Mihaela Pertea, Ph.D. - Publications

Affiliations: 
2002 Johns Hopkins University, Baltimore, MD 
Area:
Computer Science

31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
2018 Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biology. 19: 208. PMID 30486838 DOI: 10.1186/s13059-018-1590-2  1
2016 Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols. 11: 1650-1667. PMID 27560171 DOI: 10.1038/nprot.2016.095  1
2015 Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Research. 25: 1401-9. PMID 26290535 DOI: 10.1101/gr.193607.115  1
2015 Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 33: 290-5. PMID 25690850 DOI: 10.1038/nbt.3122  1
2015 Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Ghiaur G, Lai J, McHugh HL, Hao H, Zhang H, Margolick JB, Gurer C, Murphy AJ, Valenzuela DM, Yancopoulos GD, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature. 517: 381-5. PMID 25561180 DOI: 10.1038/nature14053  1
2014 Salzberg SL, Pertea M, Fahrner JA, Sobreira N. DIAMUND: direct comparison of genomes to detect mutations. Human Mutation. 35: 283-8. PMID 24375697 DOI: 10.1002/humu.22503  1
2011 Pertea M, Pertea GM, Salzberg SL. Detection of lineage-specific evolutionary changes among primate species Bmc Bioinformatics. 12. PMID 21726447 DOI: 10.1186/1471-2105-12-274  1
2010 Salzberg SL, Pertea M. Do-it-yourself genetic testing Genome Biology. 11. PMID 20932271 DOI: 10.1186/gb-2010-11-10-404  1
2010 Pertea M, Salzberg SL. Between a chicken and a grape: estimating the number of human genes. Genome Biology. 11: 206. PMID 20441615 DOI: 10.1186/gb-2010-11-5-206  1
2009 Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, ... ... Pertea M, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 460: 352-8. PMID 19606141 DOI: 10.1038/nature08160  1
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  0.52
2009 Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: A comprehensive database of predicted operons in microbial genomes Nucleic Acids Research. 37. PMID 18948284 DOI: 10.1093/nar/gkn784  1
2008 Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology. 9: R7. PMID 18190707 DOI: 10.1186/gb-2008-9-1-r7  1
2007 Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, ... ... Pertea M, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/science.1145406  1
2007 Pertea M, Mount SM, Salzberg SL. A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. Bmc Bioinformatics. 8: 159. PMID 17517127 DOI: 10.1186/1471-2105-8-159  1
2007 Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, ... ... Pertea M, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/science.1138878  1
2007 Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, ... ... Pertea M, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (New York, N.Y.). 315: 207-12. PMID 17218520 DOI: 10.1126/science.1132894  1
2006 Allen JE, Majoros WH, Pertea M, Salzberg SL. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions Genome Biology. 7. PMID 16925843  1
2005 Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, ... ... Pertea M, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 438: 1151-6. PMID 16372009 DOI: 10.1038/nature04332  1
2005 Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, et al. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research. 15: 1284-91. PMID 16109971 DOI: 10.1101/gr.3869505  1
2005 Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, ... ... Pertea M, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (New York, N.Y.). 309: 134-7. PMID 15994558 DOI: 10.1126/science.1110439  1
2005 Majoros WH, Pertea M, Delcher AL, Salzberg SL. Efficient decoding algorithms for generalized hidden Markov model gene finders. Bmc Bioinformatics. 6: 16. PMID 15667658 DOI: 10.1186/1471-2105-6-16  1
2005 Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, ... ... Pertea M, et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (New York, N.Y.). 307: 1321-4. PMID 15653466 DOI: 10.1126/science.1103773  1
2004 Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M, Fosker N, Fraser A, Harris D, Larke N, Murphy L, Humphray S, O'Neil S, Pertea M, Price C, et al. Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genetics and Biology : Fg & B. 41: 443-53. PMID 14998527 DOI: 10.1016/j.fgb.2003.12.003  1
2004 Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Research. 14: 142-8. PMID 14707176 DOI: 10.1101/gr.1562804  1
2003 Majoros WH, Pertea M, Antonescu C, Salzberg SL. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Research. 31: 3601-4. PMID 12824375  1
2002 Pertea M, Salzberg SL. Using GlimmerM to find genes in eukaryotic genomes. Current Protocols in Bioinformatics. Unit 4.4. PMID 18792941 DOI: 10.1002/0471250953.bi0404s00  1
2002 Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, ... ... Pertea M, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature. 419: 531-4. PMID 12368868 DOI: 10.1038/nature01094  1
2002 Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/nature01099  1
2002 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, ... ... Pertea M, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419: 498-511. PMID 12368864 DOI: 10.1038/nature01097  1
2002 Pertea M, Salzberg SL. Computational gene finding in plants. Plant Molecular Biology. 48: 39-48. PMID 11860211  1
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