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Here you will find an archive of publications published by our group members.

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Publications by authors:

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

Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes

Mitchell SN, Kakani EG, South A, Howell PI, Waterhouse RM, Catteruccia F.
Science
PMID: 25722409

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.
PMID: 25660540

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
PMID: 25554792

Extensive introgression in a malaria vector species complex revealed by phylogenomics

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ.
Science
PMID: 25431491

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.
PMID: 25428351

Phylogenetic analysis of the oriental-Palearctic-Afrotropical members of Anopheles (Culicidae: Diptera) based on nuclear rDNA an

Karimian F, Oshaghi MA, Sedaghat MM, Waterhouse RM, Vatandoost H, Hanafi-Bojd AA, Ravasan NM, Chavshin AR.
Jpn J Infect Dis
PMID: 25241686

The evolution of the anopheles 16 genomes project

Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ.
PMID: 23708298

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

Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1.

Nishimura T, Molinard G, Petty TJ, Broger L, Gabus C, Halazonetis TD, Thore S, Paszkowski J.
PLoS Genet
PMID: 22346760

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

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.

Petty TJ, Emamzadah S, Costantino L, Petkova I, Stavridi ES, Saven JG, Vauthey E, Halazonetis TD.
EMBO J. 2011 Jun 1;30(11):2167-76. Epub 2011 Apr 26.
PMID: 21522129

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

Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins

Waterhouse RM, Povelones M, Christophides GK.
BMC Genomics
PMID: 20920294

X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 protein.

Petty TJ, Nishimura T, Emamzadah S, Gabus C, Paszkowski J, Halazonetis TD, Thore S.
Acta Crystallogr Sect F Struct Biol Cryst Commun.
PMID: 20693667

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

A caspase-like decoy molecule enhances the activity of a paralogous caspase in the yellow fever mosquito, Aedes aegypti.

Bryant B, Ungerer MC, Liu Q, Waterhouse RM, Clem RJ.
Insect Biochem Mol Biol.
PMID: 20417712

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

Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae.

Pinto SB, Lombardo F, Koutsos AC, Waterhouse RM, McKay K, An C, Ramakrishnan C, Kafatos FC, Michel K.
Proc Natl Acad Sci U S A.
PMID: 19940242

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

Emamzadah S, Petty TJ, De Almeida V, Nishimura T, Joly J, Ferrer JL, Halazonetis TD
Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):913-20.
PMID: 19690369

Identification of the active form of endothelial lipase, a homodimer in a head-to-tail conformation.

Griffon N, Jin W, Petty TJ, Millar J, Badellino KO, Saven JG, Marchadier DH, Kempner ES, Billheimer J, Glick JM, Rader DJ
J Biol Chem. 2009 Aug 28;284(35):23322-30.
PMID: 19567873

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

Leucine-Rich Repeat Protein Complex Activates Mosquito Complement in Defense Against Plasmodium Parasites

Povelones M, Waterhouse RM, Kafatos FC, Christophides GK
Science
PMID: 19264986

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon.

Junier P, Kim OS, Junier T, Ahn TS, Imhoff JS, and Witzel KP
Applied Microbiology and Biotechnology
PMID: 19274459

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

Composition of diazotrophic bacterial assemblages in bean-planted soil compared to unplanted soil

Junier P, Junier T, Witzel KP, Carú M
European Journal of Soil Biology

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

TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets

Junier P, Junier T, Witzel KP
Applied and Environmental Microbiology
PMID: 18757578

Experience using web services for biological sequence analysis

Stockinger H, Attwood T, Chohan S, Côté R, Cudré-Mauroux P, Falquet L, Fernandes P, Finn R, Hupponen T, Korpelainen E, Labarga A, Laugraud A, Lima T, Pafilis E, Pagni M, Pettifer S, Phan I, Rahman N
Briefings in Bioinformatics
PMID: 18621748

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

Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species.

González N, Heeb S, Valverde C, Kay E, Reimmann C, Junier T, Haas D.
BMC Genomics
PMID: 18405392

Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxi

Junier P, Kim OS, Molina V, Limburg P, Junier T, Imhoff JF, Witzel KP.
FEMS Microbiology Ecology

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

Protein Folding, Misfolding and Aggregation: Classical Themes and Novel Approaches

Lehmann A, Lanci CJ, Petty TJ, Kang SG & Saven JG
RSC Biomolecular Sciences Book Series

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

Biased distributions and decay of long interspersed nuclear elements in the chicken genome.

Abrusán G, Krambeck HJ, Junier T, Giordano J, Warburton PE.
Genetics
PMID: 17947446

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

CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome

Yakhnin H, Pandit P, Petty TJ, Baker CS, Romeo T, Babitzke P
Mol Microbiol. 2007 Jun;64(6):1605-20.
PMID: 17555441

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

Deep metazoan phylogeny

Gerlach D, Wolf M, Dandekar T, Müller T, Pokorny A, Rahmann S
In Silico Biology 7, 0015 (2007)
PMID: 17688440

Insights into social insects from the genome of the honeybee Apis mellifera

Honeybee Genome Sequencing Consortium
Nature. 2006 Oct 26;443(7114):931-49
PMID: 17073008

Quantification of insect genome divergence

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

Effects of a GTP-insensitive mutation of glutamate dehydrogenase on insulin secretion in transgenic mice.

Li C, Matter A, Kelly A, Petty TJ, Najafi H, MacMullen C, Daikhin Y, Nissim I, Lazarow A, Kwagh J, Collins HW, Hsu BY, Nissim I, Yudkoff M, Matschinsky FM, Stanley CA
J Biol Chem. 2006 Jun 2;281(22):15064-72.
PMID: 16574664

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

A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota

Schultz J, Maisel S, Gerlach D, Muller T, Wolf M
RNA. 2005 Apr;11(4):361-4
PMID: 15769870

Cloning, characterization and analysis by RNA interference of various genes of the Chelonus inanitus polydnavirus

Bonvin M, Marti D, Wyder S, Kojic D, Annaheim M, Lanzrein B
J Gen Virol. 2005 Apr;86(Pt 4):973-83
PMID: 15784890

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

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium
Nature. 2004 Dec 9;432(7018):695-716. Erratum in: Nature. 2005 Feb 17;433(7027):777
PMID: 15592404

Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks.

Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD
Nature. 2004 Nov 18;432(7015):406-11.
PMID: 15525939

Stage-dependent expression of Chelonus inanitus polydnavirus genes in the host and the parasitoid

Bonvin M, Kojic D, Blank F, Annaheim M, Wehrle I, Wyder S, Kaeslin M, Lanzrein B
J Insect Physiol. 2004 Nov;50(11):1015-26
PMID: 15607504

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome Sequencing Consortium
Nature. 2004 Apr 1;428(6982):493-521
PMID: 15057822

Free Full Text A genome-wide survey of human pseudogenes

Torrents D, Suyama M, Zdobnov E, Bork P
Genome Res. 2003 Dec;13(12):2559-67
PMID: 14656963

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

Ovary development and polydnavirus morphogenesis in the parasitic wasp Chelonus inanitus. I. Ovary morphogenesis, amplification

Marti D, Grossniklaus-Burgin C, Wyder S, Wyler T, Lanzrein B
J Gen Virol. 2003 May;84(Pt 5):1141-50
PMID: 12692279

Fate of polydnavirus DNA of the egg-larval parasitoid Chelonus inanitus in the host Spodoptera littoralis

Wyder S, Blank F, Lanzrein B
J Insect Physiol. 2003 May;49(5):491-500
PMID: 12770628

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

Immunity-related genes and gene families in Anopheles gambiae

Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Muller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC.
Science. 2002 Oct 4;298(5591):159-65
PMID: 12364793

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

Interactive InterPro-based comparisons of proteins in whole genomes.

Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics. 2002 Feb;18(2):374-5
PMID: 11847096

The EBI SRS server--recent developments

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

Characterization of Chelonus inanitus polydnavirus segments: sequences and analysis, excision site and demonstration of clusteri

Wyder S, Tschannen A, Hochuli A, Gruber A, Saladin V, Zumbach S, Lanzrein B
J Gen Virol. 2002 Jan;83(Pt 1):247-56
PMID: 11752722

mmsearch: a motif arrangement language and search program

Junier T, Pagni M, Bucher P.
Bioinformatics. 2001 Dec;17(12):1234-5
PMID: 11751236

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole gen

Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic Acids Res. 2001 Jan 1;29(1):44-8.
PMID: 11125045

trEST, trGEN and Hits: access to databases of predicted protein sequences

Pagni M,Iseli C,Junier T,Falquet L,Jongeneel V,Bucher P
Nucleic Acids Res. 2001 Jan 1;29(1):148-51
PMID: 11125074

Dotlet: diagonal plots in a web browser

Junier T, Pagni M
Bioinformatics. 2000 Feb;16(2):178-9
PMID: 10842741

The eukaryotic promoter database (EPD)

Perier RC, Junier T, Bonnard C, Bucher P
Nucleic Acids Res. 2000 Jan 1;28(1):302-3
PMID: 10592254

The Eukaryotic Promoter Database (EPD): recent developments

Perier RC, Junier T, Bonnard C, Bucher P
Nucleic Acids Res. 1999 Jan 1;27(1):307-9
PMID: 9847211

Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA

Roulot E, Fisch I, Junier T, Bucher P, Mermod N
In Silico Biol. 1998;1(1):21-8
PMID: 11471239

SEView: a Java applet for browsing molecular sequence data

Junier T, Bucher P
In Silico Biol. 1998;1(1):13-20
PMID: 11471238

The Eukaryotic Promoter Database EPD

Cavin Perier R, Junier T, Bucher P
Nucleic Acids Res. 1998 Jan 1;26(1):353-7
PMID: 9399872

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