Publications
Driller, M., Brown, T., Currie, S.E., Hiller, M., Winkler, S., Pippel, M., Voigt, C.C., Fickel, J., Mazzoni, C.J. (2024)
A haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839).
DNA Research.
Bein, B., Chrysostomakis, I., Arantes, L.S., Brown, T., Gerheim, C., Schell, T., Schneider, C., et al. (2024)
Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.
bioRxiv.
Arantes, L.S, Caccavo, J.A., Sullivan, J.K., Sparmann, S., Mbedi, S., Höner, O.P., Mazzoni, C.J. (2023)
Scaling-up RADseq methods for large datasets of non-invasive samples.
Molecular Ecology Resources.
Mazzoni, C. J., Ciofi, C., Waterhouse, R. M. (2023)
Biodiversity: An Atlas of European Reference Genomes.
Nature 2023, 619 (7969), 252–252.
Danabalan, R., Merkel, K., Bærholm Schnell, I., Arandjelovic, M., Boesch, C., Brazzola, G., Dieguez, P., Dupain, J., Kambale-Vyalengerera, M., Kühl, H. S., Hoffmann, C., Lapuente, J., Ngoc Thinh, V., Zimmermann, F., Leendertz, F. H., Gilbert, M. T. P., Roos, C., Mazzoni, C., Gogarten, J. F., Calvignac-Spencer, S. (2023)
Mammal Mitogenomics from Invertebrate-Derived DNA.
Environmental DNA
Danabalan, R., Planillo, A., Butschkau, S., Deeg, S., Pierre, G., Thion, C., Calvignac-Spencer, S., Kramer-Schadt, S., Mazzoni, C. (2023)
Comparison of Mosquito and Fly Derived DNA as a Tool for Sampling Vertebrate Biodiversity in Suburban Forests in Berlin, Germany.
Environmental DNA
Bentley, B. P., Carrasco-Valenzuela, T., Ramos, E. K. S., Pawar, H., Souza Arantes, L., Alexander, A., Banerjee, S. M., Masterson, P., Kuhlwilm, M., Pippel, M., Mountcastle, J., Haase, B., Uliano-Silva, M., Formenti, G., Howe, K., Chow, W., Tracey, A., Sims, Y., Pelan, S., Wood, J., Yetsko, K., Perrault, J. R., Stewart, K., Benson, S. R., Levy, Y., Todd, E. V., Shaffer, H. B., Scott, P., Henen, B. T., Murphy, R. W., Mohr, D. W., Scott, A. F., Duffy, D. J., Gemmell, N. J., Suh, A., Winkler, S., Thibaud-Nissen, F., Nery, M. F., Marques-Bonet, T., Antunes, A., Tikochinski, Y., Dutton, P. H., Fedrigo, O., Myers, E. W., Jarvis, E. D., Mazzoni, C. J.*, Komoroske, L. M.* (2023)
Divergent Sensory and Immune Gene Evolution in Sea Turtles with Contrasting Demographic and Life Histories.
Proc. Natl. Acad. Sci. U.S.A. 120 (7), e2201076120. *co-last authors
Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., Jentoft, S., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Secomandi, S., Theofanopoulou, C., de Vries, J., Waldvogel, A.-M., Zhang, G., Jarvis, E. D., Bálint, M., Ciofi, C., Waterhouse, R. M., Mazzoni, C. J., Höglund, J. (2023).
How Genomics Can Help Biodiversity Conservation.
Trends in Genetics S0168952523000203.
Vilaça, S. T., Maroso, F., Lara, P., de Thoisy, B., Chevallier, D., Arantes, L. S., Santos, F. R., Bertorelle, G., Mazzoni, C. J. (2023).
Evidence of Backcross Inviability and Mitochondrial DNA Paternal Leakage in Sea Turtle Hybrids.
Molecular Ecology 32 (3), 628–643.
Damas J, M Corbo, J Kim, J Turner-Maier, M Farré, DM Larkin, OA Ryder, C Steiner, ML Houck, S Hall, L Shiue, S Thomas, T Swale, M Daly, J Korlach, M Uliano-Silva, CJ Mazzoni, BW Birren, DP Genereux, J Johnson, K Lindblad-Toh, EK Karlsson, MT Nweeia, RN Johnson, Zoonomia Consortium, HA Lewin (2022).
Evolution of the ancestral mammalian karyotype and syntenic regions.
Proceedings of the National Academy of Sciences USA 119:e22091391.
De Panis D, SA Lambertucci, G Wiemeyer, H Dopazo, FC Almeida, CJ Mazzoni, M Gut, I Gut, J Padró (2022)
Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures.
Scientific Reports 11:17109.
Lewin H.A. et al.. (2022)
The Earth BioGenome Project 2020: starting the clock.
Proceedings of the National Academy of Sciences USA 118:e2115635118
Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M, The European Reference Genome Atlas (ERGA) Consortium (2022).
The era of reference genomes in conservation genomics.
Trends in Ecology and Evolution.
Mazzoni C, Carrasco-Valenzuela T, Uliano-Silva M, Winkler S, Formenti G, Mountcastle J, Haase B, Pelan S, Sims Y, Tikochinski Y, Howe K, Fedrigo O, Myers G, Jarvis E, D. (2020).
Chelonia mydas isolate rCheMyd1, whole genome shotgun sequencing project.
Driller M, Vilaca ST, Souza Arantes L, Carrasco Valenzuela T, Heeger F, Chevallier D, De Thoisy B, Mazzoni CJ (2020)
Optimization of ddRAD-like data leads to high quality sets of reduced representation single copy orthologs (R2SCOS) in a sea turtle multi-species analysis.
Biorxiv, Pre-Print.
Arantes LS, ST Vilaça, CJ Mazzoni, FR Santos (2020).
New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil.
Journal of Heredity 5:444–456
Arantes LS, LCL Ferreira, M Driller, FPMR Filho, CJ Mazzoni, FR Santos (2020)
Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output.
Scientific Reports 10:12847.
Arantes LS, ST Vilaça, CJ Mazzoni, FR Santos (2020)
New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil.
Journal of Heredity esaa024
Heeger F, C Wurzbacher, EC Bourne, CJ Mazzoni, MT Monaghan (2019)
Combining the 5.8S and ITS2 to improve classification of fungi.
Methods in Ecology and Evolution 10:1702-1711.
Vilaça ST, CS Lima, CJ Mazzoni, FR Santos, B de Thoisy (2019)
Manatee genomics supports a special conservation area along the Guianas coastline under the influence of the Amazon River plume.
Estuarine, Coastal and Shelf Science 226:106286.
Heeger F, EC Bourne, C Baschien, A Yurkov, B Bunk, C Spröer, J Overmann, CJ Mazzoni, MT Monaghan (2018)
Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments.
Molecular Ecology Resources 18:1500-1514.
Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G (2018)
A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).
Heredity 10.1038/s41437-018-0070-5.
Blankers T, Vilaça ST, Waurick I, Gray DA, Hennig RM, Mazzoni CJ, Mayer F, Berdan EL (2018)
Demography and selection shape transcriptomic divergence in field crickets.
Evolution 72:553-567.
Uliano-Silva M, Dondero F, Otto TD, Costa I, Lima NCB, Americo JA, Mazzoni CJ, Prosdocimi F, de Freitas Rebelo M. (2017)
A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei.
GigaScience 7:gix128.
Schwensow NI, Detering H, Pederson S, Mazzoni CJ, Sinclair R, Peacock D, Kovaliski J, Cooke B, Fickel J, Sommer S (2017)
Resistance to RHD virus in wild Australian rabbits: comparison of susceptible and resistant individuals using a genome‐wide approach.
Molecular Ecology 26:4551–4561.
Berdan EL, Finck J, Johnston PR, Waurick I, Mazzoni CJ, Mayer F (2017)
Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus.
PLoS One 12:e0177367.
Nikolin VM, Olarte-Castillo XA, Osterrieder N, Hofer H, Dubovi E, Mazzoni CJ, Brunner E, Goller KV, Fyumagwa RD, Moehlman PD, Thierer D, East ML (2017)
Canine distemper virus in the Serengeti ecosystem: molecular adaptation to different carnivore species.
Molecular Ecology 26:2111–2130.
Schwensow NI, Mazzoni CJ, Marmesat E, Fickel J, Peacock D, Kovaliski J, Sinclair R, Cassey P, Cooke B, Sommer S (2017)
High adaptive variability and virus-driven selection on Major Histocompatibility Complex (MHC) genes in invasive wild rabbits in Australia
Biological Invasions 19:1255–1271.
Schuster AC, Herde A, Mazzoni CJ, Eccard JA, Sommer S (2016)
Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations.
Immunogenetics 68:429-437.
Marmesat E, Soriano L, Mazzoni CJ, Sommer S, Godoy JA (2016)
PCR strategies for complete allele calling in multigene families using high-throughput sequencing approaches.
PLoS One 11:e0157402.
Berdan E, Blaneers T, Waurick I, Mazzoni CJ, Mayer F (2016)
A genes eye view of ontogeny: De novo assembly and profiling of the Gryllus rubens transcriptome.
Molecular Ecology Resources 16:1478–1490.
Obara, I, Nielsen M, Jeschek M, Nijhof A, Mazzoni CJ, Svitek N, Steinaa L, Awino E, Olds C, Jabbar A, Clausen P-H, Bishop, RP (2016)
Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters.
Immunogenetics 68:339-352.
Clozato CL, Mazzoni CJ, Moraes-Barros N, Morgante JS, Sommer S (2015)
Spatial pattern of adaptive and neutral genetic diversity across different biomes in the lesser anteater (Tamandua tetradactyla).
Ecology and Evolution 21:4932–4948.
Hartmann S, Hasenkamp N, Mayer J, Michaux J, Morand S, Mazzoni CJ, Roca AL, Greenwood AD (2015)
Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse.
BMC Genomics 16:613.
Berdan E, Mazzoni CJ, Waurick I, Roehr J, Mayer F (2015)
A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence.
Molecular Ecology 24:3918-3930.
Escalera-Zamudio M, Zepeda Mendoza L, Heeger F, Loza-Rubio E, Rojas-Anaya E, Méndez-Ojeda ML, Taboada B, Mazzoni CJ, Arias CF, Greenwood AD (2015)
A novel endogenous betaretrovirus in the commmon vampire bat (Desmondus rotundus) suggests multiple independent infection and cross-species transmission events.
Journal of Virology 89:5180-5184.
Olarte-Castillo XA, Heeger F, Mazzoni CJ, Greenwood AD, Fyumagwa RD, Moehlmann PD, Hofer H, East ML (2015)
Molecular characterization of canine kobuvirus in wild carnivores and the domestic dog in Africa.
Virology 477:89–97.
Weyrich A, Schüllermann T, Heeger F, Jeschek M, Mazzoni CJ, Chen W, Schumann K, Fickel J (2014)
Whole genome sequencing and methylome analysis of the wild guinea pig.
BMC Genomics 15:1036.
Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V, Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, Derisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder N, Greenwood AD (2014). Polar Bear Encephalitis: Establishment of a Comprehensive Next-generation Pathogen Analysis Pipeline for Captive and Free-living Wildlife.
Journal of Comparative Pathology; 150(4):474-88.
Araki AS, Ferreira GE, Mazzoni CJ, Souza NA, Machado RC, Bruno RV, Peixoto AA (2013) Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil.
PLoS Negl Trop Dis 7(10):e2495.
Sommer S, Courtiol A, Mazzoni CJ (2013). MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout.
BMC Genomics. 2013 Aug 9;14:542.
Mayer J, Tsangaras K, Heeger F, Avila-Arcos M, Stenglein MD, Chen W, Sun W, Mazzoni CJ, Osterrieder N, Greenwood AD (2013). A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca).
Virology 443(1):1-10.
Dadheech PK, Glöckner G, Casper P, Kotut K, Mazzoni CJ, Mbedi S, Krienitz L (2013). Cyanobacterial diversity in the hot spring, pelagic and benthic habitats of a tropical soda lake.
FEMS Microbiol Ecol. 2013 Aug;85(2):389-401. doi: 10.1111/1574-6941.12128. Epub 2013 Apr 25. PubMed PMID: 23586739.
Mazzoni CJ*, Mayer J*, Greenwood AD (2012). Comparing PreXMRV-2 gag sequence diversity in laboratory and wild mice using deep sequencing.
Virus Research. 169(1):30-7.
Azevedo RVDM, Dias DBS, Bretas JAC, Mazzoni CJ, Souza NA, Albano RM, Wagner G, Davila AMR, Peixoto AA (2012). The Transcriptome of Lutzomyia longipalpis (Diptera: Psychodidae) Male Reproductive Organs.
PloS ONE 7(3)e34495.
Laukkanen-Ninios R, Didelot X, Jolley K A, Morelli G, Sangal V, Kristo P, Brehony C, Imori PFM, Fukushima H , Siitonen A , Tseneva G , Voskressenskaya E, Falcao JP, Korkeala, H, Maiden MCJ , Mazzoni C, Carniel E , Skurnik M, Achtman M (2011). Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing.
Environmental Microbiology. 13(12):3114-3127.
Mazzoni CJ*, Morelli G*, Song Y*, Eppinger M*, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E & Achtman M (2010). Phylogenetic diversity and historical patterns of pandemic spread of Yersinia pestis.
Nature Genetics 42:1140-3.
Sangal, V, Harbottle, H, Mazzoni, CJ, Helmuth, R, Guerra, B, Didelot, X, Paglietti, B, Rabsch, W, Brisse, S, Weill, FX, Roumagnac, P, Achtman, M (2010). Evolution and population structure of Salmonella enterica serovar Newport.
Journal of Bacteriology 192:6465-76.
Song, Y, Roumagnac, P, Weill, FX, Wain, J, Dolecek, C, Mazzoni, CJ, Holt, KE and Achtman, M (2010). A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.
J. Antimicrob. Chemother. 65: 1631–1641.
Rona LD, Carvalho-Pinto CJ, Mazzoni CJ, Peixoto AA (2010). Estimation of divergence time between two sibling species of the Anopheles (Kerteszia) cruzii complex using a multilocus approach.
BMC Evol Biol. 10:91.
Holt, KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G (2008). High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.
Nature Genetics 40:987-93.
Mazzoni CJ, Araki AS, Ferreira GEM, Azevedo RVDM, Barbujani G, Peixoto AA (2008). Multilocus analysis of introgression between two sand fly vectors of leishmaniasis.
BMC Evol Biol. 8:141.
Mazzoni CJ, Souza NA, Andrade-Coelho C Kyriacou C P, Peixoto AA (2006). Molecular polymorphism, differentiation and introgression in the period gene between Lutzomyia intermedia and Lutzomyia whitmani (Diptera: Psychodidae).
BMC Evol Biol. 6:85.
Davila AMR, Lorenzini DM, Mendes PN, Satake TS, Sousa GR, Campos LM, Mazzoni CJ, Wagner GW, Pires PF, Grisard EC, Cavalcantis MCR, Campos MLM (2005). GARSA: Genomic Analysis Resources for Sequence Annotation.
Bioinformatics. 21:4302-4303.
Mazzoni, CJ, Gomes, CA, Souza, NA, Queiroz, RG, Justiniano, SCB, Ward, RD, Kyriacou, CP, Peixoto, AA (2002). Molecular evolution of the period gene in sandflies.
Journal of Molecular Evolution. 55(5):553-62.
