Summaries:  Google Scholar or Europe PMC

key:  more than 100 citations.  » new, not yet highly cited

Selected Publications

2023: » 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 [Internet]. 2023 May 12; Available from: | abstract | PDF

2023: » 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 Mar;19(3):e1011230. DOI | abstract | PDF

2022: » Strong effects of parasite genotype on drug susceptibility in the Indian subcontinent
Cooper Grace, João Reis-Cunha, Daniel Jeffares. bioRxiv 2022.08.17.504263; doi:

2022: » Grace, Cooper Alastair and Carvalho, Kátia Silene Sousa and Lima, Mayara Ingrid Sousa and Costa Silva, Vladimir and Reis Cuhna, Joâo Luís and Brune, Matthew J. and Forrester, Sarah J. and Pedrozo e Silva de Azevedo, Conceição de Maria and Costa, Dorcas Lamounier and Speed, Doug and Mottram, Jeremy C. and Jeffares, Daniel C. and Costa, Carlos H. N., Leishmania infantum Genotype is a Major Factor in Visceral Leishmaniasis Mortality in Brazil.
MBio (in press). DOI: | abstract | PDF.

2021: » Cooper Alastair Grace, Sarah Forrester, Vladimir Costa Silva, Katia Silene Sousa Carvalho, Hannah Kilford, Yen Peng Chew, Sally James, Dorcas L. Costa, Jeremy C. Mottram, Carlos C. H. N. Costa, and Daniel C. Jeffares (2021). Candidates for Balancing Selection in Leishmania donovani Complex Parasites. Genome Biol. Evol. 13(12) DOI: 10.1093/gbe/evab265  | abstract | pdf

2021: » Harnqvist SE, Grace CA, Jeffares DC. Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe. J Mol Evol. 2021. doi:10.1007/s00239-021-10028-y | abstract | pdf

2021: » T. Mourier, D. A. M. de Alvarenga, A. Kaushik, A. de Pina-Costa, O. Douvropoulou, Q. Guan, F. J. Guzmán-Vega, S. Forrester, F. V. S. de Abreu, C. B. Júnior, J. C. de Souza Junior, S. B. Moreira, Z. M. B. Hirano, A. Pissinatti, M. de F. Ferreira-da-Cruz, R. L. de Oliveira, S. T. Arold, D. C. Jeffares, P. Brasil, C. F. A. de Brito, R. Culleton, C. T. Daniel-Ribeiro, A. Pain, The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching. BMC Biol. 19, 219 (2021). | abstract | pdf

2021: » David A. Ellis, Félix Reyes-Martín, María Rodríguez-López, Cristina Cotobal, Xi-Ming Sun, Daniel C. Jeffares, Samuel Marguerat, Víctor A. Tallada, Jürg Bähler (2021). R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements. PLOS Genetics 31 Aug 2021, 17(8):e1009784 | abstract | pdf

2021: » Sarah Hendrickx,João Luís Reis-Cunha,Sarah Forrester, Daniel C. Jeffares, Guy Caljon (2021). Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms. Microorganisms 2021, 9(8), 1546; | abstract | pd.

2021: » Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, Sorana Morrissy, Laura Sycuro, Guang Yang, Daniel Jeffares, Quan Long (2021). Reconstruction of microbial haplotypes by integration of statistical and physical linkage in scaffolding. Molecular Biology and Evolution 38(6):2660–2672. | abstract | pdf

» Romain Coppée, Daniel C. Jeffares, Audrey Sabbagh, Jérôme Clain (2019). Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K1. Scientific Reports Jul 23;9(1):10675. doi: 10.1038/s41598-019-47034-6  | abstract PDF

» Leanne Grech, Daniel C Jeffares, Christoph Yves Sadee, Maria Rodriguez-Lopez, Danny Asher Bitton, Mimoza Hoti, Caroline Biagosch, Dimitra Aravani, Maarten Speekenbrink, Christopher JR Illingworth, Philipp H Schiffer, Alison L Pidoux, Pin Tong, Victor A Tallada, Robin Allshire, Henry L Levin, Jurg Bahler (2019). Fitness Landscape of the Fission Yeast Genome. Molecular Biology and Evolution 36(8): 1612-1623. doi:10.1093/molbev/msz113. abstract | PDF | data

» Juliana B. T. Carnielli, Kathryn Crouch,  Sarah Forrester,  Vladimir Costa Silva, Sílvio F. G. Carvalho, Jeziel D. Damasceno, Elaine Brown, Nicholas J. Dickens, Dorcas L. Costa, Carlos H. N. Costa, Reynaldo Dietze, Daniel C. Jeffares, Jeremy C. Mottram (2018). A Leishmania infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis. EBiomedicine 2018  abstract  | PDF

» David A. Ellis, Ville Mustonen, María Rodríguez-López, Charalampos Rallis, Michał Malecki, Daniel C. Jeffares and Jürg Bähler. Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. Genetics 301262.2018 (2018). doi:10.1534/genetics.118.301262 | abstract | PDF

» Jeffares DC (2017). The natural diversity and ecology of fission yeast. Yeast doi:10.1002/yea.3293 | abstract | PDF 

» Jeffares DC, Jolly C, Hoti M, Speed D, Liam Shaw, Rallis D, Francois Balloux, Dessimoz C, Bähler J, Sedlazeck F (2016). Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications 8:14061. doi:10.1038/ncomms14061. abstract | PDF 

» Leanne Bischof, Martin Převorovský, Charalampos Rallis, Daniel C. Jeffares, Yulia Arzhaeva and Jürg Bähler (2016). Spotsizer: High-throughput quantitative analysis of microbial growth. BioTechniques 61(4):191–20. abstract | PDF | Get the software

» Benito A, Jeffares DC, Palomero F, Calderón F, Bai F-Y, Bähler J, Benito S (2016). Selected Schizosaccharomyces pombe strains have characteristics that are beneficial for winemaking. PLoS ONE 11(3): e0151102. doi:10.1371/journal.pone.0151102. abstract | PDF

» Poole AM,  Jeffares DC, Hoeppner M & Penny D (2015). Does the ribosome challenge our understanding of the RNA World? Journal of Molecular Evolution 82(1):1-4. Abstract | PDF

» Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, [more authors], Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J (2015). The Genomic and Phenotypic Diversity of Schizosaccharomyces pombe. Nature Genetics 47(3):235-241. doi: 10.1038/ng.3215. abstract | PDF 

» Bitton DA, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat S, Bähler J (2014). LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. Genome Res. 24(7):1169-79. abstract | PDF

» 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. (2010). Long- and short-term selective forces on malaria parasite genomes. PLOS Genetics 6(9): e1001099. abstract PDF

Jeffares DC, Penkett CJ, Bähler J (2008). Rapidly regulated genes are intron poor. Trends in Genetics24(8): 375-378. abstractPDF

 Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall, K, Uhlemann A-C, Kyes S, Krishna S, Newbold C, Dermitzakis ET, Berriman M (2007). Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nature Genetics 39(1): 120-125. abstractPDF

 Peacock et al. (2007). Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nature Genetics 39(7): 839-847. abstractPDF

 Jeffares DC,  Mourier T, and Penny, D (2006). The biology of intron gain and loss. Trends in Genetics 22(1):16-22.  abstractPDF

 Mourier T and Jeffares DC (2003). Eukaryotic intron loss. Science 300 (5624): 1393. abstractPDF

 Poole A, Jeffares DC and Penny D (1998). The path from the RNA world. Journal of Molecular Evolution 46(1):1-17. abstractPDF

 Jeffares DC, Poole AM, and Penny D (1998). Relics from the RNA world. Journal of Molecular Evolution 46(1):18–36. abstractPDF