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Items: 49

1.

Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape.

Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang SH, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho YC.

Cell Host Microbe. 2017 Apr 12;21(4):494-506.e4. doi: 10.1016/j.chom.2017.03.008.

2.

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL.

Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11.

3.

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT.

Genome Res. 2015 Sep;25(9):1401-9. doi: 10.1101/gr.193607.115.

4.

Severe thoracic impalement injury: Survival in a case with delayed surgical definitive care.

Lunca S, Morosanu C, Alexa O, Pertea M.

Ulus Travma Acil Cerrahi Derg. 2015 Mar;21(2):152-6. doi: 10.5505/tjtes.2015.38354.

5.

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL.

Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18.

6.

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.

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, Deeks SG, Strowig T, Kumar P, Siliciano JD, Salzberg SL, Flavell RA, Shan L, Siliciano RF.

Nature. 2015 Jan 15;517(7534):381-5. doi: 10.1038/nature14053. Epub 2015 Jan 7.

7.

DIAMUND: direct comparison of genomes to detect mutations.

Salzberg SL, Pertea M, Fahrner JA, Sobreira N.

Hum Mutat. 2014 Mar;35(3):283-8. doi: 10.1002/humu.22503.

8.

The human transcriptome: an unfinished story.

Pertea M.

Genes (Basel). 2012 Sep;3(3):344-60. doi: 10.3390/genes3030344.

9.

[Functional reeducation of flexor tendons with associated lesions in zone II--comparative study].

Topa I, Tamaş C, Perţea M, Stamate T.

Rev Med Chir Soc Med Nat Iasi. 2011 Jul-Sep;115(3):851-7. Romanian.

PMID:
22046798
10.

[Regeneration capacity of the peripheral nerve: experimental study--final results].

Perţea M, Luncă S.

Rev Med Chir Soc Med Nat Iasi. 2011 Apr-Jun;115(2):418-27. Romanian.

PMID:
21870734
11.

Detection of lineage-specific evolutionary changes among primate species.

Pertea M, Pertea GM, Salzberg SL.

BMC Bioinformatics. 2011 Jul 4;12:274. doi: 10.1186/1471-2105-12-274.

12.

Do-it-yourself genetic testing.

Salzberg SL, Pertea M.

Genome Biol. 2010;11(10):404. doi: 10.1186/gb-2010-11-10-404. Epub 2010 Oct 7.

13.

[Capacity for peripheral nerve regeneration. Experimental study--preliminary results].

Perţea M, Luncă S.

Rev Med Chir Soc Med Nat Iasi. 2010 Jan-Mar;114(1):135-41. Romanian.

PMID:
20509290
14.

Between a chicken and a grape: estimating the number of human genes.

Pertea M, Salzberg SL.

Genome Biol. 2010;11(5):206. doi: 10.1186/gb-2010-11-5-206. Epub 2010 May 5. Review.

15.

The genome of the blood fluke Schistosoma mansoni.

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, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM.

Nature. 2009 Jul 16;460(7253):352-8. doi: 10.1038/nature08160.

16.

Sim4cc: a cross-species spliced alignment program.

Zhou L, Pertea M, Delcher AL, Florea L.

Nucleic Acids Res. 2009 Jun;37(11):e80. doi: 10.1093/nar/gkp319. Epub 2009 May 8.

17.

[Postmastectomy breast reconstruction--outcome on 33 consecutive cases].

Curic L, Azzena B, Bassetto F, Perţea M, Luncă S.

Rev Med Chir Soc Med Nat Iasi. 2009 Apr-Jun;113(2):453-8. Romanian.

PMID:
21495351
18.

OperonDB: a comprehensive database of predicted operons in microbial genomes.

Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL.

Nucleic Acids Res. 2009 Jan;37(Database issue):D479-82. doi: 10.1093/nar/gkn784. Epub 2008 Oct 23.

19.

[Axillary wound with complete vasculo-nervous section. Functional outcomes].

Perţea M, Luncă S, Moroşanu C.

Rev Med Chir Soc Med Nat Iasi. 2008 Oct-Dec;112(4):999-1002. Romanian.

PMID:
20209776
20.

Using GlimmerM to find genes in eukaryotic genomes.

Pertea M, Salzberg SL.

Curr Protoc Bioinformatics. 2002 Nov;Chapter 4:Unit 4.4. doi: 10.1002/0471250953.bi0404s00.

PMID:
18792941
21.

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR.

Genome Biol. 2008 Jan 11;9(1):R7. doi: 10.1186/gb-2008-9-1-r7.

22.

Draft genome of the filarial nematode parasite Brugia malayi.

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, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

23.
24.

Genome sequence of Aedes aegypti, a major arbovirus vector.

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, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW.

Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.

25.

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.

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, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ.

Science. 2007 Jan 12;315(5809):207-12.

26.

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

Allen JE, Majoros WH, Pertea M, Salzberg SL.

Genome Biol. 2006;7 Suppl 1:S9.1-13. Epub 2006 Aug 7.

27.

Abdominal wall actinomycosis associated with prolonged use of an intrauterine device: a case report and review of the literature.

Lunca S, Bouras G, Romedea NS, Pertea M.

Int Surg. 2005 Sep-Oct;90(4):236-40. Review.

PMID:
16548322
28.

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

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, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Latgé JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Córdoba S, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW.

Nature. 2005 Dec 22;438(7071):1151-6. Erratum in: Nature. 2006 Jan 26;439(7075):502. Lafton, Anne [corrected to Lafon, Anne].

PMID:
16372009
29.

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

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, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O'Shaughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S; Rice Chromosome 3 Sequencing Consortium.

Genome Res. 2005 Sep;15(9):1284-91. Epub 2005 Aug 18.

30.

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.

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, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V.

Science. 2005 Jul 1;309(5731):134-7.

31.

Morbid obesity: a surgical perspective.

Lunca S, Perţea M, Bouras G, Dumitru L, Hatjissalatas SG.

Rom J Gastroenterol. 2005 Jun;14(2):151-8. Review.

32.

Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.

Majoros WH, Pertea M, Salzberg SL.

Bioinformatics. 2005 May 1;21(9):1782-8. Epub 2005 Feb 2.

PMID:
15691859
33.

Efficient decoding algorithms for generalized hidden Markov model gene finders.

Majoros WH, Pertea M, Delcher AL, Salzberg SL.

BMC Bioinformatics. 2005 Jan 24;6:16.

34.

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

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, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW.

Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13.

35.

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.

Majoros WH, Pertea M, Salzberg SL.

Bioinformatics. 2004 Nov 1;20(16):2878-9. Epub 2004 May 14.

PMID:
15145805
36.

Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster.

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, Rabbinowitsch E, Rajandream MA, Salzberg S, Saunders D, Seeger K, Sharp S, Warren T, Denning DW, Barrell B, Hall N.

Fungal Genet Biol. 2004 Apr;41(4):443-53.

PMID:
14998527
37.

Computational gene prediction using multiple sources of evidence.

Allen JE, Pertea M, Salzberg SL.

Genome Res. 2004 Jan;14(1):142-8.

38.

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.

Majoros WH, Pertea M, Antonescu C, Salzberg SL.

Nucleic Acids Res. 2003 Jul 1;31(13):3601-4.

39.

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.

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, Granger D, Fujii C, Hansen C, Pederson J, Feldblyum T, Peterson J, Suh B, Angiuoli S, Pertea M, Allen J, Selengut J, White O, Cummings LM, Smith HO, Adams MD, Venter JC, Carucci DJ, Hoffman SL, Fraser CM.

Nature. 2002 Oct 3;419(6906):531-4.

PMID:
12368868
40.

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.

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, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ.

Nature. 2002 Oct 3;419(6906):512-9.

PMID:
12368865
41.

Genome sequence of the human malaria parasite Plasmodium falciparum.

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, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B.

Nature. 2002 Oct 3;419(6906):498-511.

42.

Computational gene finding in plants.

Pertea M, Salzberg SL.

Plant Mol Biol. 2002 Jan;48(1-2):39-48. Review.

PMID:
11860211
43.

Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.

Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR.

Plant Physiol. 2001 Mar;125(3):1166-74.

44.

GeneSplicer: a new computational method for splice site prediction.

Pertea M, Lin X, Salzberg SL.

Nucleic Acids Res. 2001 Mar 1;29(5):1185-90.

45.

Finding genes in Plasmodium falciparum.

Pertea M, Salzberg SL, Gardner MJ.

Nature. 2000 Mar 2;404(6773):34; discussion 34-5. No abstract available.

PMID:
10716431
46.

Interpolated Markov models for eukaryotic gene finding.

Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H.

Genomics. 1999 Jul 1;59(1):24-31.

PMID:
10395796
47.

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.

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, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Adams MD, Venter JC, Hoffman SL.

Science. 1998 Nov 6;282(5391):1126-32. Erratum in: Science 1998 Dec 4;282(5395):1827.

48.

[A study of pyramidone suppositories].

Mihalache M, Perţea M, Verbuţă A.

Rev Med Chir Soc Med Nat Iasi. 1990 Apr-Jun;94(2):389-92. Romanian.

PMID:
2100858
49.

[Considerations on drug nomenclator during the past 20 years].

Năstasă V, Voitcu M, Pertea M.

Rev Med Chir Soc Med Nat Iasi. 1987 Apr-Jun;91(2):335-40. Romanian. No abstract available.

PMID:
3685699

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