| Year |
Citation |
Score |
| 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 |
0.41 |
|
| 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 |
0.787 |
|
| 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 |
0.49 |
|
| 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 |
0.651 |
|
| 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 |
0.506 |
|
| 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 |
0.518 |
|
| 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 |
0.382 |
|
| 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 |
0.513 |
|
| 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 |
0.682 |
|
| 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 |
0.584 |
|
| 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 |
0.71 |
|
| 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 |
0.787 |
|
| 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 |
0.691 |
|
| 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 |
0.635 |
|
| 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 |
0.311 |
|
| 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 |
0.562 |
|
| 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 |
0.624 |
|
| 2020 |
Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000research. 9: 304. PMID 32489650 DOI: 10.12688/F1000Research.23297.1 |
0.46 |
|
| 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 |
0.649 |
|
| 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 |
0.548 |
|
| 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 |
0.807 |
|
| 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 |
0.706 |
|
| 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 |
0.523 |
|
| 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 |
0.583 |
|
| 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 |
0.469 |
|
| 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 |
0.602 |
|
| 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 |
0.597 |
|
| 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 |
0.663 |
|
| 2010 |
Salzberg SL, Pertea M. Do-it-yourself genetic testing Genome Biology. 11. PMID 20932271 DOI: 10.1186/Gb-2010-11-10-404 |
0.576 |
|
| 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 |
0.689 |
|
| 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 |
0.369 |
|
| 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 |
0.627 |
|
| 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 |
0.548 |
|
| 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 |
0.67 |
|
| 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 |
0.767 |
|
| 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 |
0.33 |
|
| 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 |
0.565 |
|
| 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 |
0.761 |
|
| 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 |
0.755 |
|
| 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 |
0.741 |
|
| 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 |
0.525 |
|
| 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 |
0.691 |
|
| 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 |
0.653 |
|
| 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 |
0.814 |
|
| 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 |
0.488 |
|
| 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 |
0.616 |
|
| 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 |
0.798 |
|
| 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 |
0.623 |
|
| 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 |
0.71 |
|
| 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 |
0.776 |
|
| 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 |
0.542 |
|
| 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 |
0.682 |
|
| 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 |
0.78 |
|
| 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 |
0.817 |
|
| 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 |
0.831 |
|
| 2002 |
Pertea M, Salzberg SL. Computational gene finding in plants. Plant Molecular Biology. 48: 39-48. PMID 11860211 DOI: 10.1023/A:1013770123580 |
0.71 |
|
| 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 |
0.579 |
|
| 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 |
0.364 |
|
| 2000 |
Pertea M, Salzberg SL, Gardner MJ. Finding genes in Plasmodium falciparum. Nature. 404: 34; discussion 34-5. PMID 10716431 DOI: 10.1038/35003643 |
0.501 |
|
| 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 |
0.566 |
|
| 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 |
0.701 |
|
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