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Items: 24

1.

Erratum: Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999-2015.

Bialosuknia SM, Tan Y, Zink SD, Koetzner CA, Maffei JG, Halpin RA, Mueller EA, Novotny M, Shilts M, Fedorova NB, Amedeo P, Das SR, Pickett B, Kramer LD, Ciota AT.

Virus Evol. 2019 Aug 20;5(2):vez035. doi: 10.1093/ve/vez035. eCollection 2019 Jul.

2.

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999-2015.

Bialosuknia SM, Tan Y, Zink SD, Koetzner CA, Maffei JG, Halpin RA, Muller E, Novatny M, Shilts M, Fedorova NB, Amedeo P, Das SR, Pickett B, Kramer LD, Ciota AT.

Virus Evol. 2019 Jul 21;5(2):vez020. doi: 10.1093/ve/vez020. eCollection 2019 Jul. Erratum in: Virus Evol. 2019 Aug 20;5(2):vez035.

3.

Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes.

Bose ME, Shrivastava S, He J, Nelson MI, Bera J, Fedorova N, Halpin R, Town CD, Lorenzi HA, Amedeo P, Gupta N, Noyola DE, Videla C, Kok T, Buys A, Venter M, Vabret A, Cordey S, Henrickson KJ.

PLoS One. 2019 Jul 18;14(7):e0220057. doi: 10.1371/journal.pone.0220057. eCollection 2019.

4.

Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains.

Shrivastava S, Puri V, Dilley KA, Ngouajio E, Shifflett J, Oldfield LM, Fedorova NB, Hu L, Williams T, Durbin A, Amedeo P, Rashid S, Shabman RS, Pickett BE.

Sci Rep. 2018 Oct 26;8(1):15843. doi: 10.1038/s41598-018-34147-7.

5.

Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.

Tan Y, Pickett BE, Shrivastava S, Gresh L, Balmaseda A, Amedeo P, Hu L, Puri V, Fedorova NB, Halpin RA, LaPointe MP, Cone MR, Heberlein-Larson L, Kramer LD, Ciota AT, Gordon A, Shabman RS, Das SR, Harris E.

PLoS Negl Trop Dis. 2018 Jul 30;12(7):e0006670. doi: 10.1371/journal.pntd.0006670. eCollection 2018 Jul.

6.

Sequences of Zika Virus Genomes from a Pediatric Cohort in Nicaragua.

Oldfield LM, Fedorova N, Puri V, Shrivastava S, Amedeo P, Durbin A, Rocchi I, Williams T, Shabman RS, Tan GS, Balmaseda A, Kuan G, Saborio S, Gordon A, Harris E, Pickett BE.

Genome Announc. 2018 Jun 14;6(24). pii: e00498-18. doi: 10.1128/genomeA.00498-18.

7.

Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells.

Moser LA, Oldfield LM, Fedorova N, Puri V, Shrivastava S, Amedeo P, Isom R, Hu L, Durbin A, Rocchi I, Williams T, Tan GS, Shabman RS, Bernard KA, Pickett BE.

Genome Announc. 2018 Jan 25;6(4). pii: e01528-17. doi: 10.1128/genomeA.01528-17.

8.

Identification of Dezidougou Virus in a DAK AR 41524 Zika Virus Stock.

Shrivastava S, Puri V, Fedorova N, Amedeo P, Stockwell TB, Shabman RS, Rashid S, Pickett BE.

Genome Announc. 2017 Jul 27;5(30). pii: e00605-17. doi: 10.1128/genomeA.00605-17.

9.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.

Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.

10.

New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information.

Lorenzi HA, Puiu D, Miller JR, Brinkac LM, Amedeo P, Hall N, Caler EV.

PLoS Negl Trop Dis. 2010 Jun 15;4(6):e716. doi: 10.1371/journal.pntd.0000716.

11.

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM.

Nature. 2008 Oct 9;455(7214):757-63. doi: 10.1038/nature07327.

12.

What can comparative genomics tell us about species concepts in the genus Aspergillus?

Rokas A, Payne G, Fedorova ND, Baker SE, Machida M, Yu J, Georgianna DR, Dean RA, Bhatnagar D, Cleveland TE, Wortman JR, Maiti R, Joardar V, Amedeo P, Denning DW, Nierman WC.

Stud Mycol. 2007;59:11-7. doi: 10.3114/sim.2007.59.02.

13.

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC.

PLoS Genet. 2008 Apr 11;4(4):e1000046. doi: 10.1371/journal.pgen.1000046.

14.

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.

15.

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.

16.

Whole genome comparison of the A. fumigatus family.

Wortman JR, Fedorova N, Crabtree J, Joardar V, Maiti R, Haas BJ, Amedeo P, Lee E, Angiuoli SV, Jiang B, Anderson MJ, Denning DW, White OR, Nierman WC.

Med Mycol. 2006 Sep 1;44(Supplement_1):S3-S7. doi: 10.1080/13693780600835799.

PMID:
30408921
17.

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E.

PLoS Biol. 2006 Sep;4(9):e286.

18.

The genome of the protist parasite Entamoeba histolytica.

Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillén N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N.

Nature. 2005 Feb 24;433(7028):865-8.

19.
20.

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.

21.

Endogenous targets of transcriptional gene silencing in Arabidopsis.

Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, Paszkowski J.

Plant Cell. 2000 Jul;12(7):1165-78.

22.

Disruption of the plant gene MOM releases transcriptional silencing of methylated genes.

Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J.

Nature. 2000 May 11;405(6783):203-6.

PMID:
10821279
23.
24.

[Pharmacological cardiac arrest in open heart surgery (experimental study)].

PAOLO M, NICOLA M, GIANPAOLO N, AMEDEO P, ANACLETO V.

Archivio Chir Torace. 1959 Apr-Jun;16:191-204. Italian. No abstract available.

PMID:
14430235

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