2025

Krasilnikova, M. , Marques, C. A. , Briggs, E., Lapsley, C., Hamilton, G., Beraldi, D., Crouch, K. and McCulloch, R. (2025) Nanopore sequencing reveals that DNA replication compartmentalisation dictates genome stability and instability in Trypanosoma brucei. Nature Communications, 16, 751. (doi: 10.1038/s41467-025-56087-3)

2024

Damasceno, J. , LA. Silva, G., Marques, C. A. , Krasilnikova, M. , Lapsley, C., Beraldi, D. and McCulloch, R. (2024) Nuclear DNA replication in Leishmania major relies on a single constitutive origin per chromosome supplemented by thousands of stochastic initiation events. bioRxiv, (doi: 10.1101/2024.11.14.623610)

Damasceno, J. D. , Briggs, E. M., Krasilnikova, M. , Marques, C. A. , Lapsley, C. and McCulloch, R. (2024) R-loops acted on by RNase H1 are a determinant of chromosome length-associated DNA replication timing and genome stability in Leishmania. bioRxiv, (doi: 10.1101/2024.04.29.591643)

Reis-Cunha, J. L., Pimenta-Carvalho, S. A., Almeida, L. V., Coqueiro-Dos-Santos, A., Marques, C. A. , Black, J. A., Damasceno, J. , McCulloch, R. , Bartholomeu, D. C. and Jeffares, D. C. (2024) Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites. Genome Research, 34(3), pp. 441-453. (doi: 10.1101/gr.278550.123) (PMID:38604731) (PMCID:PMC11067883)

2023

Faria, J. R.C., Tinti, M., Marques, C. A. , Zoltner, M., Yoshikawa, H., Field, M. C. and Horn, D. (2023) An allele-selective inter-chromosomal protein bridge supports monogenic antigen expression in the African trypanosome. Nature Communications, 14, 8200. (doi: 10.1038/s41467-023-44043-y) (PMID:38081826) (PMCID:PMC10713589)

Girasol, M. J. et al. (2023) RAD51-mediated R-loop formation acts to repair transcription associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America, 120(48), e230930612. (doi: 10.1073/pnas.2309306120) (PMID:37988471) (PMCID:PMC10691351)

Girasol, M. J., Briggs, E., Marques, C. A. , Batista, J. M., Beraldi, D., Buchmore, R., Lemgruber, L. and McCulloch, R. (2023) Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Research, 51(20), pp. 11123-11141. (doi: 10.1093/nar/gkad836) (PMID:37843098) (PMCID:PMC10639054)

Briggs, E. M., Marques, C. A. , Oldrieve, G. R., Hu, J., Otto, T. D. and Matthews, K. R. (2023) Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single cell transcriptomics. eLife, 12, e86325. (doi: 10.7554/eLife.86325) (PMID:37166108) (PMCID:PMC10212563)

2022

Marques, C. A. , Ridgway, M., Tinti, M., Cassidy, A. and Horn, D. (2022) Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects. Nature Communications, 13, 5326. (doi: 10.1038/s41467-022-33109-y) (PMID:36088375) (PMCID:PMC9464253)

2021

Damasceno, J. D. , Marques, C. A. , Black, J., Briggs, E. and McCulloch, R. (2021) Read, write, adapt: challenges and opportunities during kinetoplastid genome replication. Trends in Genetics, 37(1), pp. 21-34. (doi: 10.1016/j.tig.2020.09.002) (PMID:32993968) (PMCID:PMC9213392)

2020

Damasceno, J. D. , Marques, C. A. , Beraldi, D., Crouch, K. , Lapsley, C., Obonaga, R., Tosi, L. R.O. and McCulloch, R. (2020) Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife, 9, e58030. (doi: 10.7554/eLife.58030) (PMID:32897188) (PMCID:PMC7511235)

Marques, C. A. , Tinti, M., Cassidy, A. and Horn, D. (2020) Genome-scale functional profiling of cell cycle controls in African trypanosomes. bioRxiv, (doi: 10.1101/2020.07.16.206698)

de Araujo, C. B. et al. (2020) Replication origin location might contribute to genetic variability in Trypanosoma cruzi. BMC Genomics, 21, 414. (doi: 10.1186/s12864-020-06803-8) (PMID:32571205) (PMCID:PMC7310030)

Briggs, E. M., Marques, C. , Reis-Cunha, J., Black, J., Campbell, S., Damasceno, J. , Bartholomeu, D., Crouch, K. and McCulloch, R. (2020) Next-generation analysis of trypanosomatid genome stability and instability. In: Michels, P. A.M., Ginger, M. L. and Zilberstein, D. (eds.) Trypanosomatids: Methods and Protocols. Series: Methods in Molecular Biology (2116). Springer, pp. 225-262. ISBN 9781071602935 (doi: 10.1007/978-1-0716-0294-2_15)

2019

Glover, L., Marques, C. A. , Suska, O. and Horn, D. (2019) Persistent DNA damage foci and DNA replication with a broken chromosome in the African trypanosome. mBio, 10(4), e01252-19. (doi: 10.1128/mbio.01252-19) (PMID:31289179) (PMCID:PMC6747728)

2018

Marques, C. A. and McCulloch, R. (2018) Conservation and variation in strategies for DNA replication of kinetoplastid nuclear genomes. Current Genomics, 19(2), pp. 98-109. (doi: 10.2174/1389202918666170815144627) (PMID:29491738) (PMCID:PMC5814967)

2017

da Silva, M. S., Pavani, R. S., Damasceno, J. D. , Marques, C. A. , McCulloch, R. , Tosi, L. R. O. and Elias, M. C. (2017) Nuclear DNA replication in trypanosomatids: there are no easy methods for solving difficult problems. Trends in Parasitology, 33(11), pp. 858-874. (doi: 10.1016/j.pt.2017.08.002) (PMID:28844718) (PMCID:PMC5662062)

Devlin, R., Marques, C. A. and McCulloch, R. (2017) Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome? Current Genetics, 63(3), pp. 441-449. (doi: 10.1007/s00294-016-0662-7) (PMID:27822899) (PMCID:PMC5422504)

2016

Marques, C. A. , Tiengwe, C., Lemgruber Soares, L. , Damasceno, J. D., Scott, A., Paape, D. , Marcello, L. and McCulloch, R. (2016) Diverged composition and regulation of the Trypanosoma brucei origin recognition complex that mediates DNA replication initiation. Nucleic Acids Research, 44(10), pp. 4763-4784. (doi: 10.1093/nar/gkw147) (PMID:26951375) (PMCID:PMC4889932)

Devlin, R., Marques, C. A. , Paape, D. , Prorocic, M., Zurita-Leal, A. C., Campbell, S. J., Lapsley, C., Dickens, N. and McCulloch, R. (2016) Mapping replication dynamics in Trypanosoma brucei reveals a link with telomere transcription and antigenic variation. eLife, 5, e12765. (doi: 10.7554/eLife.12765) (PMID:27228154) (PMCID:PMC4946898)

2015

Marques, C. A. , Dickens, N. J. , Paape, D. , Campbell, S. J. and McCulloch, R. (2015) Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. Genome Biology, 16, 230. (doi: 10.1186/s13059-015-0788-9) (PMID:26481451) (PMCID:PMC4612428)

Calderano, S.G., Drosopoulos, W.C., Quaresma, M. M., Marques, C.A. , Kosiyatrakul, S., McCulloch, R. , Schildkraut, C.L. and Elias, M.C. (2015) Single molecule analysis of Trypanosoma brucei DNA replication dynamics. Nucleic Acids Research, 43(5), pp. 2655-2665. (doi: 10.1093/nar/gku1389) (PMID:25690894) (PMCID:PMC4357695)

2014

Machado, C. R. et al. (2014) Nucleotide excision repair in Trypanosoma brucei: specialization of transcription-coupled repair due to multigenic transcription. Molecular Microbiology, 92(4), pp. 756-776. (doi: 10.1111/mmi.12589) (PMID:24661334) (PMCID:PMC4138998)

Tiengwe, C., Marques, C. A. and McCulloch, R. (2014) Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends in Parasitology, 30(1), pp. 27-36. (doi: 10.1016/j.pt.2013.10.009)

2009

Vale, N. et al. (2009) Imidazoquines as antimalarial and antipneumocystis agents. Journal of Medicinal Chemistry, 52(23), pp. 7800-7807. (doi: 10.1021/jm900738c) (PMID:19799426) (PMCID:PMC2788672)

Prudêncio, M., Derbyshire, E. T., Marques, C. A. , Krishna, S., Mota, M. M. and Staines, H. M. (2009) Plasmodium berghei-infection induces volume-regulated anion channel-like activity in human hepatoma cells. Cellular Microbiology, 11(10), pp. 1492-1501. (doi: 10.1111/j.1462-5822.2009.01342.x) (PMID:19496788) (PMCID:PMC2774480)

Articles

Krasilnikova, M. , Marques, C. A. , Briggs, E., Lapsley, C., Hamilton, G., Beraldi, D., Crouch, K. and McCulloch, R. (2025) Nanopore sequencing reveals that DNA replication compartmentalisation dictates genome stability and instability in Trypanosoma brucei. Nature Communications, 16, 751. (doi: 10.1038/s41467-025-56087-3)

Damasceno, J. , LA. Silva, G., Marques, C. A. , Krasilnikova, M. , Lapsley, C., Beraldi, D. and McCulloch, R. (2024) Nuclear DNA replication in Leishmania major relies on a single constitutive origin per chromosome supplemented by thousands of stochastic initiation events. bioRxiv, (doi: 10.1101/2024.11.14.623610)

Damasceno, J. D. , Briggs, E. M., Krasilnikova, M. , Marques, C. A. , Lapsley, C. and McCulloch, R. (2024) R-loops acted on by RNase H1 are a determinant of chromosome length-associated DNA replication timing and genome stability in Leishmania. bioRxiv, (doi: 10.1101/2024.04.29.591643)

Reis-Cunha, J. L., Pimenta-Carvalho, S. A., Almeida, L. V., Coqueiro-Dos-Santos, A., Marques, C. A. , Black, J. A., Damasceno, J. , McCulloch, R. , Bartholomeu, D. C. and Jeffares, D. C. (2024) Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites. Genome Research, 34(3), pp. 441-453. (doi: 10.1101/gr.278550.123) (PMID:38604731) (PMCID:PMC11067883)

Faria, J. R.C., Tinti, M., Marques, C. A. , Zoltner, M., Yoshikawa, H., Field, M. C. and Horn, D. (2023) An allele-selective inter-chromosomal protein bridge supports monogenic antigen expression in the African trypanosome. Nature Communications, 14, 8200. (doi: 10.1038/s41467-023-44043-y) (PMID:38081826) (PMCID:PMC10713589)

Girasol, M. J. et al. (2023) RAD51-mediated R-loop formation acts to repair transcription associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America, 120(48), e230930612. (doi: 10.1073/pnas.2309306120) (PMID:37988471) (PMCID:PMC10691351)

Girasol, M. J., Briggs, E., Marques, C. A. , Batista, J. M., Beraldi, D., Buchmore, R., Lemgruber, L. and McCulloch, R. (2023) Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Research, 51(20), pp. 11123-11141. (doi: 10.1093/nar/gkad836) (PMID:37843098) (PMCID:PMC10639054)

Briggs, E. M., Marques, C. A. , Oldrieve, G. R., Hu, J., Otto, T. D. and Matthews, K. R. (2023) Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single cell transcriptomics. eLife, 12, e86325. (doi: 10.7554/eLife.86325) (PMID:37166108) (PMCID:PMC10212563)

Marques, C. A. , Ridgway, M., Tinti, M., Cassidy, A. and Horn, D. (2022) Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects. Nature Communications, 13, 5326. (doi: 10.1038/s41467-022-33109-y) (PMID:36088375) (PMCID:PMC9464253)

Damasceno, J. D. , Marques, C. A. , Black, J., Briggs, E. and McCulloch, R. (2021) Read, write, adapt: challenges and opportunities during kinetoplastid genome replication. Trends in Genetics, 37(1), pp. 21-34. (doi: 10.1016/j.tig.2020.09.002) (PMID:32993968) (PMCID:PMC9213392)

Damasceno, J. D. , Marques, C. A. , Beraldi, D., Crouch, K. , Lapsley, C., Obonaga, R., Tosi, L. R.O. and McCulloch, R. (2020) Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife, 9, e58030. (doi: 10.7554/eLife.58030) (PMID:32897188) (PMCID:PMC7511235)

Marques, C. A. , Tinti, M., Cassidy, A. and Horn, D. (2020) Genome-scale functional profiling of cell cycle controls in African trypanosomes. bioRxiv, (doi: 10.1101/2020.07.16.206698)

de Araujo, C. B. et al. (2020) Replication origin location might contribute to genetic variability in Trypanosoma cruzi. BMC Genomics, 21, 414. (doi: 10.1186/s12864-020-06803-8) (PMID:32571205) (PMCID:PMC7310030)

Glover, L., Marques, C. A. , Suska, O. and Horn, D. (2019) Persistent DNA damage foci and DNA replication with a broken chromosome in the African trypanosome. mBio, 10(4), e01252-19. (doi: 10.1128/mbio.01252-19) (PMID:31289179) (PMCID:PMC6747728)

Marques, C. A. and McCulloch, R. (2018) Conservation and variation in strategies for DNA replication of kinetoplastid nuclear genomes. Current Genomics, 19(2), pp. 98-109. (doi: 10.2174/1389202918666170815144627) (PMID:29491738) (PMCID:PMC5814967)

da Silva, M. S., Pavani, R. S., Damasceno, J. D. , Marques, C. A. , McCulloch, R. , Tosi, L. R. O. and Elias, M. C. (2017) Nuclear DNA replication in trypanosomatids: there are no easy methods for solving difficult problems. Trends in Parasitology, 33(11), pp. 858-874. (doi: 10.1016/j.pt.2017.08.002) (PMID:28844718) (PMCID:PMC5662062)

Devlin, R., Marques, C. A. and McCulloch, R. (2017) Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome? Current Genetics, 63(3), pp. 441-449. (doi: 10.1007/s00294-016-0662-7) (PMID:27822899) (PMCID:PMC5422504)

Marques, C. A. , Tiengwe, C., Lemgruber Soares, L. , Damasceno, J. D., Scott, A., Paape, D. , Marcello, L. and McCulloch, R. (2016) Diverged composition and regulation of the Trypanosoma brucei origin recognition complex that mediates DNA replication initiation. Nucleic Acids Research, 44(10), pp. 4763-4784. (doi: 10.1093/nar/gkw147) (PMID:26951375) (PMCID:PMC4889932)

Devlin, R., Marques, C. A. , Paape, D. , Prorocic, M., Zurita-Leal, A. C., Campbell, S. J., Lapsley, C., Dickens, N. and McCulloch, R. (2016) Mapping replication dynamics in Trypanosoma brucei reveals a link with telomere transcription and antigenic variation. eLife, 5, e12765. (doi: 10.7554/eLife.12765) (PMID:27228154) (PMCID:PMC4946898)

Marques, C. A. , Dickens, N. J. , Paape, D. , Campbell, S. J. and McCulloch, R. (2015) Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. Genome Biology, 16, 230. (doi: 10.1186/s13059-015-0788-9) (PMID:26481451) (PMCID:PMC4612428)

Calderano, S.G., Drosopoulos, W.C., Quaresma, M. M., Marques, C.A. , Kosiyatrakul, S., McCulloch, R. , Schildkraut, C.L. and Elias, M.C. (2015) Single molecule analysis of Trypanosoma brucei DNA replication dynamics. Nucleic Acids Research, 43(5), pp. 2655-2665. (doi: 10.1093/nar/gku1389) (PMID:25690894) (PMCID:PMC4357695)

Machado, C. R. et al. (2014) Nucleotide excision repair in Trypanosoma brucei: specialization of transcription-coupled repair due to multigenic transcription. Molecular Microbiology, 92(4), pp. 756-776. (doi: 10.1111/mmi.12589) (PMID:24661334) (PMCID:PMC4138998)

Tiengwe, C., Marques, C. A. and McCulloch, R. (2014) Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends in Parasitology, 30(1), pp. 27-36. (doi: 10.1016/j.pt.2013.10.009)

Vale, N. et al. (2009) Imidazoquines as antimalarial and antipneumocystis agents. Journal of Medicinal Chemistry, 52(23), pp. 7800-7807. (doi: 10.1021/jm900738c) (PMID:19799426) (PMCID:PMC2788672)

Prudêncio, M., Derbyshire, E. T., Marques, C. A. , Krishna, S., Mota, M. M. and Staines, H. M. (2009) Plasmodium berghei-infection induces volume-regulated anion channel-like activity in human hepatoma cells. Cellular Microbiology, 11(10), pp. 1492-1501. (doi: 10.1111/j.1462-5822.2009.01342.x) (PMID:19496788) (PMCID:PMC2774480)

Book Sections

Briggs, E. M., Marques, C. , Reis-Cunha, J., Black, J., Campbell, S., Damasceno, J. , Bartholomeu, D., Crouch, K. and McCulloch, R. (2020) Next-generation analysis of trypanosomatid genome stability and instability. In: Michels, P. A.M., Ginger, M. L. and Zilberstein, D. (eds.) Trypanosomatids: Methods and Protocols. Series: Methods in Molecular Biology (2116). Springer, pp. 225-262. ISBN 9781071602935 (doi: 10.1007/978-1-0716-0294-2_15)