Publications
Maître assistant - Fonds National & SIB
Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders.
 
2017, Ioannidis P, Simao FA, Waterhouse RM , Manni M, Seppey M, Robertson HM, Misof B, Niehuis O, Zdobnov EM​.
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OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.
 
2017, Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM , Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV​.
  1. Title 1
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Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface.
 
2016, McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, Mitchell RF, Waterhouse RM , Ahn SJ, Arsala D, Benoit JB, et al.
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Evolutionary dynamics of abundant stop codon readthrough.
 
2016, Jungreis I, Chan CS, Waterhouse RM , Fields G, Lin MF, & Kellis M.

In-depth analysis of Anopheles 16 genomes project data.
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Tick genome assembled: new opportunities for research on tick-host-pathogen interactions.
 
2016, de la Fuente J, Waterhouse RM , Sonenshine DE, Roe RM, Ribeiro JM, Sattelle DB, & Hill CA.
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Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.
 
2016, Kanost MR, Arrese EL, Cao X, Chen Y, Chellapilla S, Goldsmith MR,  Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, et al.
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Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomised Hox genes and super-dynamic intron evolution.
 
2016, 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.
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Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
 
2016, Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM , Sattelle DB, de la Fuente J, Ribeiro JM, et al.
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Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.
 
2016, Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, et al.
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The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
 
2016, SIB Swiss Institute of Bioinformatics Members.
OrthoDB contributor.
  1. Title 1
Publications
Marie Curie International Outgoing Fellow
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
 
2015, Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, et al.
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A maturing understanding of the composition of the insect gene repertoire.
 
2015,  Waterhouse RM.
 
COIS review series on Insect Genomics
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Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution.
 
2015, Chen XG, Jiang X, Gu J, Xu M, Wu Y, Deng Y, Zhang C, Bonizzoni M, Dermauw W, et al.
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Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.
 
2015, Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DST, Lee SF, Perry T, et al.
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
 
2015, Simão FA•, Waterhouse RM•, Ioannidis P, Kriventseva EV, Zdobnov EM.
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Genomic signatures of evolutionary transitions from solitary to group living.
 
2015, Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, et al.
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A depauperate immune repertoire precedes evolution of sociality in bees.
 
2015, Barribeau SM, Sadd BM, du Plessis L, Brown MJF, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, et al.
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The genomes of two key bumblebee species with primitive eusocial organisation.
 
2015, Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, et al.
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Long non-coding RNA discovery across the genus Anopheles reveals conserved secondary structures within and beyond the Gambiae complex.
 
2015, Jenkins AM, Waterhouse RM , Muskavitch MAT.
  1. lnRNAs1
  2. lnRNAs2
  3. lnRNAs3
  4. lnRNAs4
  5. lnRNAs5
  6. lnRNAs6
Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes.
 
2015, Mitchell SN, Kakani EG, South A, Howell PI, Waterhouse RM , Catteruccia F.
  1. mozsex1
  2. mozsex2
  3. mozsex3
  4. mozsex4
  5. mozsex5
A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.
 
2015, Zhao C, Escalante LN, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM , Wheeler D, Andersson MN, et al.
  1. Mdest1
  2. Mdest2
  3. Mdest3
  4. Mdest4
Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
 
2015, Neafsey DE•, Waterhouse RM•, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, et al.
  1. Ano16-1
  2. Ano16-2
  3. Ano16-3
  4. Ano16-4
  5. Ano16-5
  6. Ano16-6
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Extensive introgression in a malaria vector species complex revealed by phylogenomics.
 
2015, Fontaine MC, Pease JB, Steele A, Waterhouse RM , Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, et al.
  1. gamintro1
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  4. gamintro4
  5. gamintro5
  6. gamintro6
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Scaffold assembly based on genome rearrangement analysis.
 
2015, Aganezov S, Sitdykova N, AGC Consortium, Alekseyev MA.
  1. assemb1
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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.
 
2015, Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM , Simão FA, Pozdnyakov IA, Ioannidis P, & Zdobnov EM.
  1. ODB-2015-1
  2. ODB-2015-2
  3. ODB-2015-3
  4. ODB-2015-4
Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
 
2014, Jiang X, Peery A, Hall A, Sharma A, Chen XG, Waterhouse RM , Komissarov A, Riehl MM, Shouche Y, Sharakhova MV, et al.
  1. stephensi1
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  3. stephensi3
  4. stephensi4
  5. stephensi5
  6. stephensi6
  7. stephensi7
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  9. stephensi9
Phylogenetic analysis of the oriental-Palearctic-Afrotropical members of Anopheles (Culicidae: Diptera) based on nuclear rDNA and mitochondrial DNA characteristics.
2014, Karimian F, Oshaghi MA, Sedaghat MM, Waterhouse RM , Vatandoost H, Hanafi-Bojd AA, Ravasan NM, & Chavshin AR.
  1. iran1
  2. iran2
  3. iran3
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
 
2014, Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, et al.
  1. mcinx1
  2. mcinx2
  3. mcinx3
  4. mcinx4
  5. mcinx5
  6. mcinx6
  7. mcinx7
  8. mcinx8
  9. mcinx9
Big data and other challenges in the quest for orthologs.
 
2014, Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, & Quest for Orthologs consortium.
  1. QfO2
  2. QfO1
Finding the missing honey bee genes: lessons learned from a genome upgrade.
 
2014, Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, et al.
  1. HB-upgrade4
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  3. HB-upgrade2
  4. HB-upgrade1
Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae.
 
2013, Rinker DC, Zhou X, Pitts RJ, AGC Consortium, Rokas A, & Zwiebel LJ.
  1. Antenna1
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  4. Antenna4
  5. Antenna5
  6. Antenna6
  7. Antenna7
The Evolution of the Anopheles 16 Genomes Project.
 
2013, 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.
  1. G3-16ano2
  2. G3-16ano1
Publications
Swiss National Science Foundation Postdoctoral Researcher
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.
 
2013, Simola DF, Wissler L, Donahue G, Waterhouse RM , Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, et al.
  1. ants1
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  3. ants3
  4. ants4
  5. ants5
  6. ants6
OrthoDB: a hierarchical catalog of animal, fungal, and bacterial orthologs.
 
2013,  Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, & Kriventseva EV.
  1. ODB-2013-2
  2. ODB-2013-1
  3. ODB-2013-3
  4. ODB-2013-4
A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits.
 
2011, Li J,  Waterhouse RM, & Zdobnov EM.
  1. tipE1
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  3. tipE3
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi.
 
2011,  Waterhouse RM, Zdobnov EM, & Kriventseva EV.
  1. gbe1
  2. gbe2
  3. gbe3
  4. gbe4
  5. gbe5
  6. gbe6
  7. gbe7
  8. gbe8
  9. gbe9
  10. gbe10
  11. gbe11
  12. gbe12
  13. gbe13
  14. gbe14
  15. gbe15
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.
 
2011,  Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, & Kriventseva EV.
  1. odb1
  2. odb2
  3. odb3
  4. odb4
  5. odb5
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
 
2010, Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, et al.
  1. culex1
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  3. culex3
  4. culex4
  5. culex5
Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens.
 
2010, Bartholomay LC•, Waterhouse RM•, Mayhew GF, Campbell CL, Michel K, Zou Z, Ramirez JL, Das S, Alvarez K, et al.
  1. CxPatho1
  2. CxPatho2
  3. CxPatho3
  4. CxPatho4
  5. CxPatho5
  6. CxPatho6
  7. CxPatho7
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.
 
2010, Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, et al.
  1. louse1
  2. louse2
  3. louse3
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
 
2010, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, et al.
  1. Nasonia1
  2. Nasonia2
Bioinformatics: A Swiss Perspective. Comparative Genome Analysis.
 
2009, Waterhouse RM, Kriventseva EV, & Zdobnov EM.
  1. swiss_bioinf
Publications
Wellcome Trust Doctoral Fellow
Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins.
 
2010, Waterhouse RM, Povelones M, & Christophides GK.
  1. LRIMs1
  2. LRIMs2
  3. LRIMs3
  4. LRIMs4
A caspase-like decoy molecule enhances the activity of a paralogous caspase in the yellow fever mosquito, Aedes aegypti.
 
2010, Bryant B, Ungerer MC, Liu Q, Waterhouse RM, & Clem RJ.
  1. casp1
  2. casp2
  3. casp3
  4. casp4
  5. casp5
Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae.
 
2009, Pinto SB, Lombardo F, Koutsos AC, Waterhouse RM, McKay K, An C, Ramakrishnan C, Kafatos FC, & Michel K.
  1. hemo1
Leucine-rich repeat protein complex activates mosquito complement in defence against Plasmodium parasites.
 
2009, Povelones M,  Waterhouse RM, Kafatos FC, & Christophides GK.
  1. LRIM.1
  2. LRIM.2
  3. LRIM.3
  4. LRIM.4
Insect Infection and Immunity. Comparative Genomics of Insect Immunity.
 
2009, Kafatos FC,  Waterhouse RM, Zdobnov EM & Christophides GK.
  1. insect_infection_immunity
The genome of the model beetle and pest Tribolium castaneum.
 
2008, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Bucher G, et al.
  1. Trib1
The Aedes aegypti genome: a comparative perspective.
 
2008, Waterhouse RM, Wyder S, & Zdobnov EM.
  1. Aedes1
  2. Aedes2
  3. Aedes3
  4. Aedes4
  5. Aedes5
Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes.
 
2007, Waterhouse RM, Kriventseva EV, Meister S, Xi Z, Alvarez KS, Bartholomay LC, Barillas-Mury C, Bian G, Blandin S, et al.
  1. evodyn1A
  2. evodyn1B
  3. evodyn2A
  4. evodyn2B
  5. evodyn3
  6. evodyn4
  7. evodyn5
  8. evodyn6
  9. evodyn7