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Social insect genomes: dramatic evolution in gene composition & regulation, preserving regulatory features linked to sociality

Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad K, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva E, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Munos-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie C, 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 Research
PMID: 23636946

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

Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV.
Nucleic Acids Res.
PMID: 23180791

Identification of Site-Specific Adaptations Conferring Increased Neural Cell Tropism during Human Enterovirus 71 Infection.

Cordey S, Petty TJ, Schibler M, Martinez Y, Gerlach D, van Belle S, Turin L, Zdobnov EM, Kaiser L, Tapparel C.
PLoS Pathog
PMID: 22910880

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

Li J, Waterhouse RM and Zdobnov EM
BMC Evolutionary Biology 2011, 11:337 (18 November 2011)
PMID: 22098672

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

Tapparel C, Cordey S, Junier T, Farinelli L, Van Belle S, Soccal PM, Aubert JD, Zdobnov EM, Kaiser L.
PLoS One
PMID: 21713005

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.
Molecular & Cellular Proteomics
PMID: 20467044

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
PMID: 21385848

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
PMID: 21292972

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.

Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV.
Nucleic Acids Res.
PMID: 20972218

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

Waterhouse RM, Zdobnov EM, Kriventseva EV.
Genome Biol Evol
PMID: 21148284

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
PMID: 20929811

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
PMID: 20929810

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, Krause 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 Jun 21. [Epub ahead of print]
PMID: 20566863

The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell

Junier T, Zdobnov EM
Bioinformatics. 2010 May 13
PMID: 20472542

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
PMID: 20485673

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 5(4): e10263
PMID: 20428235

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 Computational Biology 6(1):e1000652
PMID: 20126523

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

Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SY, Goodisman MAD
Journal of Molecular Biology and Evolution 27(3):497-500
PMID: 20110264

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

The Nasonia Genome Working Group (incl. Junier T, Gerlach D, Waterhouse RM, Kriventseva EV, Wyder S, Zdobnov EM)
Science. 2010 Jan 15;327(5963):343-8.
PMID: 20075255

Integration of microRNA miR-122 in hepatic circadian gene expression

Gatfield D, Le Martelot G, Vejnar CE, Gerlach D, Schaad O, Fleury-Olela F, Ruskeepää AL, Oresic M, Esau CC, Zdobnov EM, Schibler U
Genes Dev. 2009 June 1;23(11):1313-1326
PMID: 19487572

The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection

Yerly S, Junier T, Gayet-Ageron A, Amari EB, von Wyl V, Günthard HF, Hirschel B, Zdobnov EM, Kaiser L, and the Swiss HIV Cohort Study.
AIDS. 2009 May 29. [Epub ahead of print]
PMID: 19487906

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

The Bovine Genome Sequencing and Analysis Consortium (incl. Gerlach D, Junier T, Kriventseva EV, Zdobnov EM)
Science. 2009 Apr 24;324(5926):522-528
PMID: 19390049

The bovine lactation genome: insights into the evolution of mammalian milk

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M.
Genome Biol. 2009;10(4):R43. Epub 2009 Apr 24.
PMID: 19393040

New respiratory enterovirus genotype and rhinovirus strains identified by genotyping circulating picornaviruses

Tapparel C, Junier T, Gerlach D, Van Belle S, Turin L, Cordey S, Muehlemann K, Regamey N, Aubert JD, Soccal PM, Eigenmann P, Zdobnov EM, Kaiser L
Emerg Infect Dis. 2009 May;15(5):719-726
PMID: 19402957

Expression profiles of Urbilaterian genes uniquely shared between honey bee and vertebrates

Matsui T, Yamamoto T, Wyder S, Zdobnov EM, Kadowaki T
BMC Genomics 2009, 10:17
PMID: 19138430

Sertoli cell Dicer is essential for spermatogenesis in mice

Papaioannou MD, Pitetti JL, Ro S, Park C, Aubry F, Schaad O, Vejnar CE, Kühne F, Descombes P, Zdobnov EM, McManus MT, Guillou F, Harfe BD, Yan W, Jégou B, Nef S
Dev Biol. 2008 Nov 28. Epub ahead of print
PMID: 19071104

miROrtho: computational survey of microRNA genes

Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM
Nucleic Acids Res. 2009 Jan;37(Database issue):D111-D117. Epub 2008 Oct 15
PMID: 18927110

The cis-acting replication elements define human enterovirus and rhinovirus species

Cordey S, Gerlach D, Junier T, Zdobnov EM, Kaiser L, Tapparel C.
RNA. 2008 Aug;14(8):1568-78
PMID: 18541697

The genome of the model beetle and pest Tribolium castaneum.

Tribolium Genome Sequencing Consortium; Project leader, Richards S; Principal investigators, Gibbs RA, Weinstock GM; White paper, Brown SJ, Denell R, Beeman RW, Gibbs R; Analysis leaders, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM; DNA sequence and global analysis: DNA sequencing, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R; EST sequencing, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA; genome assembly, Liu Y, Worley K, Weinstock G; G+C content, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D; repetitive DNA, transposons and telomeres, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S; gene prediction and consensus gene set, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM; global gene content analysis, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P; Developmental processes and signalling pathways, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X; Pest biology, senses, Medea and RNAi: ligand gated ion channels, Jones AK, Sattelle DB; oxidative phosphorylation, Ebert PR; P450 genes, Nelson D, Scott JG, Beeman RW; chitin and cuticular proteins, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R; digestive proteinases, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C; immunity, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H; neurohormones and GPCRs, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P; neuropeptide processing enzymes, Raible F, Bork P; opsins, Friedrich M; odorant receptors and gustatory receptors, Walden KK, Robertson HM; odorant binding and chemosensory proteins, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA; Medea, Beeman RW, Lorenzen M; systemic RNAi, Tomoyasu Y, Miller SC, Grossmann D, Bucher G.
Nature. 2008 Mar 23
PMID: 18362917

The Aedes aegypti genome: a comparative perspective

Waterhouse RM, Wyder S, Zdobnov EM
Insect Mol Biol. 2008 Feb;17(1):1-8
PMID: 18237279

OrthoDB: the hierarchical catalog of eukaryotic orthologs

Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM
Nucleic Acids Res. 2008 Jan;36(Database issue):D271-5. Epub 2007 Oct 18
PMID: 17947323

Quantification of ortholog losses in insects and vertebrates

Wyder S, Kriventseva EV, Schroder R, Kadowaki T and Zdobnov EM
Genome Biol. 2007 Nov 16;8(11):R242
PMID: 18021399

Evolution of genes and genomes on the Drosophila phylogeny

Drosophila 12 Genomes Consortium (Zdobnov EM)
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features

Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM and Kaiser L
BMC Genomics. 2007 Jul 10; 8(1):224
PMID: 17623054

Evolutionary dynamics of immune-related genes and pathways in disease vector mosquitoes

Waterhouse RM, Kriventseva EV, Meister S, Xi Z, Alvarez KS, Bartholomay LC, Carolina Barillas-Mury C, Bian G, Blandin S, Bruce M. Christensen BM, Dong Y, Jiang H, Kanost MR, Koutsos AC, Levashina EA, Li J, Ligoxygakis P, MacCallum RM, Mayhew GF, Mendes A, Michel K, Osta MA, Paskewitz S, Shin SW, Vlachou D, Wang L, Wei W, Zheng L, Zou Z, Severson DW, Raikhel AS, Kafatos FC, Dimopoulos G, Zdobnov EM George K. Christophides GK
Science. 2007 Jun 22;316(5832):1738-43.
PMID: 17588928

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Koutsos AC, Blass C, Meister S, Schmidt S, Maccallum RM, Soares MB, Collins FH, Benes V, Zdobnov EM, Kafatos FC, Christophides GK
Proc Natl Acad Sci USA. 2007 Jun 11
PMID: 17563388

Computational and transcriptional evidence for microRNAs in the honey bee genome

Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM, Samanta MP, Miller J, Elsik CG
Genome Biol. 2007 Jun 1;8(6):R97
PMID: 17543122

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, Amedo P, Arsenburger 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 SJ, 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 SB, 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, Bruce B, Fraser-Liggett CM, Severson DW.
Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.
PMID: 17510324

Quantification of insect genome divergence

Zdobnov EM, Bork P
Trends Genet. 2007 Jan;23(1):16-20. Epub 2006 Nov 9.
PMID: 17097187

Overgrowth caused by misexpression of a microRNA with dispensable wild-type function

Nairz K, Rottig C, Rintelen F, Zdobnov EM, Moser M, Hafen E.
Dev Biol. 2006 Mar 15;291(2):314-24. Epub 2006 Jan 27
PMID: 16443211

AnoEST: toward A. gambiae functional genomics

Kriventseva EV, Koutsos AC, Blass C, Kafatos FC, Christophides GK, Zdobnov EM
Genome Res. 2005 Jun;15(6):893-9. Epub 2005 May 17
PMID: 15899967

Consistency of genome-based methods in measuring Metazoan evolution

Zdobnov EM, von Mering C, Letunic I, Bork P
FEBS Lett. 2005 Jun 13;579(15):3355-61. Epub 2005 Apr 18
PMID: 15943981

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P
Nucleic Acids Res. 2005 Feb 16;33(3):946-54. Print 2005
PMID: 15716312

Genome evolution reveals biochemical networks and functional modules

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15428-33. Epub 2003 Dec 12
PMID: 14673105

The InterPro Database, 2003 brings increased coverage and new features

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM
Nucleic Acids Res. 2003 Jan 1;31(1):315-8
PMID: 12520011

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium; Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES
Nature. 2002 Dec 5;420(6915):520-62
PMID: 12466850

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

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
Science. 2002 Oct 4;298(5591):149-59
PMID: 12364792

The genome sequence of the malaria mosquito Anopheles gambiae

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
Science. 2002 Oct 4;298(5591):129-49
PMID: 12364791

The EBI SRS server-new features

Zdobnov EM, Lopez R, Apweiler R, Etzold T
Bioinformatics. 2002 Aug;18(8):1149-50
PMID: 12176845

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8179-84
PMID: 12060762

The EBI SRS server--recent developments

Zdobnov EM, Lopez R, Apweiler R, Etzold T
Bioinformatics. 2002 Feb;18(2):368-73
PMID: 11847095

Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain

Minyat EE, Khomyakova EB, Petrova MV, Zdobnov EM, Ivanov VI.
J Biomol Struct Dyn. 1995 Dec;13(3):523-7
PMID: 8825732

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Zdobnov EM | Wyder S | Waterhouse RM | Kriventseva EV | Junier T | Gerlach D | Rahman N | Vejnar CE | Tegenfeldt FP | Li J | Petty TJ