, 264.

Research output: Contribution to journalArticle

Breast Neoplasms
Messenger RNA
Transcriptional Regulatory Elements
Calnexin
Osteonectin
2011

Genome assembly has a major impact on gene content: A comparison of annotation in two bos Taurus assemblies

Florea, L. D., Souvorov, A., Kalbfleisch, T. S. & Salzberg, S. L., 2011, In : PLoS One. 6, 6, e21400.

Research output: Contribution to journalArticle

genome assembly
Genes
Genome
cattle
Molecular Sequence Annotation

MicroRNA silencing of tumor suppressor DLC-1 promotes efficient hepatitis C virus replication in primary human hepatocytes

Banaudha, K., Kaliszewski, M., Korolnek, T., Florea, L. D., Yeung, M. L., Jeang, K. T. & Kumar, A., Jan 2011, In : Hepatology. 53, 1, p. 53-61 9 p.

Research output: Contribution to journalArticle

Virus Replication
MicroRNAs
Hepacivirus
Hepatocytes
Virus Diseases

Sim4db and Leaff: Utilities for fast batch spliced alignment and sequence indexing

Walenz, B. & Florea, L. D., Jul 2011, In : Bioinformatics. 27, 13, p. 1869-1870 2 p., btr285.

Research output: Contribution to journalArticle

Sequence Alignment
Indexing
Batch
Genome
Alignment
2010

Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L. D. & 51 others, Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y. & Reed, K. M., Sep 2010, In : PLoS Biology. 8, 9, e1000475.

Research output: Contribution to journalArticle

genome assembly
Turkey
Turkey (country)
Genes
Genome
2009
RNA Splice Sites
Vertebrates
Strongylocentrotus purpuratus
Messenger RNA
Trans-Splicing

A whole-genome assembly of the domestic cow, Bos taurus

Zimin, A. V., Delcher, A. L., Florea, L. D., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A. & Salzberg, S. L., Apr 24 2009, In : Genome Biology. 10, 4, R42.

Research output: Contribution to journalArticle

genome assembly
genome
Genome
Synteny
cows

Corrigendum to "Novel Splice Variants of sFlt1 are Upregulated in Preeclampsia [Placenta 30 (3) (2009) 250-255]" (DOI: 10.1016/j.placenta.2008.12.010)

Heydarian, M., McCaffrey, T., Florea, L. D., Yang, Z., Ross, M. M., Zhou, W. & Maynard, S. E., Apr 2009, In : Placenta. 30, 4, p. 377 1 p.

Research output: Contribution to journalArticle

Pre-Eclampsia
Placenta
corrigendum

Novel Splice Variants of sFlt1 are Upregulated in Preeclampsia

Heydarian, M., McCaffrey, T., Florea, L. D., Yang, Z., Ross, M. M., Zhou, W. & Maynard, S. E., Mar 2009, In : Placenta. 30, 3, p. 250-255 6 p.

Research output: Contribution to journalArticle

Vascular Endothelial Growth Factor Receptor-1
Pre-Eclampsia
Exons
Placenta
Trophoblasts

Sim4cc: A cross-species spliced alignment program

Zhou, L., Pertea, M., Delcher, A. L. & Florea, L. D., 2009, In : Nucleic Acids Research. 37, 11, e80.

Research output: Contribution to journalArticle

Genome
Complementary DNA
Fagus
Expressed Sequence Tags
Genes
2008

Effective cluster-based seed design for cross-species sequence comparisons

Zhou, L., Mihai, I. & Florea, L. D., Dec 2008, In : Bioinformatics. 24, 24, p. 2926-2927 2 p.

Research output: Contribution to journalArticle

Sequence Comparison
Seed
Seeds
Genes
Genome

Universal seeds for cDNA-to-genome comparison

Zhou, L., Stanton, J. & Florea, L. D., Jan 23 2008, In : BMC Bioinformatics. 9, 36.

Research output: Contribution to journalArticle

CDNA
Seed
Seeds
Genome
Complementary DNA
2007

Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment

Zhou, L. & Florea, L. D., Mar 2007, In : Journal of Computational Biology. 14, 2, p. 113-130 18 p.

Research output: Contribution to journalArticle

Messenger RNA
Seed
Seeds
Genome
Alignment

Improving gene annotation using peptide mass spectrometry

Tanner, S., Shen, Z., Ng, J., Florea, L. D., Guigó, R., Briggs, S. P. & Bafna, V., Feb 2007, In : Genome Research. 17, 2, p. 231-239 9 p.

Research output: Contribution to journalArticle

Molecular Sequence Annotation
Mass Spectrometry
Exons
Peptides
Proteomics
2006

Bioinformatics of alternative splicing and its regulation

Florea, L. D., Mar 2006, In : Briefings in Bioinformatics. 7, 1, p. 55-69 15 p.

Research output: Contribution to journalArticle

Alternative Splicing
Bioinformatics
Computational Biology
Genes
Cataloging
2005

Differences in gene content between Salmonella enterica serovar enteritidis isolates and comparison to closely related serovars gallinarum and Dublin

Porwollik, S., Santiviago, C. A., Cheng, P., Florea, L. D., Jackson, S. & McClelland, M., Sep 2005, In : Journal of Bacteriology. 187, 18, p. 6545-6555 11 p.

Research output: Contribution to journalArticle

Salmonella enteritidis
Genes
Bacteriophages
Poultry
Serogroup

Finding anchors for genomic sequence comparison

Lippert, R. A., Zhao, X., Florea, L. D., Mobarry, C. & Istrail, S., Jul 2005, In : Journal of Computational Biology. 12, 6, p. 762-776 15 p.

Research output: Contribution to journalArticle

Sequence Comparison
Anchors
Genomics
Genome
Genes

Gene and alternative splicing annotation with AIR

Florea, L. D., Di Francesco, V., Miller, J., Turner, R., Yao, A., Harris, M., Walenz, B., Mobarry, C., Merkulov, G. V., Charlab, R., Dew, I., Deng, Z., Istrail, S., Li, P. & Sutton, G., Jan 2005, In : Genome Research. 15, 1, p. 54-66 13 p.

Research output: Contribution to journalArticle

Molecular Sequence Annotation
Alternative Splicing
Genome
Messenger RNA
Genomics

List of lists-annotated (LOLA): A database for annotation and comparison of published microarray gene lists

Cahan, P., Ahmad, A. M., Burke, H., Fu, S., Lai, Y., Florea, L. D., Dharker, N., Kobrinski, T., Kale, P. & McCaffrey, T. A., Oct 24 2005, In : Gene. 360, 1, p. 78-82 5 p.

Research output: Contribution to journalArticle

Databases
Genes
Search Engine
Cell Aging
Internet
2004

Characterization of Salmonella enterica subspecies I genovars by use of microarrays

Porwollik, S., Boyd, E. F., Choy, C., Cheng, P., Florea, L. D., Proctor, E. & McClelland, M., Sep 2004, In : Journal of Bacteriology. 186, 17, p. 5883-5898 16 p.

Research output: Contribution to journalArticle

Salmonella enterica
Salmonella Infections
Salmonella
Genes
Host Specificity

Comparative immunopeptidomics of humans and their pathogens

Istrail, S., Florea, L. D., Halldórsson, B. V., Kohlbacher, O., Schwartz, R. S., Yap, V. B., Yewdell, J. W. & Hoffman, S. L., Sep 7 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 36, p. 13268-13272 5 p.

Research output: Contribution to journalArticle

Proteome
Peptides
T-Lymphocytes
Major Histocompatibility Complex
Proteins

Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid

McClelland, M., Sanderson, K. E., Clifton, S. W., Latreille, P., Porwollik, S., Sabo, A., Meyer, R., Bieri, T., Ozersky, P., McLellan, M., Harkins, C. R., Wang, C., Nguyen, C., Berghoff, A., Elliott, G., Kohlberg, S., Strong, C., Du, F., Carter, J., Kremizki, C. & 15 others, Layman, D., Leonard, S., Sun, H., Fulton, L., Nash, W., Miner, T., Minx, P., Delehaunty, K., Fronick, C., Magrini, V., Nhan, M., Warren, W., Florea, L. D., Spieth, J. & Wilson, R. K., Dec 2004, In : Nature Genetics. 36, 12, p. 1268-1274 7 p.

Research output: Contribution to journalArticle

Salmonella enterica
Typhoid Fever
Genome
Genes
Pseudogenes

Finding anchors for genomic sequence comparison

Lippert, R. A., Zhao, X., Florea, L. D., Mobarry, C. & Istrail, S., 2004, Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB. Vol. 8. p. 233-241 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Anchors
Genes
Genome
Chromosome Mapping
Human Genome

Whole-genome shotgun assembly and comparison of human genome assemblies

Istrail, S., Sutton, G. G., Florea, L. D., Halpern, A. L., Mobarry, C. M., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J. R., Flanigan, M. J., Edwards, N. J., Bolanos, R., Fasulo, D., Halldorsson, B. V., Hannenhalli, S., Turner, R., Yooseph, S., Lu, F., Nusskern, D. R. & 16 others, Shue, B. C., Zheng, X. H., Zhong, F., Delcher, A. L., Huson, D. H., Kravitz, S. A., Mouchard, L., Reinert, K., Remington, K. A., Clark, A. G., Waterman, M. S., Eichler, E. E., Adams, M. D., Hunkapiller, M. W., Myers, E. W. & Venter, J. C., Feb 17 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 7, p. 1916-1921 6 p.

Research output: Contribution to journalArticle

Firearms
Human Genome
Information Centers
Genome
Biotechnology
2003

A non-redundant microarray of genes for two related bacteria

Porwollik, S., Frye, J., Florea, L. D., Blackmer, F. & McClelland, M., Apr 1 2003, In : Nucleic Acids Research. 31, 7, p. 1869-1876 8 p.

Research output: Contribution to journalArticle

Open Reading Frames
Bacteria
Genome
Genes
Salmonella enterica

EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae

Florea, L. D., McClelland, M., Riemer, C., Schwartz, S. & Miller, W., Jul 1 2003, In : Nucleic Acids Research. 31, 13, p. 3527-3532 6 p.

Research output: Contribution to journalArticle

Enterobacteriaceae
Genome
Sequence Alignment
Data Display
Molecular Sequence Annotation

Epitope prediction algorithms for peptide-based vaccine design

Florea, L. D., Halldórsson, B., Kohlbacher, O., Schwartz, R., Hoffman, S. & Istrail, S., 2003, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., p. 17-26 10 p. 1227293

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Epitopes
Vaccines
Peptides
Antigen-antibody reactions
Immune system

Epitope prediction algorithms for peptide-based vaccine design.

Florea, L., Halldórsson, B., Kohlbacher, O., Schwartz, R., Hoffman, S. & Istrail, S., 2003, In : Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference.. 2, p. 17-26 10 p.

Research output: Contribution to journalArticle

Subunit Vaccines
Epitopes
Peptides
Linear Programming
Computer-Aided Design
2002

PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences

Elnitski, L., Riemer, C., Petrykowska, H., Florea, L. D., Schwartz, S., Miller, W. & Hardison, R., 2002, In : Genomics. 80, 6, p. 681-690 10 p.

Research output: Contribution to journalArticle

Data Display
Molecular Sequence Annotation
Conserved Sequence
Sequence Alignment
Deoxyribonuclease I