Daniel Jeffares

Search results

• 2025

  Molecular Insights into Cell-Mediated Immunity in Atypical Non-Ulcerated Cutaneous Leishmaniasis

  Batista, L. F. S., Sandoval Pacheco, C. M., Flores, G. V. A., Ferreira, F. M., Gonçalves, A. N. A., Sosa-Ochoa, W. H., da Matta, V. L. R., Gomes, C. M. C., Zúniga, C., Corbett, C. E. P., Jeffares, D. C., Nakaya, H. I., Silveira, F. T. & Laurenti, M. D., 13 Feb 2025, In: Microorganisms. 13, 2, 413.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2024

  Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

  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. & Jeffares, D. C., 11 Apr 2024, (E-pub ahead of print) In: Genome Research. 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Detecting complex infections in trypanosomatids using whole genome sequencing

  Reis-Cunha, J. L. & Jeffares, D. C., 29 Oct 2024, In: BMC Genomics. 25, 15 p., 1011.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites

  Dirkx, L., Van Acker, S., Nicolaes, Y., Cunha, J. L. R., Ahmad, R., Hendrickx, R., Caljon, B., Imamura, H., Ebo, D. G., Jeffares, D. C., Sterckx, Y.G.-J., Maes, L., Hendrickx, S. & Caljon, G., 24 Apr 2024, (E-pub ahead of print) In: PLOS PATHOGENS. 20, 4, e1012181.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata

  Smit, S. J., Whitehead, C., James, S. R., Jeffares, D. C., Godden, G., Peng, D., Sun, H. & Lichman, B. R., 7 Oct 2024, In: G3: Genes, Genomes, Genetics. 14, 10, 10 p., jkae172.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2023

  Co-infection of Leishmania infantum and a Crithidia-related species in a case of refractory relapsed visceral leishmaniasis with non-ulcerated cutaneous manifestation in Brazil

  Rogerio, L. A., Takahashi, T. Y., Cardoso, L., Takamiya, N. T., de Melo, E. V., de Jesus, A. R., de Oliveira, F. A., Forrester, S., Jeffares, D. C., da Silva, J. S., Ribeiro, J. M., Almeida, R. P. & Maruyama, S. R., 12 May 2023, In: International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases. 133, p. 85-88 4 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies

  Pilling, O. A., Reis-Cunha, J. L., Grace, C. A., Berry, A. S. F., Mitchell, M. W., Yu, J. A., Malekshahi, C. R., Krespan, E., Go, C. K., Lombana, C., Song, Y. S., Amorim, C. F., Lago, A. S., Carvalho, L. P., Carvalho, E. M., Brisson, D., Scott, P., Jeffares, D. C. & Beiting, D. P., 1 Mar 2023, In: PLOS PATHOGENS. 19, 3, p. e1011230 e1011230.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2022

  Parasite Genotype Is a Major Predictor of Mortality from Visceral Leishmaniasis

  Grace, C. A., Sousa Carvalho, K. S., Sousa Lima, M. I., Silva, V. C., Reis-Cunha, J. L., Brune, M. J., Forrester, S., de Maria Pedrozo, C., de Azevedo, S., Costa, D. L., Speed, D., Mottram, J. C., Jeffares, D. C. & Costa, C. H. N., Dec 2022, In: MBio. 13, 6, p. e0206822 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2021

  Candidates for Balancing Selection in Leishmania donovani Complex Parasites

  Grace, C. A., Forrester, S. J., Costa Silva, V., Carvalho, K. S. S., Kilford, H., Chew, Y. P., James, S., Costa, D. L., Mottram, J. C., Costa, C. H. N. & Jeffares, D., 2 Dec 2021, In: Molecular Biology and Evolution. 13, 12, 15 p., evab265.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms

  Hendrickx, S., Reis-Cunha, J. L., Forrester, S., Jeffares, D. C. & Caljon, G., 21 Jul 2021, In: Microorganisms. 9, 8, 14 p., 1546.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Identification of individual root-knot nematodes using low coverage long-read sequencing

  Sellers, G. S., Jeffares, D. C., Lawson, B., Prior, T. & Lunt, D. H., 1 Dec 2021, In: PLOS one. 16, 12 December, e0253248.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

  Cao, C., He, J., Mak, L., Perera, D., Kwok, D., Wang, J., Li, M., Mourier, T., Gavriliuc, S., Greenberg, M., Morrissy, A. S., Sycuro, L. K., Yang, G., Jeffares, D. C. & Long, Q., 19 May 2021, In: Molecular Biology and Evolution. 38, 6, p. 2660-2672 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements

  Ellis, D. A., Reyes-Martín, F., Rodríguez-López, M., Cotobal, C., Sun, X. M., Saintain, Q., Jeffares, D. C., Marguerat, S., Tallada, V. A. & Bähler, J., 31 Aug 2021, In: PLoS Genetics. 17, 8, 28 p., 1009784.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching

  Mourier, T., de Alvarenga, D. A. M., Kaushik, A., de Pina-Costa, A., Douvropoulou, O., Guan, Q., Guzmán-Vega, F. J., Forrester, S., de Abreu, F. V. S., Júnior, C. B., de Souza Junior, J. C., Moreira, S. B., Hirano, Z. M. B., Pissinatti, A., Ferreira-da-Cruz, M. D. F., de Oliveira, R. L., Arold, S. T., Jeffares, D. C., Brasil, P. & de Brito, C. F. A. & 3 others, Culleton, R., Daniel-Ribeiro, C. T. & Pain, A., 1 Oct 2021, In: BMC Biology. 19, 1, 219.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe

  Harnqvist, S. E., Grace, C. A. & Jeffares, D. C., Dec 2021, In: Journal of molecular evolution. 89, 9-10, p. 601-610

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2019

  Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

  Tusso, S., Nieuwenhuis, B. P. S., Sedlazeck, F. J., Davey, J. W., Jeffares, D. C. & Wolf, J. B. W., 9 Sept 2019, In: Molecular Biology and Evolution. 36, 9, p. 1975–1989 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13

  Coppée, R., Jeffares, D. C., Miteva, M. A., Sabbagh, A. & Clain, J., 23 Jul 2019, In: Scientific Reports. 9, 1, p. 10675 10675.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Fitness Landscape of the Fission Yeast Genome

  Grech, L., Jeffares, D., Sadee, C. Y., Rodriguez-Lopez, M., Bitton, D. A., Hoti, M., Biagosch, C., Aravani, D., Speekenbrink, M., Illingworth, C. J. R., Schiffer, P. H., Pidoux, A. L., Tong, P., Tallada, V. A., Allshire, R., Levin, H. L. & Bahler, J., 1 Aug 2019, In: Molecular Biology and Evolution. 36, 8, p. 1612-1623 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2018

  A Leishmania infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis

  Mottram, J. C., Jeffares, D., Brambilla Carnielli Trindade, J., Crouch, K., Forrester, S. J., Costa Silva, V., Carvalho, S. F. G., Damasceno, J. D., Brown, E., Dickens, N. J., Costa, D. L., Costa, C. H. N. & Dietze, R., 27 Sept 2018, In: EBioMedicine. 36, 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• The natural diversity and ecology of fission yeast

  Jeffares, D. C., 8 Feb 2018, In: Yeast (Chichester, England). p. 1-21 21 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells

  Ellis, D. A., Mustonen, V., Rodríguez-López, M., Rallis, C., Malecki, M., Jeffares, D. C. & Bähler, J., 1 Sept 2018, In: Genetics. 209, 4, 39 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2017

  Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

  Jeffares, D. C., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J. & Sedlazeck, F. J., 24 Jan 2017, In: Nature Communications. 8, 11 p., 14061.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2016

  Does the Ribosome Challenge our Understanding of the RNA World?

  Poole, A. M., Jeffares, D. C., Hoeppner, M. P. & Penny, D., 1 Jan 2016, In: Journal of molecular evolution. 82, 1, p. 1-4 4 p.

  Research output: Contribution to journal › Article › peer-review

• Selected Schizosaccharomyces pombe strains have characteristics that are beneficial for winemaking

  Benito, Á., Jeffares, D., Palomero, F., Calderón, F., Bai, F. Y., Bähler, J. & Benito, S., 1 Mar 2016, In: PLoS ONE. 11, 3, p. e0151102 19 p., e0151102.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Spotsizer: High-throughput quantitative analysis of microbial growth

  Bischof, L., Prěvorovský, M., Rallis, C., Jeffares, D. C., Arzhaeva, Y. & Bähler, J., Oct 2016, In: Biotechniques. 61, 4, p. 191-201 11 p.

  Research output: Contribution to journal › Article › peer-review
• 2015

  A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome

  Jeffares, D. C., Tomiczek, B., Sojo, V. & dos Reis, M., 2015, In: Methods in Molecular Biology. 1201, p. 65-90 26 p.

  Research output: Contribution to journal › Article › peer-review

• The genomic and phenotypic diversity of Schizosaccharomyces pombe

  Jeffares, D. C., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F. X., Iqbal, Z., Lau, W., Cheng, T. M. K., Pracana, R., Mülleder, M., Lawson, J. L. D., Chessel, A., Bala, S., Hellenthal, G., O'Fallon, B., Keane, T., Simpson, J. T. & Bischof, L. & 22 others, Tomiczek, B., Bitton, D. A., Sideri, T., Codlin, S., Hellberg, J. E. E. U., Van Trigt, L., Jeffery, L., Li, J. J., Atkinson, S., Thodberg, M., Febrer, M., McLay, K., Drou, N., Brown, W., Hayles, J., Salas, R. E. C., Ralser, M., Maniatis, N., Balding, D. J., Balloux, F., Durbin, R. & Bähler, J., 9 Feb 2015, In: Nature genetics. 47, 3, p. 235-241 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2014

  LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

  Bitton, D. A., Rallis, C., Jeffares, D. C., Smith, G. C., Chen, Y. Y. C., Codlin, S., Marguerat, S. & Bähler, J., Jul 2014, In: Genome Research. 24, 7, p. 1169-1179 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2011

  PoolHap: Inferring haplotype frequencies from pooled samples by next generation sequencing

  Long, Q., Jeffares, D. C., Zhang, Q., Ye, K., Nizhynska, V., Ning, Z., Tyler-Smith, C. & Nordborg, M., 2011, In: PLoS ONE. 6, 1, p. e15292 e15292.

  Research output: Contribution to journal › Article › peer-review
• 2010

  Long- and short-term selective forces on malaria parasite genomes.

  Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, A., Otto, T. D., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, E. T. & Jeffares, D. C., 1 Sept 2010, In: PLoS Genetics. 6, 9, p. e1001099 e1001099.

  Research output: Contribution to journal › Article › peer-review
• 2009

  An overview of the introns-first theory

  Penny, D., Hoeppner, M. P., Poole, A. M. & Jeffares, D. C., Nov 2009, In: Journal of molecular evolution. 69, 5, p. 527-540 14 p.

  Research output: Contribution to journal › Article › peer-review

• Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes

  Hoeppner, M. P., White, S., Jeffares, D. C. & Poole, A. M., 5 Nov 2009, In: Genome biology and evolution. 1, p. 420-8 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2008

  Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

  Mourier, T., Carret, C., Kyes, S., Christodoulou, Z., Gardner, P. P., Jeffares, D. C., Pinches, R., Barrell, B., Berriman, M., Griffiths-Jones, S., Ivens, A., Newbold, C. & Pain, A., 1 Feb 2008, In: Genome Research. 18, 2, p. 281-292 12 p.

  Research output: Contribution to journal › Article › peer-review

• Rapidly regulated genes are intron poor

  Jeffares, D. C., Penkett, C. J. & Bähler, J., Aug 2008, In: Trends in Genetics. 24, 8, p. 375-378 4 p.

  Research output: Contribution to journal › Article › peer-review
• 2007

  Comparative genomic analysis of three Leishmania species that cause diverse human disease

  Peacock, C. S., Seeger, K., Harris, D., Murphy, L., Ruiz, J. C., Quail, M. A., Peters, N., Adlem, E., Tivey, A., Aslett, M., Kerhornou, A., Ivens, A., Fraser, A., Rajandream, M. A., Carver, T., Norbertczak, H., Chillingworth, T., Hance, Z., Jagels, K. & Moule, S. & 22 others, Ormond, D., Rutter, S., Squares, R., Whitehead, S., Rabbinowitsch, E., Arrowsmith, C., White, B., Thurston, S., Bringaud, F., Baldauf, S. L., Faulconbridge, A., Jeffares, D., Depledge, D. P., Oyola, S. O., Hilley, J. D., Brito, L. O., Tosi, L. R. O., Barrell, B., Cruz, A. K., Mottram, J. C., Smith, D. F. & Berriman, M., Jun 2007, In: Nature genetics. 39, 7, p. 839-847 9 p.

  Research output: Contribution to journal › Article › peer-review

• Genome variation and evolution of the malaria parasite Plasmodium falciparum

  Jeffares, D. C., Pain, A., Berry, A., Cox, A. V., Stalker, J., Ingle, C. E., Thomas, A., Quail, M. A., Siebenthall, K., Uhlemann, A. C., Kyes, S., Krishna, S., Newbold, C., Dermitzakis, E. T. & Berriman, M., Jan 2007, In: Nature genetics. 39, 1, p. 120-125 6 p.

  Research output: Contribution to journal › Article › peer-review

• Outsourcing the nucleus: nuclear pore complex genes are no longer encoded in nucleomorph genomes

  Neumann, N., Jeffares, D. C. & Poole, A. M., 27 Feb 2007, In: Evolutionary bioinformatics online. 2, p. 23-34 12 p.

  Research output: Contribution to journal › Article › peer-review

• 2006

  The biology of intron gain and loss

  Jeffares, D. C., Mourier, T. & Penny, D., Jan 2006, In: Trends in Genetics. 22, 1, p. 16-22 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2004

  A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context

  Jeffares, D. C., Phillips, M. J., Moore, S. & Veit, B., 1 Mar 2004, In: Development genes and evolution. 214, 3, p. 149-158 10 p.

  Research output: Contribution to journal › Article › peer-review

• Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes

  Zagrobelny, M., Jeffares, D. C. & Arctander, P., 14 Apr 2004, In: Gene. 330, 1-2, p. 61-66 6 p.

  Research output: Contribution to journal › Article › peer-review

• Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture.

  Jacobsen, N., Nielsen, P. S., Jeffares, D. C., Eriksen, J., Ohlsson, H., Arctander, P. & Kauppinen, S., Apr 2004, In: Nucleic Acids Research. 32, 7, p. e64

  Research output: Contribution to journal › Article › peer-review

• Diversification of genes encoding mei2-like RNA binding proteins in plants

  Anderson, G. H., Alvarez, N. D. G., Gilman, C., Jeffares, D. C., Trainor, V. C. W., Hanson, M. R. & Veit, B., 1 Mar 2004, In: Plant Molecular Biology. 54, 5, p. 653-670 18 p.

  Research output: Contribution to journal › Article › peer-review
• 2003

  Eukaryotic intron loss

  Mourier, T. & Jeffares, D. C., 1 May 2003, In: Science. 300, 5624, p. 1393 1 p.

  Research output: Contribution to journal › Article › peer-review

• 2002

  JAWS: just add water system - a device for detection of nucleic acids in Martian ice caps

  Hansen, A. J., Willerslev, E., Mørk, S., Hedegaard, M. M., Rønn, R. & Jeffares, D. C., 1 Nov 2002, In: Exo-Astrobiology. 518, p. 309-312 4 p.

  Research output: Contribution to journal › Article › peer-review

• 1999

  Early evolution: prokaryotes, the new kids on the block

  Poole, A., Jeffares, D. C. & Penny, D., 1999, In: Bioessays. 21, 10, p. 880-889 10 p.

  Research output: Contribution to journal › Article › peer-review

• 1998

  Relics from the RNA world

  Jeffares, D. C., Poole, A. M. & Penny, D., 1998, In: Journal of molecular evolution. 46, 1, p. 18-36 19 p.

  Research output: Contribution to journal › Article › peer-review

• Temperature-dependence of carbon acquisition and demand in relation to shoot growth of kiwifruit (Actinidia deliciosa) vines grown in controlled environments

  Greer, D. & Jeffares, D. C., 1998, In: Australian Journal of Plant Physiology. 25, 7, p. 843-850 8 p.

  Research output: Contribution to journal › Article › peer-review

• The path from the RNA world

  Poole, A., Jeffares, D. C. & Penny, D., 1998, In: Journal of molecular evolution.

  Research output: Contribution to journal › Article › peer-review

• 1996

  PCR amplification of the fas-1 gene for the detection of virulent strains of Rhodococcus fascians

  Stange, R., Jeffares, D. C., Young, C., Scott, D., Eason, J. & Jameson, P., 1996, In: Molecular Plant Pathology. 45, 3, p. 407-417 11 p.

  Research output: Contribution to journal › Article › peer-review

• 1995

  Pre-rRNA processing and the path from the RNA world

  Jeffares, D. C., Poole, A. M. & Penny, D., 1 Aug 1995, In: Trends in biochemical sciences. 20, 8, p. 298-299 2 p.

  Research output: Contribution to journal › Article › peer-review