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Liliana D. Florea, Ph.D. - Publications

Affiliations: 
2000 Pennsylvania State University, State College, PA, United States 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 He Z, Chen O, Phillips N, Pasquesi GIM, Sabunciyan S, Florea L. Predicting exonization in the human genome with a deep learning model. Biorxiv : the Preprint Server For Biology. PMID 38260329 DOI: 10.1101/2024.01.03.574099  0.381
2019 Song L, Sabunciyan S, Yang G, Florea L. A multi-sample approach increases the accuracy of transcript assembly. Nature Communications. 10: 5000. PMID 31676772 DOI: 10.1038/S41467-019-12990-0  0.306
2018 Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, et al. Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer. Bioinformatics (Oxford, England). PMID 29342249 DOI: 10.1093/Bioinformatics/Bty004  0.344
2017 Afsari B, Guo T, Considine M, Kelley D, Flam E, Florea L, Ha P, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer Cancer Research. 77: 3577-3577. DOI: 10.1158/1538-7445.Am2017-3577  0.304
2016 Song L, Shankar DS, Florea L. Rascaf: Improving Genome Assembly with RNA Sequencing Data. The Plant Genome. 9. PMID 27902792 DOI: 10.3835/Plantgenome2016.03.0027  0.473
2016 Song L, Sabunciyan S, Florea L. CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Research. PMID 26975657 DOI: 10.1093/Nar/Gkw158  0.412
2015 Song L, Florea L. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience. 4: 48. PMID 26500767 DOI: 10.1186/S13742-015-0089-Y  0.369
2013 Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000research. 2: 188. PMID 24555089 DOI: 10.12688/F1000Research.2-188.V2  0.304
2013 Florea LD, Salzberg SL. Genome-guided transcriptome assembly in the age of next-generation sequencing. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1234-40. PMID 24524156 DOI: 10.1109/Tcbb.2013.140  0.478
2013 Song L, Florea L. CLASS: constrained transcript assembly of RNA-seq reads. Bmc Bioinformatics. 14: 1-8. PMID 23734605 DOI: 10.1186/1471-2105-14-S5-S14  0.387
2013 Eswaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SA, Polyak K, Florea LD, Kumar R. RNA sequencing of cancer reveals novel splicing alterations. Scientific Reports. 3: 1689. PMID 23604310 DOI: 10.1038/Srep01689  0.301
2012 Guerrero-Preston R, McClelland M, Sidransky D, Florea L. Abstract A12: Web-based tools for visualization of the Human Papilloma Virus genome dynamics: A computational approach to cancer prevention and control Cancer Prevention Research. 5. DOI: 10.1158/1940-6207.Prev-12-A12  0.301
2011 Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL. Genome assembly has a major impact on gene content: A comparison of annotation in two bos Taurus assemblies Plos One. 6. PMID 21731731 DOI: 10.1371/Journal.Pone.0021400  0.481
2011 Walenz B, Florea L. Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. Bioinformatics (Oxford, England). 27: 1869-70. PMID 21551146 DOI: 10.1093/bioinformatics/btr285  0.43
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Florea L, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  0.512
2010 Zhou L, Mihai I, Florea L. Spaced Seeds for Cross-species CDNA-to-genome Sequence Alignment Communications in Information and Systems. 10: 115-136. DOI: 10.4310/Cis.2010.V10.N2.A4  0.508
2010 Florea L, Souvorov A, Salzberg SL. Genes and genomes, an imperfect world: comparison of gene annotations of two Bos taurus draft assemblies Genome Biology. 11: 13. DOI: 10.1186/Gb-2010-11-S1-P13  0.461
2009 Buckley KM, Florea LD, Smith LC. 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: 318. PMID 19607703 DOI: 10.1186/1471-2164-10-318  0.456
2009 Zhou L, Pertea M, Delcher AL, Florea L. Sim4cc: a cross-species spliced alignment program. Nucleic Acids Research. 37: e80. PMID 19429899 DOI: 10.1093/Nar/Gkp319  0.477
2009 Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42  0.436
2009 Heydarian M, McCaffrey T, Florea L, Yang Z, Ross MM, Zhou W, Maynard SE. Novel splice variants of sFlt1 are upregulated in preeclampsia. Placenta. 30: 250-255. PMID 19147226 DOI: 10.1016/J.Placenta.2008.12.010  0.327
2008 Zhou L, Mihai I, Florea L. Effective cluster-based seed design for cross-species sequence comparisons Bioinformatics. 24: 2926-2927. PMID 18940827 DOI: 10.1093/Bioinformatics/Btn547  0.417
2008 Zhou L, Stanton J, Florea LD. Universal seeds for cDNA-to-genome comparison. Bmc Bioinformatics. 9: 36-36. PMID 18215286 DOI: 10.1186/1471-2105-9-36  0.413
2007 Zhou L, Florea LD. Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment. Journal of Computational Biology. 14: 113-130. PMID 17456011 DOI: 10.1089/Cmb.2006.0130  0.426
2007 Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Research. 17: 231-9. PMID 17189379 DOI: 10.1101/Gr.5646507  0.408
2006 Florea LD. Bioinformatics of alternative splicing and its regulation Briefings in Bioinformatics. 7: 55-69. PMID 16761365 DOI: 10.1093/Bib/Bbk005  0.403
2005 Porwollik S, Santiviago CA, Cheng P, Florea L, Jackson S, McClelland M. Differences in Gene Content between Salmonella enterica Serovar Enteritidis Isolates and Comparison to Closely Related Serovars Gallinarum and Dublin Journal of Bacteriology. 187: 6545-6555. PMID 16159788 DOI: 10.1128/Jb.187.18.6545-6555.2005  0.43
2005 Cahan P, Ahmad AM, Burke H, Fu S, Lai Y, Florea L, Dharker N, Kobrinski T, Kale P, McCaffrey TA. List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists. Gene. 360: 78-82. PMID 16140476 DOI: 10.1016/J.Gene.2005.07.008  0.417
2005 Lippert RA, Zhao X, Florea L, Mobarry C, Istrail S. Finding anchors for genomic sequence comparison. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 762-76. PMID 16108715 DOI: 10.1089/Cmb.2005.12.762  0.469
2005 Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G. Gene and alternative splicing annotation with AIR. Genome Research. 15: 54-66. PMID 15632090 DOI: 10.1101/Gr.2889405  0.469
2004 McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, ... ... Florea L, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nature Genetics. 36: 1268-74. PMID 15531882 DOI: 10.1038/Ng1470  0.469
2004 Porwollik S, Boyd EF, Choy C, Cheng P, Florea L, Proctor E, McClelland M. Characterization of Salmonella enterica subspecies I genovars by use of microarrays. Journal of Bacteriology. 186: 5883-98. PMID 15317794 DOI: 10.1128/Jb.186.17.5883-5898.2004  0.305
2004 Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the National Academy of Sciences of the United States of America. 101: 1916-21. PMID 14769938 DOI: 10.1073/Pnas.0307971100  0.465
2003 Florea L, McClelland M, Riemer C, Schwartz S, Miller W. EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Research. 31: 3527-32. PMID 12824359 DOI: 10.1093/Nar/Gkg551  0.599
2003 Porwollik S, Frye J, Florea LD, Blackmer F, McClelland M. A non-redundant microarray of genes for two related bacteria. Nucleic Acids Research. 31: 1869-76. PMID 12655003 DOI: 10.1093/Nar/Gkg298  0.468
2002 Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 80: 681-90. PMID 12504859 DOI: 10.1006/Geno.2002.7018  0.602
2001 McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, ... ... Florea L, et al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 Nature. 413: 852-856. PMID 11677609 DOI: 10.1038/35101614  0.554
2001 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Florea L, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040  0.502
2000 McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, Churcher C, Dougan G, Wilson RK, Miller W. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Research. 28: 4974-86. PMID 11121489 DOI: 10.1093/Nar/28.24.4974  0.608
2000 Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M. Web-based visualization tools for bacterial genome alignments Nucleic Acids Research. 28: 3486-3496. PMID 10982867 DOI: 10.1093/Nar/28.18.3486  0.608
2000 Florea L, Li M, Riemer C, Giardine B, Miller W, Hardison R. Validating Computer Programs for Functional Genomics in Gene Regulatory Regions Current Genomics. 1: 11-27. DOI: 10.2174/1389202003351733  0.546
1999 Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, Goodman M, Miller W, Hardison R. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions Nucleic Acids Research. 27: 3899-3910. PMID 10481030 DOI: 10.1093/Nar/27.19.3899  0.552
1998 Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research. 8: 967-74. PMID 9750195 DOI: 10.1101/Gr.8.9.967  0.601
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