Publications

Jeffares Group at the University of York

Summaries

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Recent

Latest:[59] Thiam R, Ceballos MS, Beneke T, Kuk N, Pasquier G, Crobu L, Jeffares DC, Vergnes B, Barckmann B, Sterkers Y. A novel Leishmania infantum reference strain for gene editing and the study of visceral leishmaniasis. PLoS One 2025;20:e0327390

[58] Batista LFS, Sandoval Pacheco CM, Araujo Flores GV, Ferreira FM, Gonçalves ANA, Sosa-Ochoa W, da Matta VD, Gomes C, Zúniga C, Corbett CP, Jeffares D, Nakaya HI, Silveira FT, Laurenti M. Molecular insights into cell-mediated immunity in atypical non-ulcerated cutaneous leishmaniasis. Microorganisms 2025;13:413

[57] Reis-Cunha JL, Grace CA, Ahmed S, Harnqvist SE, Lynch CM, Boité MC, Barcellos G, Lachaud L, Bastien P, Munt H, Mottram JC, Cupolillo E, Jeffares DC. The global dispersal of visceral leishmaniasis occurred within human history. bioRxiv 2024:2024.10. 30.621037

[56] Reis-Cunha JL, Jeffares DC. Detecting complex infections in trypanosomatids using whole genome sequencing. BMC Genomics 2024;25:1011

Highly cited

Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017 Jan 24;8(1):14061. Available from: http://dx.doi.org/10.1038/ncomms14061

Jeffares DC, Penkett CJ, Bähler J. Rapidly regulated genes are intron poor. Trends Genet. 2008 Aug;24(8):375–8. https://doi.org/10.1016/j.tig.2008.05.006

Jeffares, Daniel C., Charalampos Rallis, Adrien Rieux, Doug Speed, Martin Převorovský, Tobias Mourier, Francesc X. Marsellach, et al. 2015. The Genomic and Phenotypic Diversity of Schizosaccharomyces Pombe. Nature Genetics 47, no. 3 (March): 235–41. https://doi.org/10.1038/ng.3215

Jeffares, Daniel C., Arnab Pain, Andrew Berry, Anthony V. Cox, James Stalker, Catherine E. Ingle, Alan Thomas, et al. 2007. Genome Variation and Evolution of the Malaria Parasite Plasmodium Falciparum. Nature Genetics 39, no. 1 (January): 120–25. https://doi.org/10.1038/ng1931

Mourier, Tobias, and Daniel C. Jeffares. 2003. Eukaryotic Intron Loss. Science (New York, N.Y.) 300, no. 5624 (May): 1393. https://www.science.org/doi/pdf/10.1126/science.1080559

The full list

[59] Thiam R, Ceballos MS, Beneke T, Kuk N, Pasquier G, Crobu L, Jeffares DC, Vergnes B, Barckmann B, Sterkers Y. A novel Leishmania infantum reference strain for gene editing and the study of visceral leishmaniasis. PLoS One 2025;20:e0327390

[58] Batista LFS, Sandoval Pacheco CM, Araujo Flores GV, Ferreira FM, Gonçalves ANA, Sosa-Ochoa W, da Matta VD, Gomes C, Zúniga C, Corbett CP, Jeffares D, Nakaya HI, Silveira FT, Laurenti M. Molecular insights into cell-mediated immunity in atypical non-ulcerated cutaneous leishmaniasis. Microorganisms 2025;13:413

[57] Reis-Cunha JL, Grace CA, Ahmed S, Harnqvist SE, Lynch CM, Boité MC, Barcellos G, Lachaud L, Bastien P, Munt H, Mottram JC, Cupolillo E, Jeffares DC. The global dispersal of visceral leishmaniasis occurred within human history. bioRxiv 2024:2024.10. 30.621037

[56] Reis-Cunha JL, Jeffares DC. Detecting complex infections in trypanosomatids using whole genome sequencing. BMC Genomics 2024;25:1011

[55] Nicoll AG, Ford H, Grace CA, Reis-Cunha JL, Jeffares DC, Constable GWA. Estimating the rate of sexual reproduction and the inbreeding rate in Leishmania. bioRxiv 2024:2024.10. 15.618469. https://doi.org/10.1101/2024.10.15.618469.

[54] Smit SJ, Whitehead C, James SR, Jeffares DC, Godden G, Peng D, Sun H, Lichman BR. Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata. G3: Genes, Genomes, Genetics 2024:jkae172

[53] Reis-Cunha JL, Pimenta-Carvalho SA, Almeida LV, Coqueiro-Dos-Santos A, Marques CA, Black JA, Damasceno J, McCulloch R, Bartholomeu DC, Jeffares DC. Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites. Genome Res 2024;34:441–53

[52] Dirkx L, Van Acker SI, Nicolaes Y, Cunha JLR, Ahmad R, Hendrickx R, Caljon B, Imamura H, Ebo DG, Jeffares DC, Sterckx YG-J, Maes L, Hendrickx S, Caljon G. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites. PLoS Pathog 2024;20:e1012181

[51] Mbuchi M, Hogg K, Osuna F, Jeffares D, Matano D, Chebotibin J, Ichugu C, Biwott W, Chebet E, Cunha J, Wiggins R, Kaye P, Mbui J. PA-682 Overcoming diverse challenges associated with innovative multicountry collaborative initiatives: the Kenyan experience of the Prev_PKDL project. BMJ Global Health: 17 December 2023

[50] Rogerio LA, Takahashi TY, Cardoso L, Takamiya NT, de Melo EV, de Jesus AR, de Oliveira FA, Forrester S, Jeffares DC, da Silva JS, Ribeiro JM, Almeida RP, Maruyama SR. 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. Int J Infect Dis 2023;133:85–8

[49] Pilling OA, Reis-Cunha JL, Grace CA, Berry ASF, Mitchell MW, Yu JA, Malekshahi CR, Krespan E, Go CK, Lombana C, Song YS, Amorim CF, Lago AS, Carvalho LP, Carvalho EM, Brisson D, Scott P, Jeffares DC, Beiting DP. Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies. PLoS Pathog 2023;19:e1011230

[48] Grace CA, Sousa Carvalho KS, Sousa Lima MI, Costa Silva V, Reis-Cunha JL, Brune MJ, Forrester S, Pedrozo E Silva de Azevedo C de M, Costa DL, Speed D, Mottram JC, Jeffares DC, Costa CHN. Parasite genotype is a major predictor of mortality from visceral leishmaniasis. MBio 2022;13:e0206822

[47] Grace CA, Reis-Cunha J, Jeffares D. Strong effects of parasite genotype on drug susceptibility in the Indian subcontinent. bioRxiv 2022

[46] Farnham E, Stoycheva M, Elphinstone J, Jeffares D, Friman V. Phenotypic diversity of a clonal Ralstonia solanacearum pathogen lineage is explained by accessory genome variation. Access Microbiol 2022;4:o0197

[45] Sellers GS, Jeffares DC, Lawson B, Prior T, Lunt DH. Identification of individual root-knot nematodes using low coverage long-read sequencing. PLoS One 2021;16:e0253248

[44] Grace CA, Forrester S, Silva VC, Carvalho KSS, Kilford H, Chew YP, James S, Costa DL, Mottram JC, Costa CC, Jeffares DC. Candidates for Balancing Selection in Leishmania donovani Complex Parasites. Genome Biol Evol 2021;13:evab265

[43] Harnqvist SE, Grace CA, Jeffares DC. Variables influencing differences in sequence conservation in the fission yeast Schizosaccharomyces pombe. J Mol Evol 2021;89:601–10

[42] Mourier T, de Alvarenga DAM, Kaushik A, de Pina-Costa A, Douvropoulou O, Guan Q, Guzmán-Vega FJ, Forrester S, de Abreu FVS, Júnior CB, de Souza Junior JC, Moreira SB, Hirano ZMB, Pissinatti A, Ferreira-da-Cruz M de F, de Oliveira RL, Arold ST, Jeffares DC, Brasil P, de Brito CFA, Culleton R, Daniel-Ribeiro CT, Pain A. The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching. BMC Biol 2021;19:219

[41] Ellis DA, Reyes-Martín F, Rodríguez-López M, Cotobal C, Sun X-M, Saintain Q, Jeffares DC, Marguerat S, Tallada VA, Bähler J. R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements. PLoS Genet 2021;17:e1009784

[40] Hendrickx S, Reis-Cunha J, Forrester S, Jeffares D, Caljon G. Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms. Microorganisms 2021;9:1546

[39] Cao C, He J, Mak L, Perera D, Kwok D, Wang J, Li M, Mourier T, Gavriliuc S, Greenberg M, Morrissy A, Sycuro L, Yang G, Jeffares D, Long Q. Reconstruction of microbial haplotypes by integration of statistical and physical linkage in scaffolding. Mol Biol Evol 2021;38:2660–72

[37] Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral admixture is the main determinant of global biodiversity in fission yeast. Mol Biol Evol 2019;36:1975–89

[36] Grech L, Jeffares DC, Sadée CY, Rodríguez-López M, Bitton DA, Hoti M, Biagosch C, Aravani D, Speekenbrink M, Illingworth CJR, Schiffer PH, Pidoux AL, Tong P, Tallada VA, Allshire R, Levin HL, Bähler J. Fitness landscape of the fission yeast genome. Mol Biol Evol 2019;36:1612–23.

[35] Coppée R, Jeffares DC, Miteva MA, Sabbagh A, Clain J. Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13. Scientific Reports 2019;9:10675.

[34] Carnielli JBT, Crouch K, Forrester S, Silva VC, Carvalho SFG, Damasceno JD, Brown E, Dickens NJ, Costa DL, Costa CHN, Dietze R, Jeffares DC, Mottram JC. A Leishmania infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis. EBioMedicine 2018;36:83–91

[33] Ellis DA, Mustonen V, Rodríguez-López M, Rallis C, Malecki M, Jeffares DC, Bähler J. Uncovering natural longevity alleles from intercrossed pools of aging fission yeast cells. Genetics 2018;210:733–44

[32] Jeffares DC. The natural diversity and ecology of fission yeast. Yeast 2018;35:253–60

[31] Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun 2017;8:14061

[30] Benito Á, Jeffares D, Palomero F, Calderón F, Bai F-Y, Bähler J, Benito S. Selected Schizosaccharomyces pombe strains have characteristics that are beneficial for winemaking. PLoS One 2016;11:e0151102

[29] Poole AM, Jeffares DC, Hoeppner MP, Penny D. Does the Ribosome Challenge our Understanding of the RNA World? J Mol Evol 2016;82:1–4

[28] Jeffares D, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach F-X, Iqbal Z, Lau W, Cheng TMK, Pracana R, Mülleder M, Lawson JLD, Chessel A, Bala S, Hellenthal G, O’Fallon BD, Keane TM, Simpson J, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JEE, van Trigt L, Jeffery L, Li J, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Salas RC, Ralser M, Maniatis N, Balding D, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet 2015;47:235–41

[27] Jeffares DC, Tomiczek B, Sojo V, dos Reis M. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods Mol Biol 2015;1201:65–90

[26] Bitton DA, Rallis C, Jeffares D, Smith GC, Chen YYC, Codlin S, Marguerat S, Bähler J. LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. Genome Res 2014;24:1169–79

[25] Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C, Nordborg M. PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing. PLoS One 2011;6:e15292

[24] Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC. Long- and short-term selective forces on malaria parasite genomes. PLoS Genet 2010;6:e1001099

[23] Penny D, Hoeppner MP, Poole AM, Jeffares DC. An overview of the introns-first theory. J Mol Evol 2009;69:527–40

[22] Hoeppner MP, White S, Jeffares DC, Poole AM. Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes. Genome Biology and Evolution 2009;1:420–8

[21] Jeffares DC, Penkett CJ, Bähler J. Rapidly regulated genes are intron poor. Trends Genet 2008;24:375–8

[20] Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Res 2008;18:281–92

[19] Mourier T, Jeffares DC. Intron Loss and Gain. Encyclopedia of Life Sciences 2007

[18] Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, 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, Ormond D, Rutter S, Squares R, Whitehead S, Rabbinowitsch E, Arrowsmith C, White B, Thurston S, Bringaud F, Baldauf SL, Faulconbridge A, Jeffares D, Depledge DP, Oyola SO, Hilley JD, Brito LO, Tosi LRO, Barrell B, Cruz AK, Mottram JC, Smith DF, Berriman M. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet 2007;39:839–47

[17] Jeffares D, Pain A, Berry A, Cox A, Stalker J, Ingle CE, Thomas A, Quail M, Siebenthall KT, Uhlemann A, Kyes S, Krishna S, Newbold C, Dermitzakis E, Berriman M. Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet 2007;39:120–5

[16] Jeffares DC, Mourier T, Penny D. The origin of introns 2006;1:16–22.

[15] Neumann N, Jeffares D, Poole A. Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes. Evolutionary Bioinformatics Online 2006;2:23–34

[14] Jeffares DC, Mourier T, Penny D. The biology of intron gain and loss. Trends Genet 2006;22:16–22

[13] Kauppinen S, Alsbo C, Nielsen P, Jeffares D, Mourier T, Mork S, Arctander P, Tommerup N, Tolstrup N, Vissing H. Oligonucleotides useful for detecting and analyzing nucleic acids of interest. 20040219565:A1, 2004.

[12] Zagrobelny M, Jeffares DC, Arctander P. Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes. Gene 2004;330:61–6. https://doi.org/10.1016/j.gene.2004.01.003.

[11] Anderson GH, Alvarez N, Gilman C, Jeffares D, Trainor V, Hanson M, Veit B. Diversification of genes encoding Mei2-like RNA binding proteins in plants. Plant Mol Biol 2004;54:653–70

[10] Jeffares D, Phillips M, Moore S, Veit B. A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context. Dev Genes Evol 2004;214:149–58

[9] Jacobsen N, Nielsen PS, Jeffares DC. Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyanate‐lysed cell extracts using locked nucleic acid‐oligo(T) capture. Nucleic Acids 2004.

[8] Mourier T, Jeffares DC. Eukaryotic intron loss. Science 2003;300:1393

[7] Hansen AJ, Willerslev E, Mørk S, Hedegaard MM, Rønn R, Jeffares DC. JAWS: just add water system-a device for detection of nucleic acids in Martian ice caps. Proceedings of the Second European Workshop on Exo/Astrobiology, Graz, Austria, ESA SP-518, pp. 309-311

[6] Jeffares D, Poole A. Were bacteria the first forms of life on Earth? Action Bioscience

[5] Poole A, Jeffares D, Penny D. Early evolution: prokaryotes, the new kids on the block. Bioessays 1999;21:880–9

[4] Poole AM, Jeffares DC, Penny D. The path from the RNA world. J Mol Evol 1998;46:1–17

[3] Jeffares DC, Poole AM, Penny D. Relics from the RNA world. J Mol Evol 1998;46:18–36

[2] Greer DH, Jeffares D. Temperature-dependence of carbon acquisition and demand in relation to shoot growth of kiwifruit (Actinidia deliciosa) vines grown in controlled environments. Funct Plant Biol 1998;25:843

[1] Jeffares DC, Poole AM, Penny D. Pre-rRNA processing and the path from the RNA world. Trends Biochem Sci 1995;20:298–9