AREA OF EXPERTISE

Plant genomics, epigenomics and bioinformatics

  • Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch, TB, Van de Peer Y (2016).The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 530(7590):331-5.
  • Zuccolo A, Scofield DG, De Paoli E, Morgante M (2015). The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution. Gene. 2015 Aug 15;568(1):89-99. doi: 10.1016/j.gene.2015.05.028. Epub 2015 May 14.
  • Montes RA*, de Fátima Rosas-Cárdenas F*, De Paoli E*, Accerbi M, Rymarquis LA, Mahalingam G, Marsch-Martínez N, Meyers BC, Green PJ, de Folter S (2014). Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs.NATURE COMMUNICATIONS. 2014 Apr 23;5:3722. doi: 10.1038/ncomms4722.

*equally contributed

  • Larsson H, De Paoli E, Morgante M, Lascoux M, Gyllenstrand N (2013). The Hypomethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Piceaabies). TREE GENETICS & GENOMES, 9:601–612,ISSN: 1614-2942.
  • Albert VA, Barbazuk WB, dePamphilis CW, Der JP, Leebens-Mack J, Ma H, Palmer JD, Rounsley S, Sankoff D, Schuster SC, Soltis DE, Soltis PS, Wessler SR, Wing RA, Albert VA, Ammiraju JS, Barbazuk WB, Chamala S, Chanderbali AS, dePamphilis CW, Der JP, Determann R, Leebens-Mack J, Ma H, Ralph P, Rounsley S, Schuster SC, Soltis DE, Soltis PS, Talag J, Tomsho L, Walts B, Wanke S, Wing RA, Albert VA, Barbazuk WB, Chamala S, Chanderbali AS, Chang TH, Determann R, Lan T, Soltis DE, Soltis PS, Arikit S, Axtell MJ, Ayyampalayam S, Barbazuk WB, Burnette JM 3rd, Chamala S, De Paoli E, dePamphilis CW, Der JP, Estill JC, Farrell NP, Harkess A, Jiao Y, Leebens-Mack J, Liu K, Mei W, Meyers BC, Shahid S, Wafula E, Walts B, Wessler SR, Zhai J, Zhang X, Albert VA, Carretero-Paulet L, dePamphilis CW, Der JP, Jiao Y, Leebens-Mack J, Lyons E, Sankoff D, Tang H, Wafula E, Zheng C, Albert VA, Altman NS, Barbazuk WB, Carretero-Paulet L, dePamphilis CW, Der JP, Estill JC, Jiao Y, Leebens-Mack J, Liu K, Mei W, Wafula E, Altman NS, Arikit S, Axtell MJ, Chamala S, Chanderbali AS, Chen F, Chen JQ, Chiang V, De Paoli E, dePamphilis CW, Der JP, Determann R, Fogliani B, Guo C, Harholt J, Harkess A, Job C, Job D, Kim S, Kong H, Leebens-Mack J, Li G, Li L, Liu J, Ma H, Meyers BC, Park J, Qi X, Rajjou L, Burtet-Sarramegna V, Sederoff R, Shahid S, Soltis DE, Soltis PS, Sun YH, Ulvskov P, Villegente M, Xue JY, Yeh TF, Yu X, Zhai J, Acosta JJ, Albert VA, Barbazuk WB, Bruenn RA, Chamala S, de Kochko A, dePamphilis CW, Der JP, Herrera-Estrella LR, Ibarra-Laclette E, Kirst M, Leebens-Mack J, Pissis SP, Poncet V, Schuster SC, Soltis DE, Soltis PS, Tomsho L. (2013). The Amborella genome and the evolution of flowering plants. Science. 2013 Dec 20;342(6165):1241089. doi: 10.1126/science.1241089.
  • Prezza N, Del Fabbro C, Vezzi F, De Paoli E, Polocriti A (2012). ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet. PROCEEDINGS OF THE 2012 ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE.
  • Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang M, Leto JA, Menda N, Strickler S, Mao L, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong S, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie WR, Lippman ZB, Chia JM, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson LK, Chang SB, Royer SM, Shearer LA, Stack SM, Rose JK, Xu Y, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigó R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop GJ, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal JK, Pandit A, Singh PK, Mahato AK, Gaikwad VD, Sharma RR, Mohapatra T, Singh NK, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latché A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez del Carmen A, Monforte A, Granell A, Fernandez-Muñoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek MG, Feron RM, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJ, Janssen A, van Haaren MJ, Jungeun Kim SH, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jöcker A, Warfsmann J, Göbel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EG, van de Belt J, van Haarst JC, Peters SA, van Staveren MA, Henkens MH, Mooyman PJ, Hesselink T, van Ham RC, Jiang G, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuñiga S, Wang G, Cade R, Dietrich RA, Rogers J, Knapp S, Fei Z, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers BC, Gurazada AB, Green PJ, Vyas SM, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi AK, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk WB, Li J, Guo H, Lee TH, Wang Y, Zhang D, Paterson AH, Wang X, Tang H, Barone A, Chiusano ML, Ercolano MR, D'Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour GB, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe BA, Vezzi A, D'Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson DR, De Paoli E, Szinay D, de Jong HH, Bai Y, Visser RG, Klein R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. NATURE. 2012 May 30;485(7400):635-41. doi: 10.1038/nature11119.
  • Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ. (2011). Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage.PLANT CELL. 2011 Dec;23(12):4185-207. doi: 10.1105/tpc.111.089045.
  • Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, Gonzales AJ, Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier JD, Meyers BC (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. GENES DEV. 2011 Dec 1;25(23):2540-53. doi: 10.1101/gad.177527.111.
  • Morgante M, De Paoli E (2011). Toward the conifer genome sequence. In Genetics, Genomics and Breeding of Conifers Trees. Edited by Plomion C, Bousquet J, Kole C. New York: Edenbridge Science Publishers and CRC Press; 2011::389-403.
  • Wei F. S, Stein J. C, Liang C. Z, Zhang J. W, Fulton R. S, Baucom R. S, De Paoli E, Zhou S. G, Yang L. X, Han Y. J, Pasternak S, Narechania A, Zhang L. F, Yeh C. T, Ying K, Nagel D. H, Collura K, Kudrna D, Currie J, Lin J. K, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves T. A, Rock S. M, Adams S, Fulton L. A, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon J. M, Miguel P. S, Jiang N, Wessler S. R, Green P. J, Yu Y, Schwartz D. C, Meyers B. C, Bennetzen J. L, Martienssen R. A, Mccombie W. R, Aluru S, Clifton S. W, Schnable P. S, Ware D, Wilson R. K, Wing R. A (2010). Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet. 2009 Nov;5(11):e1000728. doi: 10.1371/journal.pgen.1000728.
  • Swaminathan K, Alabady M. S, Varala K, De Paoli E, Ho I, Rokhsar D. S, Arumuganathan A. K, Ming R, Green P. J, Meyers B. C, Moose S. P, Hudson M. E (2010). Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneaegrasse. Genome Biol. 2010;11(2):R12. doi: 10.1186/gb-2010-11-2-r12.
  • De Paoli E, Dorantes-Acosta A, Zhai J. X, Accerbi M, Jeong D. H, Park S, Meyers B. C, Jorgensen R. A, Green, P. J (2009). Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA. 2009 Nov;15(11):1965-70. doi: 10.1261/rna.1706109.
  • Vischi M, Fiori M, De Paoli E, Padovan S, Guarda M, Olivieri A (2008). Broccoli Fiolaro (Brassica oleracea), an endangered typical Italian cultivar. A genetic analysis by SSR markers. PLANT GENETIC RESOURCES, vol. 6(03), p. 215-221, ISSN: 1479-2621.
  • Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong D.H, Yen Y, Green P.J, Chandler V.L, Meyers B.C (2008). Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl AcadSci U S A. 2008 Sep 30;105(39):14958-63. doi: 10.1073/pnas.0808066105.
  • German M.A, Pillay M, Jeong D.H, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis L.A, Nobuta K, German R, De Paoli E, Lu, C. Schroth G, Meyers B.C, Green P.J (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol. 2008 Aug;26(8):941-6. doi: 10.1038/nbt1417.
  • Morgante M, De Paoli E, Radovic S (2007). Transposable elements and the plant pan-genomes. CurrOpin Plant Biol. 2007 Apr;10(2):149-55.
  • Vischi M, Arzenton F, De Paoli E, Paselli S, Tomat E, Olivieri A. M (2006). Identification of wild species of sunflower by a specific plastid DNA sequence. HELIA, vol. 29, p. 11-18, ISSN: 1018-1806
  • Heuertz M*, De Paoli E*, Kallman T*, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006). Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Piceaabies (L.) Karst]. Genetics. 2006 Dec;174(4):2095-105.

*equally contributed

  • De Paoli E*, Moroldo M*, Morgante M (2004). Marcatori molecolari e miglioramento genetico (Molecularmarkers and breeding). AGROINDUSTRIA, vol. 3,2, p. 89-100, ISSN: 1724-9015.

*equallycontributed

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