Pantelis Topalis (Staff Scientist - Bioinformatics)
The main interests of the group are a) to analyze gene expression and regulation from high throughput sequencing datasets and b) to assemble, annotate and compare newly sequenced genomes whith a special focus on insects and human pathogenes. Other interests include the development of databases and bioinformatics tools using ontologies and other sematics approaches to promote interoperability between different but related datasets.
Lima WR, Martins DC, Parreira KS, Scarpelli P, Santos de Moraes M, Topalis P, Hashimoto RF, Garcia CRS. (2017) Genome-wide analysis of the human malaria parasite Plasmodium falciparum transcription factor PfNF-YB shows interaction with a CCAAT motif. Oncotarget 8:113987-114001.
Dritsou V, Topalis P, Windbichler N, Simoni A, Hall A, Lawson D, Hinsley M, Hughes D, Napolioni V, Crucianelli F, Deligianni E, Gasperi G, Gomulski LM, Savini G, Manni M, Scolari F, Malacrida AR, Arcà B, Ribeiro JM, Lombardo F, Saccone G, Salvemini M, Moretti R, Aprea G, Calvitti M, Picciolini M, Papathanos PA, Spaccapelo R, Favia G, Crisanti A, Louis C. (2015) A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. Pathog Glob Health. 109:207-20.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S; VectorBase Consortium, Madey G, Collins FH, Lawson D. (2015) VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res. 43(Database issue):D707-13.
Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P. (2014) Non-coding RNA gene families in the genomes of anopheline mosquitoes. BMC Genomics 15:1038.
Topalis P, Mitraka E, Dritsou V, Dialynas E, Louis C. (2013) IDOMAL: the malaria ontology revisited. J Biomed Semantics 4:16.
Evi Goulielmaki, Anna Ioannidou, Maria Tsekrekou, Kalliopi Stratigi, Ioanna K. Poutakidou, Katerina Gkirtzimanaki, Michalis Aivaliotis, Konstantinos Evangelou, Pantelis Topalis, Janine Altmüller, Vassilis G. Gorgoulis, Georgia Chatzinikolaou and George A. Garinis' Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage. Nature Communications 2020 (in press).
Lima WR, Martins DC, Parreira KS, Scarpelli P, Santos de Moraes M, Topalis P, Hashimoto RF, Garcia CRS. Genome-wide analysis of the human malaria parasite
Plasmodium falciparum transcription factor PfNF-YB shows interaction with a CCAAT motif. Oncotarget. 2017 Dec 9;8(69):113987-114001. doi: 10.18632/oncotarget.23053. eCollection 2017 Dec 26. PubMed PMID: 29371963; PubMed Central PMCID: PMC5768380.
Chen XG, Jiang X, Gu J, Xu M, Wu Y, Deng Y, Zhang C, Bonizzoni M, Dermauw W, Vontas J, Armbruster P, Huang X, Yang Y, Zhang H, He W, Peng H, Liu Y, Wu K, Chen
J, Lirakis M, Topalis P, Van Leeuwen T, Hall AB, Jiang X, Thorpe C, Mueller RL, Sun C, Waterhouse RM, Yan G, Tu ZJ, Fang X, James AA. Genome sequence of the
Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5907-15. doi: 10.1073/pnas.1516410112. Epub 2015 Oct 19. Erratum in: Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):E489. PubMed PMID: 26483478; PubMed Central PMCID:PMC4640774.
Dritsou V, Topalis P, Windbichler N, Simoni A, Hall A, Lawson D, Hinsley M, Hughes D, Napolioni V, Crucianelli F, Deligianni E, Gasperi G, Gomulski LM, Savini G, Manni M, Scolari F, Malacrida AR, Arcà B, Ribeiro JM, Lombardo F, Saccone G, Salvemini M, Moretti R, Aprea G, Calvitti M, Picciolini M, Papathanos PA, Spaccapelo R, Favia G, Crisanti A, Louis C. A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. Pathog Glob Health. 2015 Jul;109(5):207-20. doi: 10.1179/2047773215Y.0000000031. Epub 2015 Sep 14. PubMed PMID: 26369436; PubMed Central PMCID: PMC4727573.
Mitraka E, Topalis P, Dritsou V, Dialynas E, Louis C. Describing the breakbone fever: IDODEN, an ontology for dengue fever. PLoS Negl Trop Dis. 2015 Feb 3;9(2):e0003479. doi: 10.1371/journal.pntd.0003479. eCollection 2015 Feb. PubMed PMID: 25646954; PubMed Central PMCID: PMC4315569.
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore
W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP,
Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ,
Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK,
Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C,
Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 2015 Jan 2;347(6217):1258522. doi:10.1126/science.1258522. Epub 2014 Nov 27. PubMed PMID: 25554792; PubMed Central PMCID: PMC4380271.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S; VectorBase Consortium, Madey G, Collins FH, Lawson D. VectorBase:
an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res. 2015 Jan;43(Database issue):D707-13. doi: 10.1093/nar/gku1117. Epub 2014 Dec 15. PubMed PMID:25510499; PubMed Central PMCID: PMC4383932.
Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P. Non-coding RNA gene families in the genomes of anopheline mosquitoes.
BMC Genomics. 2014 Nov 28;15:1038. doi: 10.1186/1471-2164-15-1038. PubMed PMID:25432596; PubMed Central PMCID: PMC4300560.
Topalis P, Mitraka E, Dritsou V, Dialynas E, Louis C. IDOMAL: the malaria ontology revisited. J Biomed Semantics. 2013 Sep 13;4(1):16. doi:10.1186/2041-1480-4-16. PubMed PMID: 24034841; PubMed Central PMCID: PMC3848731.
Parikh PP, Zheng J, Logan-Klumpler F, Stoeckert CJ Jr, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS. The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J Biomed Semantics. 2012 May 23;3(1):5. doi:10.1186/2041-1480-3-5. PubMed PMID: 22621763; PubMed Central PMCID: PMC3488002.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D; VectorBase
Consortium. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res. 2012 Jan;40(Database issue):D729-34. doi: 10.1093/nar/gkr1089. Epub 2011 Dec 1. PubMed PMID: 22135296; PubMed Central PMCID: PMC3245112.
Topalis P, Mitraka E, Bujila I, Deligianni E, Dialynas E, Siden-Kiamos I, Troye-Blomberg M, Louis C. IDOMAL: an ontology for malaria. Malar J. 2010 Aug 10;9:230. doi: 10.1186/1475-2875-9-230. PubMed PMID: 20698959; PubMed Central PMCID: PMC2925367.
Topalis P, Dialynas E, Mitraka E, Deligianni E, Siden-Kiamos I, Louis C. A set of ontologies to drive tools for the control of vector-borne diseases. J Biomed Inform. 2011 Feb;44(1):42-7. doi: 10.1016/j.jbi.2010.03.012. Epub 2010 Apr 2. PubMed PMID: 20363364; PubMed Central PMCID: PMC2953594.
Dialynas E, Topalis P, Vontas J, Louis C. MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.
PLoS Negl Trop Dis. 2009 Jun 23;3(6):e465. doi: 10.1371/journal.pntd.0000465. PubMed PMID: 19547750; PubMed Central PMCID: PMC2694272.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D583-7. doi: 10.1093/nar/gkn857. Epub 2008 Nov 21. PubMed PMID: 19028744; PubMed Central PMCID: PMC2686483.
Topalis P, Lawson D, Collins FH, Louis C. How can ontologies help vector biology? Trends Parasitol. 2008 Jun;24(6):249-52. doi: 10.1016/j.pt.2008.03.002.
Epub 2008 Apr 24. PubMed PMID: 18440275.
Topalis P, Tzavlaki C, Vestaki K, Dialynas E, Sonenshine DE, Butler R, Bruggner RV, Stinson EO, Collins FH, Louis C. Anatomical ontologies of mosquitoes
and ticks, and their web browsers in VectorBase. Insect Mol Biol. 2008 Feb;17(1):87-9. doi: 10.1111/j.1365-2583.2008.00781.x. PubMed PMID: 18237287.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Emmert D, Hammond M, Hill
CA, Kennedy RC, Lobo NF, MacCallum MR, Madey G, Megy K, Redmond S, Russo S, Severson DW, Stinson EO, Topalis P, Zdobnov EM, Birney E, Gelbart WM, Kafatos FC,
Louis C, Collins FH. VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res. 2007 Jan;35(Database issue):D503-5. Epub 2006 Dec
1. PubMed PMID: 17145709; PubMed Central PMCID: PMC1751530.
Li Y, Hernandez-Martinez S, Fernandez F, Mayoral JG, Topalis P, Priestap H, Perez M, Navare A, Noriega FG. Biochemical, molecular, and functional characterization of PISCF-allatostatin, a regulator of juvenile hormone biosynthesis in the mosquito Aedes aegypti. J Biol Chem. 2006 Nov 10;281(45):34048-55. Epub 2006 Sep 12. PubMed PMID: 16968697; PubMed Central PMCID: PMC2647716.
Topalis P, Koutsos A, Dialynas E, Kiamos C, Hope LK, Strode C, Hemingway J, Louis C. AnoBase: a genetic and biological database of anophelines. Insect Mol
Biol. 2005 Dec;14(6):591-7. PubMed PMID: 16313559.
Ribeiro JM, Topalis P, Louis C. AnoXcel: an Anopheles gambiae protein database. Insect Mol Biol. 2004 Oct;13(5):449-57. PubMed PMID: 15373803.
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G,
Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG,
Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P. Comparative genome and proteome analysis of Anopheles gambiae
and Drosophila melanogaster. Science. 2002 Oct 4;298(5591):149-59. PubMed PMID:12364792.
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002 Oct 4;298(5591):129-49. PubMed PMID: 12364791.
Bolshakov VN, Topalis P, Blass C, Kokoza E, della Torre A, Kafatos FC, Louis C. A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. Genome Res. 2002 Jan;12(1):57-66. PubMed PMID: 11779831; PubMed Central PMCID: PMC155254.
Louis C, Madueño E, Modolell J, Omar MM, Papagiannakis G, Saunders RD, Savakis C, Sidén-Kiamos I, Spanos L, Topalis P, Zhang YQ, Ashburner M, Benos P, Bolshakov VN, Deak P, Glover DM, Herrmann S, Kafatos FC. One-hundred and five new potential Drosophila melanogaster genes revealed through STS analysis. Gene. 1997 Aug 22;195(2):187-93. PubMed PMID: 9305763.