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Items: 1 to 50 of 88

1.

Using BUSCO to Assess Insect Genomic Resources.

Waterhouse RM, Seppey M, Simão FA, Zdobnov EM.

Methods Mol Biol. 2019;1858:59-74. doi: 10.1007/978-1-4939-8775-7_6.

PMID:
30414111
2.

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.

Kriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Simão FA, Zdobnov EM.

Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811. doi: 10.1093/nar/gky1053.

3.

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.

Rands CM, Starikova EV, Brüssow H, Kriventseva EV, Govorun VM, Zdobnov EM.

Environ Microbiol. 2018 Jul 16. doi: 10.1111/1462-2920.14276. [Epub ahead of print]

PMID:
30014616
4.

Human pegivirus persistence in human blood virome after allogeneic haematopoietic stem-cell transplantation.

Vu DL, Cordey S, Simonetta F, Brito F, Docquier M, Turin L, van Delden C, Boely E, Dantin C, Pradier A, Roosnek E, Chalandon Y, Zdobnov EM, Masouridi-Levrat S, Kaiser L.

Clin Microbiol Infect. 2019 Feb;25(2):225-232. doi: 10.1016/j.cmi.2018.05.004. Epub 2018 May 19.

PMID:
29787887
5.

BUSCO applications from quality assessments to gene prediction and phylogenomics.

Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM.

Mol Biol Evol. 2017 Dec 6. doi: 10.1093/molbev/msx319. [Epub ahead of print]

6.

Metagenomics analysis of red blood cell and fresh-frozen plasma units.

Lau P, Cordey S, Brito F, Tirefort D, Petty TJ, Turin L, Guichebaron A, Docquier M, Zdobnov EM, Waldvogel-Abramowski S, Lecompte T, Kaiser L, Preynat-Seauve O.

Transfusion. 2017 Jul;57(7):1787-1800. doi: 10.1111/trf.14148. Epub 2017 May 11.

PMID:
28497550
7.

Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders.

Ioannidis P, Simao FA, Waterhouse RM, Manni M, Seppey M, Robertson HM, Misof B, Niehuis O, Zdobnov EM.

Genome Biol Evol. 2017 Feb 1;9(2):415-430. doi: 10.1093/gbe/evx006.

8.

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV.

Nucleic Acids Res. 2017 Jan 4;45(D1):D744-D749. doi: 10.1093/nar/gkw1119. Epub 2016 Nov 28.

9.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, Mitchell RF, Waterhouse RM, Ahn SJ, Arsala D, Benoit JB, Blackmon H, Bledsoe T, Bowsher JH, Busch A, Calla B, Chao H, Childers AK, Childers C, Clarke DJ, Cohen L, Demuth JP, Dinh H, Doddapaneni H, Dolan A, Duan JJ, Dugan S, Friedrich M, Glastad KM, Goodisman MA, Haddad S, Han Y, Hughes DS, Ioannidis P, Johnston JS, Jones JW, Kuhn LA, Lance DR, Lee CY, Lee SL, Lin H, Lynch JA, Moczek AP, Murali SC, Muzny DM, Nelson DR, Palli SR, Panfilio KA, Pers D, Poelchau MF, Quan H, Qu J, Ray AM, Rinehart JP, Robertson HM, Roehrdanz R, Rosendale AJ, Shin S, Silva C, Torson AS, Jentzsch IM, Werren JH, Worley KC, Yocum G, Zdobnov EM, Gibbs RA, Richards S.

Genome Biol. 2016 Nov 11;17(1):227.

10.

Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology.

Cordey S, Brito F, Vu DL, Turin L, Kilowoko M, Kyungu E, Genton B, Zdobnov EM, D'Acremont V, Kaiser L.

Emerg Microbes Infect. 2016 Sep 7;5(9):e99. doi: 10.1038/emi.2016.98. No abstract available.

11.

Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology.

Cordey S, Brito F, Vu DL, Turin L, Kilowoko M, Kyungu E, Genton B, Zdobnov EM, D'Acremont V, Kaiser L.

Emerg Microbes Infect. 2016 Jul 6;5:e67. doi: 10.1038/emi.2016.67. No abstract available. Erratum in: Emerg Microbes Infect. 2016 Sep 07;5(9):e99.

12.

Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection.

Cordey S, Vu DL, Schibler M, L'Huillier AG, Brito F, Docquier M, Posfay-Barbe KM, Petty TJ, Turin L, Zdobnov EM, Kaiser L.

Emerg Infect Dis. 2016 May;22(5):846-53. doi: 10.3201/eid2205.151807.

13.

Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution.

Hoy MA, Waterhouse RM, Wu K, Estep AS, Ioannidis P, Palmer WJ, Pomerantz AF, Simão FA, Thomas J, Jiggins FM, Murphy TD, Pritham EJ, Robertson HM, Zdobnov EM, Gibbs RA, Richards S.

Genome Biol Evol. 2016 Jun 27;8(6):1762-75. doi: 10.1093/gbe/evw048.

14.

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Park Y, Rozas J, Benton R, Pedra JH, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA.

Nat Commun. 2016 Feb 9;7:10507. doi: 10.1038/ncomms10507.

15.

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, Hendershot JM, Blenau W, Predel R, Johnston PR, Ioannidis P, Waterhouse RM, Nauen R, Schorn C, Ott MC, Maiwald F, Johnston JS, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisén D, Crumière AJ, Refki PN, Santos ME, Sghaier E, Viala S, Khila A, Ahn SJ, Childers C, Lee CY, Lin H, Hughes DS, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler D, Panfilio KA, Vargas Jentzsch IM, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MA, Jones JW, Mittapalli O, Zhao C, Zhou JJ, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JM, Gibbs RA, Werren JH, Palli SR, Schal C, Richards S.

Nat Commun. 2016 Feb 2;7:10165. doi: 10.1038/ncomms10165.

16.

CEGA--a catalog of conserved elements from genomic alignments.

Dousse A, Junier T, Zdobnov EM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D96-100. doi: 10.1093/nar/gkv1163. Epub 2015 Nov 2.

17.

Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report.

Schibler M, Vetter P, Cherpillod P, Petty TJ, Cordey S, Vieille G, Yerly S, Siegrist CA, Samii K, Dayer JA, Docquier M, Zdobnov EM, Simpson AJH, Rees PSC, Sarria FB, Gasche Y, Chappuis F, Iten A, Pittet D, Pugin J, Kaiser L.

Lancet Infect Dis. 2015 Sep;15(9):1034-1040. doi: 10.1016/S1473-3099(15)00229-7. Epub 2015 Jul 19.

PMID:
26201298
18.

Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.

Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DS, Lee SF, Perry T, Stroehlein AJ, Ansell BR, Breugelmans B, Hofmann A, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ioannidis P, Waterhouse RM, Zdobnov EM, James PJ, Bagnall NH, Kotze AC, Gibbs RA, Richards S, Batterham P, Gasser RB.

Nat Commun. 2015 Jun 25;6:7344. doi: 10.1038/ncomms8344.

19.

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.

Bioinformatics. 2015 Oct 1;31(19):3210-2. doi: 10.1093/bioinformatics/btv351. Epub 2015 Jun 9.

PMID:
26059717
20.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G.

Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.

21.

A depauperate immune repertoire precedes evolution of sociality in bees.

Barribeau SM, Sadd BM, du Plessis L, Brown MJ, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, Erler S, Evans J, Helbing S, Karaus E, Lattorff HM, Marxer M, Meeus I, Näpflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse RM, Yu N, Zdobnov EM, Schmid-Hempel P.

Genome Biol. 2015 Apr 24;16:83. doi: 10.1186/s13059-015-0628-y.

22.

The genomes of two key bumblebee species with primitive eusocial organization.

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC.

Genome Biol. 2015 Apr 24;16:76. doi: 10.1186/s13059-015-0623-3.

23.

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

Zhao C, Escalante LN, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM, Wheeler D, Andersson MN, Bao R, Batterton M, Behura SK, Blankenburg KP, Caragea D, Carolan JC, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen CJ, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani SN, Johnson AJ, Kalra D, Korchina V, Kovar CL, Lara F, Lee SL, Liu X, Löfstedt C, Mata R, Mathew T, Muzny DM, Nagar S, Nazareth LV, Okwuonu G, Ongeri F, Perales L, Peterson BF, Pu LL, Robertson HM, Schemerhorn BJ, Scherer SE, Shreve JT, Simmons D, Subramanyam S, Thornton RL, Xue K, Weissenberger GM, Williams CE, Worley KC, Zhu D, Zhu Y, Harris MO, Shukle RH, Werren JH, Zdobnov EM, Chen MS, Brown SJ, Stuart JJ, Richards S.

Curr Biol. 2015 Mar 2;25(5):613-20. doi: 10.1016/j.cub.2014.12.057. Epub 2015 Feb 5.

24.

Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses.

Cordey S, Bel M, Petty TJ, Docquier M, Sacco L, Turin L, Cherpillod P, Emonet S, Louis-Simonet M, Zdobnov EM, Ambrosioni J, Kaiser L.

Clin Microbiol Infect. 2015 Apr;21(4):387.e1-4. doi: 10.1016/j.cmi.2014.11.010. Epub 2014 Nov 26.

25.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

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.

Science. 2015 Jan 2;347(6217):1258522. doi: 10.1126/science.1258522. Epub 2014 Nov 27.

26.

Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB, Ioannidis P, Zdobnov EM, Dermitzakis ET, Antonarakis SE.

Am J Hum Genet. 2014 Dec 4;95(6):660-74. doi: 10.1016/j.ajhg.2014.11.003.

27.

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D250-6. doi: 10.1093/nar/gku1220. Epub 2014 Nov 26.

28.

Repression of arginase-2 expression in dendritic cells by microRNA-155 is critical for promoting T cell proliferation.

Dunand-Sauthier I, Irla M, Carnesecchi S, Seguín-Estévez Q, Vejnar CE, Zdobnov EM, Santiago-Raber ML, Reith W.

J Immunol. 2014 Aug 15;193(4):1690-700. doi: 10.4049/jimmunol.1301913. Epub 2014 Jul 9.

29.

Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.

Petty TJ, Cordey S, Padioleau I, Docquier M, Turin L, Preynat-Seauve O, Zdobnov EM, Kaiser L.

J Clin Microbiol. 2014 Sep;52(9):3351-61. doi: 10.1128/JCM.01389-14. Epub 2014 Jul 9.

30.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

31.

Finding the missing honey bee genes: lessons learned from a genome upgrade.

Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R; HGSC production teams, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RF, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Vaerenbergh MV, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, Gibbs RA; Honey Bee Genome Sequencing Consortium.

BMC Genomics. 2014 Jan 30;15:86. doi: 10.1186/1471-2164-15-86.

32.

Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

Cosset É, Petty TJ, Dutoit V, Cordey S, Padioleau I, Otten-Hernandez P, Farinelli L, Kaiser L, Bruyère-Cerdan P, Tirefort D, Amar El-Dusouqui S, Nayernia Z, Krause KH, Zdobnov EM, Dietrich PY, Rigal E, Preynat-Seauve O.

Int J Cancer. 2014 Sep 15;135(6):1381-9. doi: 10.1002/ijc.28670. Epub 2014 May 8.

33.

miRmap web: Comprehensive microRNA target prediction online.

Vejnar CE, Blum M, Zdobnov EM.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W165-8. doi: 10.1093/nar/gkt430. Epub 2013 May 28.

34.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.

Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Muñoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J.

Genome Res. 2013 Aug;23(8):1235-47. doi: 10.1101/gr.155408.113. Epub 2013 May 1.

35.

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.

Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV.

Nucleic Acids Res. 2013 Jan;41(Database issue):D358-65. doi: 10.1093/nar/gks1116. Epub 2012 Nov 24.

36.

MiRmap: comprehensive prediction of microRNA target repression strength.

Vejnar CE, Zdobnov EM.

Nucleic Acids Res. 2012 Dec;40(22):11673-83. doi: 10.1093/nar/gks901. Epub 2012 Oct 2.

37.

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits.

Li J, Waterhouse RM, Zdobnov EM.

BMC Evol Biol. 2011 Nov 18;11:337. doi: 10.1186/1471-2148-11-337.

38.

Silencing of c-Fos expression by microRNA-155 is critical for dendritic cell maturation and function.

Dunand-Sauthier I, Santiago-Raber ML, Capponi L, Vejnar CE, Schaad O, Irla M, Seguín-Estévez Q, Descombes P, Zdobnov EM, Acha-Orbea H, Reith W.

Blood. 2011 Apr 28;117(17):4490-500. doi: 10.1182/blood-2010-09-308064. Epub 2011 Mar 8.

39.

The ecoresponsive genome of Daphnia pulex.

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.

40.

Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi.

Waterhouse RM, Zdobnov EM, Kriventseva EV.

Genome Biol Evol. 2011;3:75-86. doi: 10.1093/gbe/evq083. Epub 2010 Dec 9.

41.

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.

Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV.

Nucleic Acids Res. 2011 Jan;39(Database issue):D283-8. doi: 10.1093/nar/gkq930. Epub 2010 Oct 23.

42.

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens.

Bartholomay LC, Waterhouse RM, Mayhew GF, Campbell CL, Michel K, Zou Z, Ramirez JL, Das S, Alvarez K, Arensburger P, Bryant B, Chapman SB, Dong Y, Erickson SM, Karunaratne SH, Kokoza V, Kodira CD, Pignatelli P, Shin SW, Vanlandingham DL, Atkinson PW, Birren B, Christophides GK, Clem RJ, Hemingway J, Higgs S, Megy K, Ranson H, Zdobnov EM, Raikhel AS, Christensen BM, Dimopoulos G, Muskavitch MA.

Science. 2010 Oct 1;330(6000):88-90. doi: 10.1126/science.1193162.

43.

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.

44.

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR.

Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12168-73. doi: 10.1073/pnas.1003379107. Epub 2010 Jun 21. Erratum in: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6335. Krause, Emily [corrected to Kraus, Emily].

45.

Rhinovirus genome evolution during experimental human infection.

Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L.

PLoS One. 2010 May 11;5(5):e10588. doi: 10.1371/journal.pone.0010588.

46.

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

Junier T, Zdobnov EM.

Bioinformatics. 2010 Jul 1;26(13):1669-70. doi: 10.1093/bioinformatics/btq243. Epub 2010 May 13.

47.

Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice.

Papaioannou MD, Lagarrigue M, Vejnar CE, Rolland AD, Kühne F, Aubry F, Schaad O, Fort A, Descombes P, Neerman-Arbez M, Guillou F, Zdobnov EM, Pineau C, Nef S.

Mol Cell Proteomics. 2011 Apr;10(4):M900587MCP200. doi: 10.1074/mcp.M900587-MCP200. Epub 2010 May 13.

48.

A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes.

Hovatta O, Jaconi M, Töhönen V, Béna F, Gimelli S, Bosman A, Holm F, Wyder S, Zdobnov EM, Irion O, Andrews PW, Antonarakis SE, Zucchelli M, Kere J, Feki A.

PLoS One. 2010 Apr 23;5(4):e10263. doi: 10.1371/journal.pone.0010263.

49.

Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.

Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000652. doi: 10.1371/journal.pcbi.1000652.

50.

Sociality is linked to rates of protein evolution in a highly social insect.

Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SV, Goodisman MA.

Mol Biol Evol. 2010 Mar;27(3):497-500. doi: 10.1093/molbev/msp225. Epub 2010 Jan 28.

PMID:
20110264

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