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Pertea, Mihaela

Associate Professor
Som Biomedical Engineering

720 Rutland Ave
mpertea@jhu.edu

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About

Education
  • Ph.D. 2001, The Johns Hopkins University
  • Master of Science 1998, The Johns Hopkins University
  • Master of Science 1995, University of Bucharest
  • Bachelor of Science 1944, University of Bucharest
Experience
  • 2019 - 2019:  Associate Professor, Department of Genetic Medicine

Publications

Journal Articles
  • Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Pertea M, Salit ML, Zook JM, Salzberg SL, Salzberg SL, Salzberg SL, Salzberg SL (2020).  Assembly and annotation of an Ashkenazi human reference genome.  Genome Biology.  21(1).
  • Liu R, Yeh YHJ, Varabyou A, Collora JA, Sherrill-Mix S, Conover Talbot C, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, Ambinder RF, Hoh R, Deeks SG, Chiarella J, Spudich S, Douek DC, Bushman FD, Pertea M, Ho YC (2020).  Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target.  Science Translational Medicine.  12(543).
  • Pertea M, Pertea G (2020).  GFF Utilities: GffRead and GffCompare.  F1000Research.  9.
  • Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M (2019).  Transcriptome assembly from long-read RNA-seq alignments with StringTie2.  Genome Biology.  20(1).
  • Breitwieser FP, Pertea M, Zimin AV, Salzberg SL (2019).  Human contamination in bacterial genomes has created thousands of spurious proteins.  Genome Research.  29(6).  954-960.
  • Chiriac A, Grosu OM, Terinte C, Pertea M (2019).  Calcific uremic arteriolopathy (calciphylaxis) calls into question the validity of guidelines of diagnosis and treatment.  Journal of Dermatological Treatment.
  • Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL (2018).  CHESS: A new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.  Genome Biology.  19(1).
  • 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 (2017).  Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape.  Cell Host and Microbe.  21(4).  494-506.e4.
  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016).  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.  Nature Protocols.  11(9).  1650-1667.
  • Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT (2015).  Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.  Genome Research.  25(9).  1401-1409.
  • 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 (2015).  Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.  Nature.  517(7534).  381-385.
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015).  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.  Nature Biotechnology.  33(3).  290-295.
  • Salzberg SL, Pertea M, Fahrner JA, Sobreira N (2014).  DIAMUND: Direct comparison of genomes to detect mutations.  Human Mutation.  35(3).  283-288.
  • Pertea M (2012).  The human transcriptome: An unfinished story.  Genes.  3(3).  344-360.
  • Pertea M, Pertea GM, Salzberg SL (2011).  Detection of lineage-specific evolutionary changes among primate species.  BMC Bioinformatics.  12.
  • Topa I, Tamas C, Pertea M, Stamate T (2011).  [Functional reeducation of flexor tendons with associated lesions in zone II--comparative study]..  Revista medico-chirurgicalǎ̌ a Societǎ̌ţaii de Medici ş̧i Naturaliş̧ti din Iaş̧i.  115(3).  851-857.
  • Pertea M, Salzberg SL (2010).  Between a chicken and a grape: Estimating the number of human genes.  Genome Biology.  11(5).
  • 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 (2009).  The genome of the blood fluke Schistosoma mansoni.  Nature.  460(7253).  352-358.
  • Zhou L, Pertea M, Delcher AL, Florea L (2009).  Sim4cc: A cross-species spliced alignment program.  Nucleic Acids Research.  37(11).
  • Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL (2009).  OperonDB: A comprehensive database of predicted operons in microbial genomes.  Nucleic Acids Research.  37(SUPPL. 1).
  • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Robin CR, Wortman JR (2008).  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.  Genome Biology.  9(1).
  • 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 CKS, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin M, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DMA, 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 (2007).  Draft genome of the filarial nematode parasite Brugia malayi.  Science.  317(5845).  1756-1760.
  • Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu Z, 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 CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers Y-H, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, 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, Co...Severson DW (2007).  Genome sequence of Aedes aegypti, a major arbovirus vector.  Science.  316(5832).  1718-1723.
  • Pertea M, Mount SM, Salzberg SL (2007).  A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.  BMC Bioinformatics.  8.
  • Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UCM, 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, 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 (2007).  Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.  Science.  315(5809).  207-212.
  • Pertea M, Salzberg SL (2007).  Using protein domains to improve the accuracy of Ab Initio gene finding.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  4645 LNBI.  208-215.
  • Allen JE, Majoros WH, Pertea M, Salzberg SL (2006).  JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions..  Genome biology.  7 Suppl 1.
  • 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, Lafton A, Latgé J-P, 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 M-A, Reichard U, Renauld H, Robson GD, Rodriguez De Cordoba 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 ...Denning DW (2005).  Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.  Nature.  438(7071).  1151-1156.
  • Buell CR, McCombie WR, Wing RA, 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 J, 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 HR, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna D, Ammiraju JSS, Luo M, Goicoechea JL, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Soderlund C, Nelson W, De La Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O'haughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S (2005).  Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium.  Genome Research.  15(9).  1284-1291.
  • Gardner MJ, Bishop R, Shah T, De Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJM, 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 ELN, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V (2005).  Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.  Science.  309(5731).  134-137.
  • Majoros WH, Pertea M, Salzberg SL (2005).  Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.  Bioinformatics.  21(9).  1782-1788.
  • 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 SJM, 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 (2005).  The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.  Science.  307(5713).  1321-1324.
  • Majoros WH, Pertea M, Delcher AL, Salzberg SL (2005).  Efficient decoding algorithms for generalized hidden Markov model gene finders.  BMC Bioinformatics.  6.
  • Majoros WH, Pertea M, Salzberg SL (2004).  TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders.  Bioinformatics.  20(16).  2878-2879.
  • Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, Piccolboni A, Yang A, Tammana H, Bekiranov S, Kapranov P, Harrison R, Church G, Struhl K, Ren B, Kim TH, Barrera LO, Qu C, van Calcar S, Luna R, Glass CK, Rosenfeld MG, Guigo R, Antonarakis SE, Birney E, Brent M, Pachter L, Reymond A, Dermitzakis ET, Dewey C, Keefe D, Denoeud F, Lagarde J, Ashurst J, Hubbard T, Wesselink JJ, Castelo R, Eyras E, Myers RM, Sidow A, Batzoglou S, Trinklein ND, Hartman SJ, Aldred SF, Anton E, Schroeder DI, Marticke SS, Nguyen L, Schmutz J, Grimwood J, Dickson M, Cooper GM, Stone EA, Asimenos G, Brudno M, Dutta A, Karnani N, Taylor CM, Kim HK, Robins G, Stamatoyannopoulos G, Stamatoyannopoulos JA, Dorschner M, Sabo P, Hawrylycz M, Humbert R, Wallace J, Yu M, Navas PA, McArthur M, Noble WS, Dunham I, Koch CM, Andrews RM, Clelland GK, Wilcox S, Fowler JC, James KD, Groth P, Dovey OM, Ellis P...Harvey SC (2004).  The ENCODE (ENCyclopedia of DNA Elements) Project.  Science.  306(5696).  636-640.
  • 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 (2004).  Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster.  Fungal Genetics and Biology.  41(4).  443-453.
  • Allen JE, Pertea M, Salzberg SL (2004).  Computational gene prediction using multiple sources of evidence.  Genome Research.  14(1).  142-148.
  • Majoros WH, Pertea M, Antonescu C, Salzberg SL (2003).  GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders.  Nucleic Acids Research.  31(13).  3601-3604.
  • Yu Y, Rambo T, Currie J, Saski C, Kim HR, Collura K, Thompson S, Simmons J, Yang T-J, Nah G, Patel AJ, Thurmond S, Henry D, Oates R, Palmer M, Pries G, Gibson J, Anderson H, Paradkar M, Crane L, Dale J, Carver MB, Wood T, Frisch D, Engler F, Soderlund C, Palmer LE, Tetylman L, Nascimento L, de la Bastide M, Spiegel L, Ware D, O'Shaughnessy A, Dike S, Dedhia N, Preston R, Huang E, Ferraro K, Kuit K, Miller B, Zutavern T, Katzenberger F, Muller S, Balija V, Martienssen RA, Stein L, Minx P, Johnson D, Cordum H, Mardis E, Cheng Z, Jiang J, Wilson R, McCombie WR, Wing RA, Yuan Q, Ouyang S, Liu J, Jones KM, Gansberger K, Moffat K, Hill J, Tsitrin T, Overton L, Bera J, Kim M, Jin S, Tallon L, Ciecko A, Pai G, van Aken S, Utterback T, Reidmuller S, Bormann J, Feldblyum T, Hsiao J, Zismann V, Blunt S, de Vazeilles A, Shaffer T, Koo H, Suh B, Yang Q, Haas B, Peterson J, Pertea M, Volfovsky N, Wortman J, White O, Salzberg SL, Fraser CM, Robin Buell C, Messing J, Song R, Fuks G, Llaca V,...Dean RA (2003).  In-depth view of structure, activity, and evolution of rice chromosome 10.  Science.  300(5625).  1566-1569.
  • 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 (2002).  Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.  Nature.  419(6906).  531-534.
  • 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 (2002).  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.  Nature.  419(6906).  512-519.
  • Pertea M, Salzberg SL (2002).  Computational gene finding in plants.  Plant Molecular Biology.  48(1-2).  39-48.
  • Pertea M, Salzberg SL (2002).  Using GlimmerM to find genes in eukaryotic genomes..  Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.].  Chapter 4.
  • Pertea M, Salzberg SL (2002).  A method to improve the performance of translation start site detection and its application for gene finding.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  2452.  210-219.
  • 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 DMA, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Davis RW, Fraser CM, Barrell B (2002).  Genome sequence of the human malaria parasite Plasmodium falciparum.  Nature.  419(6906).  498-511.
  • Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR (2001).  Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species.  Plant Physiology.  125(3).  1166-1174.
  • Pertea M, Lin X, Salzberg SL (2001).  GeneSplicer: A new computational method for splice site prediction.  Nucleic Acids Research.  29(5).  1185-1190.
  • Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito M-I, Lin X, Town CD, Venter JC, Fraser CM, Tabata S, Nakamura Y, Kaneko T, Sato S, Asamizu E, Kato T, Kotani H, Sasamoto S, Ecker JR, Theologis A, Federspiel NA, Palm CJ, Osborne BI, Shinn P, Dewar K, Kim CJ, Buehler E, Dunn P, Chao Q, Chen H, Vysotskaia VS, Lenz CA, Kim CJ, Hansen NF, Liu SX, Alta H, Sakano H, Dunn P, Lam B, Pham PK, Nguyen M, Yu G, Chen H, Southwick A, Lee JM, Miranda M, Toriumi MJ, Davis RW, Palm CJ, Conway AB, Conn L, Hansen NF, Hootan A, Lam B, Wambutt R, Murphy G, Düsterhöft A, Stiekema W, Pohl T, Entian K-D, Terryn N, Volckaert G, Salanoubat M, Choisne N, Artiguenave F, Weissenbach J, Quetier F, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Wilson RK, Sekhon M, Pepin K, Murray J, Johnson D, Hillier L, de la Bastide M, Huang E, Spiegel L, Gnoj L, Habermann K, Dedhia N, Parnell L, Preston R, Marra M, McCombie WR, Chen E, Martienssen R, Mayer K, Lemcke K, Ha...Somerville C (2000).  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.  Nature.  408(6814).  796-815.
  • Pertea M, Salzberg SL, Gardner MJ, Lawson D, Bowman S, Barren B (2000).  Finding genes in Plasmodium falciparum.  Nature.  404(6773).  34-35.
  • Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H (1999).  Interpolated Markov models for eukaryotic gene finding.  Genomics.  59(1).  24-31.
  • 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 (1998).  Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.  Science.  282(5391).  1126-1132.
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