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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