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Mihaela Pertea, Ph.D. - Publications

Affiliations: 
2002 Johns Hopkins University, Baltimore, MD 
Area:
Computer Science
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69 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 Chao KH, Mao A, Salzberg SL, Pertea M. Splam: a deep-learning-based splice site predictor that improves spliced alignments. Genome Biology. 25: 243. PMID 39285451 DOI: 10.1186/s13059-024-03379-4  0.517
2024 Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, ... ... Pertea M, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods. PMID 38849569 DOI: 10.1038/s41592-024-02298-3  0.383
2024 Chao KH, Heinz JM, Hoh C, Mao A, Shumate A, Pertea M, Salzberg SL. Combining DNA and protein alignments to improve genome annotation with LiftOn. Biorxiv : the Preprint Server For Biology. PMID 38798552 DOI: 10.1101/2024.05.16.593026  0.633
2024 Erdogdu B, Varabyou A, Hicks SC, Salzberg SL, Pertea M. Detecting differential transcript usage in complex diseases with SPIT. Cell Reports Methods. 4: 100736. PMID 38508189 DOI: 10.1016/j.crmeth.2024.100736  0.525
2023 Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. Nature Computational Science. 3: 700-708. PMID 38098813 DOI: 10.1038/s43588-023-00496-1  0.595
2023 Shinder I, Hu R, Ji HJ, Chao KH, Pertea M. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes. Nature Communications. 14: 7223. PMID 37940654 DOI: 10.1038/s41467-023-43017-4  0.413
2023 Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M. CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. Genome Biology. 24: 249. PMID 37904256 DOI: 10.1186/s13059-023-03088-4  0.783
2023 Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Major data analysis errors invalidate cancer microbiome findings. Mbio. e0160723. PMID 37811944 DOI: 10.1128/mbio.01607-23  0.486
2023 Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, et al. The status of the human gene catalogue. Nature. 622: 41-47. PMID 37794265 DOI: 10.1038/s41586-023-06490-x  0.646
2023 Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Major data analysis errors invalidate cancer microbiome findings. Biorxiv : the Preprint Server For Biology. PMID 37577699 DOI: 10.1101/2023.07.28.550993  0.501
2023 Chao KH, Mao A, Salzberg SL, Pertea M. Splam: a deep-learning-based splice site predictor that improves spliced alignments. Biorxiv : the Preprint Server For Biology. PMID 37546880 DOI: 10.1101/2023.07.27.550754  0.52
2023 Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, ... ... Pertea M, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Biorxiv : the Preprint Server For Biology. PMID 37546854 DOI: 10.1101/2023.07.25.550582  0.386
2023 Erdogdu B, Varabyou A, Hicks SC, Salzberg SL, Pertea M. Detecting differential transcript usage in complex diseases with SPIT. Biorxiv : the Preprint Server For Biology. PMID 37503064 DOI: 10.1101/2023.07.10.548289  0.512
2023 Amaral P, Carbonell-Sala S, Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, et al. The status of the human gene catalogue. Arxiv. PMID 36994150  0.677
2023 Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. Biorxiv : the Preprint Server For Biology. PMID 36993373 DOI: 10.1101/2023.03.23.533704  0.585
2023 Chao KH, Zimin AV, Pertea M, Salzberg SL. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual. G3 (Bethesda, Md.). PMID 36630290 DOI: 10.1093/g3journal/jkac321  0.704
2022 Sommer MJ, Cha S, Varabyou A, Rincon N, Park S, Minkin I, Pertea M, Steinegger M, Salzberg SL. Structure-guided isoform identification for the human transcriptome. Elife. 11. PMID 36519529 DOI: 10.7554/eLife.82556  0.783
2021 Zimin AV, Shumate A, Shinder I, Heinz J, Puiu D, Pertea M, Salzberg SL. A reference-quality, fully annotated genome from a Puerto Rican individual. Genetics. PMID 34897437 DOI: 10.1093/genetics/iyab227  0.685
2021 Varabyou A, Pockrandt C, Salzberg SL, Pertea M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Genetics. PMID 33983397 DOI: 10.1093/genetics/iyab074  0.63
2021 Varabyou A, Pertea G, Pockrandt C, Pertea M. TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets. Bioinformatics (Oxford, England). PMID 33964128 DOI: 10.1093/bioinformatics/btab342  0.312
2020 Varabyou A, Salzberg SL, Pertea M. Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments. Genome Research. PMID 33361112 DOI: 10.1101/gr.266213.120  0.561
2020 Varabyou A, Pockrandt C, Salzberg SL, Pertea M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Biorxiv : the Preprint Server For Biology. PMID 32995774 DOI: 10.1101/2020.09.21.300913  0.618
2020 Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000research. 9: 304. PMID 32489650 DOI: 10.12688/F1000Research.23297.1  0.457
2020 Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Salit ML, Zook JM, Salzberg SL. Assembly and annotation of an Ashkenazi human reference genome. Genome Biology. 21: 129. PMID 32487205 DOI: 10.1186/S13059-020-02047-7  0.644
2019 Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology. 20: 278. PMID 31842956 DOI: 10.1186/S13059-019-1910-1  0.547
2019 Breitwieser FP, Pertea M, Zimin A, Salzberg SL. Human contamination in bacterial genomes has created thousands of spurious proteins. Genome Research. PMID 31064768 DOI: 10.1101/Gr.245373.118  0.806
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  0.795
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  0.707
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  0.519
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  0.582
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  0.465
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  0.599
2012 Pertea M. The human transcriptome: an unfinished story. Genes. 3: 344-60. PMID 22916334 DOI: 10.3390/Genes3030344  0.504
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  0.594
2010 Pertea M, Salzberg SL. Abstracts of Beyond the Genome: The true gene count, human evolution and disease genomics. Boston, Massachusetts, USA. October 11-13, 2010. Genome Biology. I1-14, O1-13, P1-43. PMID 21134298 DOI: 10.1186/gb-2010-11-s1-i1  0.656
2010 Salzberg SL, Pertea M. Do-it-yourself genetic testing Genome Biology. 11. PMID 20932271 DOI: 10.1186/Gb-2010-11-10-404  0.572
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  0.684
2010 Pertea M, Salzberg SL. Between a chicken and a grape: estimating the number of human genes Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-I1  0.367
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  0.622
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  0.546
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  0.664
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  0.764
2008 Pertea M. Problems and Solutions in Biological Sequence Analysis * Mark Borodovsky, Svetlana Ekisheva Briefings in Bioinformatics. 9: 550-551. DOI: 10.1093/Bib/Bbn037  0.329
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  0.83
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  0.563
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  0.756
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  0.75
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 DOI: 10.1186/Gb-2006-7-S1-S9  0.739
2006 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. Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus Nature. 439: 502-502. DOI: 10.1038/Nature04572  0.519
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  0.686
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  0.648
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  0.812
2005 Majoros WH, Pertea M, Salzberg SL. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics (Oxford, England). 21: 1782-8. PMID 15691859 DOI: 10.1093/Bioinformatics/Bti297  0.486
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  0.612
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  0.794
2004 Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics (Oxford, England). 20: 2878-9. PMID 15145805 DOI: 10.1093/Bioinformatics/Bth315  0.618
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  0.705
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  0.774
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 DOI: 10.1093/Nar/Gkg527  0.538
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  0.676
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  0.778
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  0.816
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  0.829
2002 Pertea M, Salzberg SL. Computational gene finding in plants. Plant Molecular Biology. 48: 39-48. PMID 11860211 DOI: 10.1023/A:1013770123580  0.706
2001 Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR. Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species Plant Physiology. 125: 1166-1174. PMID 11244096 DOI: 10.1104/Pp.125.3.1166  0.573
2001 Pertea M, Lin X, Salzberg SL. GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Research. 29: 1185-90. PMID 11222768 DOI: 10.1093/Nar/29.5.1185  0.365
2000 Pertea M, Salzberg SL, Gardner MJ. Finding genes in Plasmodium falciparum. Nature. 404: 34; discussion 34-5. PMID 10716431 DOI: 10.1038/35003643  0.496
1999 Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H. Interpolated Markov models for eukaryotic gene finding. Genomics. 59: 24-31. PMID 10395796 DOI: 10.1006/Geno.1999.5854  0.562
1998 Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Pederson J, Shen K, Jing J, Aston C, Lai Z, ... ... Pertea M, et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (New York, N.Y.). 282: 1126-32. PMID 9804551 DOI: 10.1126/Science.282.5391.1126  0.695
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