2024

Attenborough, Teresa, Rawlinson, Kate A., Diaz Soria, Carmen L., Ambridge, Kirsty, Sankaranarayanan, Geetha, Graham, Jennie, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Doyle, Stephen R., Rinaldi, Gabriel and Berriman, Matthew (2024) A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture. eLife, 13, RP95628. (doi: 10.7554/eLife.95628) (PMID:39190022) (PMCID:PMC11349301)

Diaz Soria, C. L. et al. (2024) Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators. Scientific Reports, 14(1), 5974. (doi: 10.1038/s41598-024-55790-3) (PMID:38472267) (PMCID:PMC10933418)

Chevalier, Frédéric D., Le Clec'h, Winka, Berriman, Matthew and Anderson, Timothy J.C. (2024) A single locus determines praziquantel response in Schistosoma mansoni. Antimicrobial Agents and Chemotherapy, 68(3), e01432-23. (doi: 10.1128/aac.01432-23) (PMID:38289079) (PMCID:PMC10916369)

Brann, T., Beltramini, A., Chaparro, C., Berriman, M., Doyle, S.R. and Protasio, A.V. (2024) Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics, 25(1), 217. (doi: 10.1186/s12864-024-10032-8) (PMID:38413905) (PMCID:PMC10900676)

Herz, M. et al. (2024) Genome-wide transcriptome analysis of Echinococcus multilocularis larvae and germinative cell cultures reveals genes involved in parasite stem cell function. Frontiers in Cellular and Infection Microbiology, 14, 1335946. (doi: 10.3389/fcimb.2024.1335946) (PMID:38333034) (PMCID:PMC10850878)

2023

Padalino, Gilda, Coghlan, Avril, Pagliuca, Giampaolo, Forde-Thomas, Josephine E., Berriman, Matthew and Hoffmann, Karl F. (2023) Using ChEMBL to complement schistosome drug discovery. Pharmaceutics, 15(5), 1359. (doi: 10.3390/pharmaceutics15051359) (PMID:37242601) (PMCID:PMC10220823)

2022

Rinaldi, Gabriel, Attenborough, Teresa, Rawlinson, Kate A. and Berriman, Matt (2022) Schistosomes go single cell. Nature Reviews Microbiology, 20, p. 705. (doi: 10.1038/s41579-022-00810-0) (PMID:36229520)

Hoshizaki, Johanna, Adjalley, Sophie H., Thathy, Vandana, Judge, Kim, Berriman, Matthew, Reid, Adam J. and Lee, Marcus C. S. (2022) A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics, 23, 780. (doi: 10.1186/s12864-022-09017-2) (PMID:36451097) (PMCID:PMC9710153)

Cortés, A. et al. (2022) The gut microbial metabolic capacity of microbiome-humanized vs. wild type rodents reveals a likely dual role of intestinal bacteria in hepato-intestinal schistosomiasis. PLoS Neglected Tropical Diseases, 16(10), e0010878. (doi: 10.1371/journal.pntd.0010878) (PMID:36279280) (PMCID:PMC9633004)

Vianney, T. J. et al. (2022) Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS Neglected Tropical Diseases, 16(8), e0010188. (doi: 10.1371/journal.pntd.0010188) (PMID:35981002) (PMCID:PMC9426917)

Coghlan, Avril, Padalino, Gilda, O'Boyle, Noel M., Hoffmann, Karl F. and Berriman, Matthew (2022) Identification of anti-schistosomal, anthelmintic and anti-parasitic compounds curated and text-mined from the scientific literature. Wellcome Open Research, 7, 193. (doi: 10.12688/wellcomeopenres.17987.1) (PMID:36003342) (PMCID:PMC9363976)

Costain, A. H. et al. (2022) Dynamics of host immune response development during Schistosoma mansoni infection. Frontiers in Immunology, 13, 906338. (doi: 10.3389/fimmu.2022.906338) (PMID:35958580) (PMCID:PMC9362740)

Aunin, Eerik, Berriman, Matthew and Reid, Adam James (2022) Characterising genome architectures using genome decomposition analysis. BMC Genomics, 23, 398. (doi: 10.1186/s12864-022-08616-3) (PMID:35610562) (PMCID:PMC9131526)

2020

Imamura, Hideo, Monsieurs, Pieter, Jara, Marlene, Sanders, Mandy, Maes, Ilse, Vanaerschot, Manu, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Dujardin, Jean-Claude and Domagalska, Malgorzata A. (2020) Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Scientific Reports, 10, 15043. (doi: 10.1038/s41598-020-71882-2) (PMID:32929126) (PMCID:PMC7490275)

2019

Sallé, G., Doyle, S.R., Cortet, J., Cabaret, J., Berriman, M., Holroyd, N. and Cotton, J.A. ORCID: https://orcid.org/0000-0001-5475-3583 (2019) The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nature Communications, 10, 4811. (doi: 10.1038/s41467-019-12695-4) (PMID:31641125) (PMCID:PMC6805936)

2018

Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Berriman, Matthew, Dalén, Love and Barnes, Ian (2018) Eradication genomics-lessons for parasite control. Science, 361(6398), pp. 130-131. (doi: 10.1126/science.aar6609) (PMID:30002241)

Sargison, Neil D., Redman, Elizabeth, Morrison, Alison A., Bartley, David J., Jackson, Frank, Naghra-van Gijzel, Hardeep, Holroyd, Nancy, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583 and Gilleard, John S. (2018) A method for single pair mating in an obligate parasitic nematode. International Journal for Parasitology, 48(2), pp. 159-165. (doi: 10.1016/j.ijpara.2017.08.010) (PMID:29111440)

2017

Iantorno, S. A. et al. (2017) Gene expression in Leishmania is regulated predominantly by gene dosage. mBio, 8(5), e01393-17. (doi: 10.1128/mBio.01393-17) (PMID:28900023) (PMCID:PMC5596349)

Dumetz, F. et al. (2017) Modulation of aneuploidy in leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. mBio, 8(3), e00599-17. (doi: 10.1128/mBio.00599-17) (PMID:28536289) (PMCID:PMC5442457)

2016

Bennuru, S. et al. (2016) Stage-specific transcriptome and proteome analyses of the filarial parasite Onchocerca volvulus and its Wolbachia endosymbiont. mBio, 7(6), e02028-16. (doi: 10.1128/mBio.02028-16) (PMID:27881553) (PMCID:PMC5137501)

Cotton, J. A. et al. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology, 2, 16216. (doi: 10.1038/nmicrobiol.2016.216) (PMID:27869790) (PMCID:PMC5310847)

Hunt, V. L. et al. (2016) The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics, 48(3), pp. 299-307. (doi: 10.1038/ng.3495) (PMID:26829753) (PMCID:PMC4948059)

Crellen, T. et al. (2016) Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Scientific Reports, 6, 20954. (doi: 10.1038/srep20954) (PMID:26879532) (PMCID:PMC4754680)

2014

Foth, B. J. et al. (2014) Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics, 46(7), pp. 693-700. (doi: 10.1038/ng.3010) (PMID:24929830) (PMCID:PMC5012510)

Attardo, G. M. et al. (2014) Genome sequence of the Tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science, 344(6182), pp. 380-386. (doi: 10.1126/science.1249656) (PMID:24763584) (PMCID:PMC4077534)

Cotton, J. A. et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology, 15(3), R43. (doi: 10.1186/gb-2014-15-3-r43) (PMID:24580726) (PMCID:PMC4054857)

Rogers, Matthew B., Downing, Tim, Smith, Barbara A., Imamura, Hideo, Sanders, Mandy, Svobodova, Milena, Volf, Petr, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583 and Smith, Deborah F. (2014) Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genetics, 10(1), e1004092. (doi: 10.1371/journal.pgen.1004092) (PMID:24453988) (PMCID:PMC3894156)

2013

Saunders, Gary Ian, Wasmuth, James David, Beech, Robin, Laing, Roz ORCID: https://orcid.org/0000-0002-6191-0759, Hunt, Martin, Naghra, Hardeep, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Berriman, Matt, Britton, Collette ORCID: https://orcid.org/0000-0002-5165-312X and Gilleard, John Stuart (2013) Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes. International Journal for Parasitology, 43(6), pp. 465-475. (doi: 10.1016/j.ijpara.2012.12.011) (PMID:23416426)

2012

Reid, A. J. et al. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens, 8(3), e1002567. (doi: 10.1371/journal.ppat.1002567) (PMID:22457617) (PMCID:PMC3310773)

Articles

Attenborough, Teresa, Rawlinson, Kate A., Diaz Soria, Carmen L., Ambridge, Kirsty, Sankaranarayanan, Geetha, Graham, Jennie, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Doyle, Stephen R., Rinaldi, Gabriel and Berriman, Matthew (2024) A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture. eLife, 13, RP95628. (doi: 10.7554/eLife.95628) (PMID:39190022) (PMCID:PMC11349301)

Diaz Soria, C. L. et al. (2024) Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators. Scientific Reports, 14(1), 5974. (doi: 10.1038/s41598-024-55790-3) (PMID:38472267) (PMCID:PMC10933418)

Chevalier, Frédéric D., Le Clec'h, Winka, Berriman, Matthew and Anderson, Timothy J.C. (2024) A single locus determines praziquantel response in Schistosoma mansoni. Antimicrobial Agents and Chemotherapy, 68(3), e01432-23. (doi: 10.1128/aac.01432-23) (PMID:38289079) (PMCID:PMC10916369)

Brann, T., Beltramini, A., Chaparro, C., Berriman, M., Doyle, S.R. and Protasio, A.V. (2024) Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics, 25(1), 217. (doi: 10.1186/s12864-024-10032-8) (PMID:38413905) (PMCID:PMC10900676)

Herz, M. et al. (2024) Genome-wide transcriptome analysis of Echinococcus multilocularis larvae and germinative cell cultures reveals genes involved in parasite stem cell function. Frontiers in Cellular and Infection Microbiology, 14, 1335946. (doi: 10.3389/fcimb.2024.1335946) (PMID:38333034) (PMCID:PMC10850878)

Padalino, Gilda, Coghlan, Avril, Pagliuca, Giampaolo, Forde-Thomas, Josephine E., Berriman, Matthew and Hoffmann, Karl F. (2023) Using ChEMBL to complement schistosome drug discovery. Pharmaceutics, 15(5), 1359. (doi: 10.3390/pharmaceutics15051359) (PMID:37242601) (PMCID:PMC10220823)

Rinaldi, Gabriel, Attenborough, Teresa, Rawlinson, Kate A. and Berriman, Matt (2022) Schistosomes go single cell. Nature Reviews Microbiology, 20, p. 705. (doi: 10.1038/s41579-022-00810-0) (PMID:36229520)

Hoshizaki, Johanna, Adjalley, Sophie H., Thathy, Vandana, Judge, Kim, Berriman, Matthew, Reid, Adam J. and Lee, Marcus C. S. (2022) A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics, 23, 780. (doi: 10.1186/s12864-022-09017-2) (PMID:36451097) (PMCID:PMC9710153)

Cortés, A. et al. (2022) The gut microbial metabolic capacity of microbiome-humanized vs. wild type rodents reveals a likely dual role of intestinal bacteria in hepato-intestinal schistosomiasis. PLoS Neglected Tropical Diseases, 16(10), e0010878. (doi: 10.1371/journal.pntd.0010878) (PMID:36279280) (PMCID:PMC9633004)

Vianney, T. J. et al. (2022) Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS Neglected Tropical Diseases, 16(8), e0010188. (doi: 10.1371/journal.pntd.0010188) (PMID:35981002) (PMCID:PMC9426917)

Coghlan, Avril, Padalino, Gilda, O'Boyle, Noel M., Hoffmann, Karl F. and Berriman, Matthew (2022) Identification of anti-schistosomal, anthelmintic and anti-parasitic compounds curated and text-mined from the scientific literature. Wellcome Open Research, 7, 193. (doi: 10.12688/wellcomeopenres.17987.1) (PMID:36003342) (PMCID:PMC9363976)

Costain, A. H. et al. (2022) Dynamics of host immune response development during Schistosoma mansoni infection. Frontiers in Immunology, 13, 906338. (doi: 10.3389/fimmu.2022.906338) (PMID:35958580) (PMCID:PMC9362740)

Aunin, Eerik, Berriman, Matthew and Reid, Adam James (2022) Characterising genome architectures using genome decomposition analysis. BMC Genomics, 23, 398. (doi: 10.1186/s12864-022-08616-3) (PMID:35610562) (PMCID:PMC9131526)

Imamura, Hideo, Monsieurs, Pieter, Jara, Marlene, Sanders, Mandy, Maes, Ilse, Vanaerschot, Manu, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Dujardin, Jean-Claude and Domagalska, Malgorzata A. (2020) Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Scientific Reports, 10, 15043. (doi: 10.1038/s41598-020-71882-2) (PMID:32929126) (PMCID:PMC7490275)

Sallé, G., Doyle, S.R., Cortet, J., Cabaret, J., Berriman, M., Holroyd, N. and Cotton, J.A. ORCID: https://orcid.org/0000-0001-5475-3583 (2019) The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nature Communications, 10, 4811. (doi: 10.1038/s41467-019-12695-4) (PMID:31641125) (PMCID:PMC6805936)

Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Berriman, Matthew, Dalén, Love and Barnes, Ian (2018) Eradication genomics-lessons for parasite control. Science, 361(6398), pp. 130-131. (doi: 10.1126/science.aar6609) (PMID:30002241)

Sargison, Neil D., Redman, Elizabeth, Morrison, Alison A., Bartley, David J., Jackson, Frank, Naghra-van Gijzel, Hardeep, Holroyd, Nancy, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583 and Gilleard, John S. (2018) A method for single pair mating in an obligate parasitic nematode. International Journal for Parasitology, 48(2), pp. 159-165. (doi: 10.1016/j.ijpara.2017.08.010) (PMID:29111440)

Iantorno, S. A. et al. (2017) Gene expression in Leishmania is regulated predominantly by gene dosage. mBio, 8(5), e01393-17. (doi: 10.1128/mBio.01393-17) (PMID:28900023) (PMCID:PMC5596349)

Dumetz, F. et al. (2017) Modulation of aneuploidy in leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. mBio, 8(3), e00599-17. (doi: 10.1128/mBio.00599-17) (PMID:28536289) (PMCID:PMC5442457)

Bennuru, S. et al. (2016) Stage-specific transcriptome and proteome analyses of the filarial parasite Onchocerca volvulus and its Wolbachia endosymbiont. mBio, 7(6), e02028-16. (doi: 10.1128/mBio.02028-16) (PMID:27881553) (PMCID:PMC5137501)

Cotton, J. A. et al. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology, 2, 16216. (doi: 10.1038/nmicrobiol.2016.216) (PMID:27869790) (PMCID:PMC5310847)

Hunt, V. L. et al. (2016) The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics, 48(3), pp. 299-307. (doi: 10.1038/ng.3495) (PMID:26829753) (PMCID:PMC4948059)

Crellen, T. et al. (2016) Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Scientific Reports, 6, 20954. (doi: 10.1038/srep20954) (PMID:26879532) (PMCID:PMC4754680)

Foth, B. J. et al. (2014) Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics, 46(7), pp. 693-700. (doi: 10.1038/ng.3010) (PMID:24929830) (PMCID:PMC5012510)

Attardo, G. M. et al. (2014) Genome sequence of the Tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science, 344(6182), pp. 380-386. (doi: 10.1126/science.1249656) (PMID:24763584) (PMCID:PMC4077534)

Cotton, J. A. et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology, 15(3), R43. (doi: 10.1186/gb-2014-15-3-r43) (PMID:24580726) (PMCID:PMC4054857)

Rogers, Matthew B., Downing, Tim, Smith, Barbara A., Imamura, Hideo, Sanders, Mandy, Svobodova, Milena, Volf, Petr, Berriman, Matthew, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583 and Smith, Deborah F. (2014) Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genetics, 10(1), e1004092. (doi: 10.1371/journal.pgen.1004092) (PMID:24453988) (PMCID:PMC3894156)

Saunders, Gary Ian, Wasmuth, James David, Beech, Robin, Laing, Roz ORCID: https://orcid.org/0000-0002-6191-0759, Hunt, Martin, Naghra, Hardeep, Cotton, James A. ORCID: https://orcid.org/0000-0001-5475-3583, Berriman, Matt, Britton, Collette ORCID: https://orcid.org/0000-0002-5165-312X and Gilleard, John Stuart (2013) Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes. International Journal for Parasitology, 43(6), pp. 465-475. (doi: 10.1016/j.ijpara.2012.12.011) (PMID:23416426)

Reid, A. J. et al. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens, 8(3), e1002567. (doi: 10.1371/journal.ppat.1002567) (PMID:22457617) (PMCID:PMC3310773)