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Items: 33

1.

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

Coppée R, Jeffares DC, Miteva MA, Sabbagh A, Clain J.

Sci Rep. 2019 Jul 23;9(1):10675. doi: 10.1038/s41598-019-47034-6.

2.

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

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW.

Mol Biol Evol. 2019 Sep 1;36(9):1975-1989. doi: 10.1093/molbev/msz126.

3.

Fitness Landscape of the Fission Yeast Genome.

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.

Mol Biol Evol. 2019 Aug 1;36(8):1612-1623. doi: 10.1093/molbev/msz113.

4.

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

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.

EBioMedicine. 2018 Oct;36:83-91. doi: 10.1016/j.ebiom.2018.09.029. Epub 2018 Sep 27.

5.

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

Ellis DA, Mustonen V, Rodríguez-López M, Rallis C, Malecki M, Jeffares DC, Bähler J.

Genetics. 2018 Oct;210(2):733-744. doi: 10.1534/genetics.118.301262. Epub 2018 Aug 2.

6.

The natural diversity and ecology of fission yeast.

Jeffares DC.

Yeast. 2018 Mar;35(3):253-260. doi: 10.1002/yea.3293. Epub 2018 Feb 8. Review.

7.

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

Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ.

Nat Commun. 2017 Jan 24;8:14061. doi: 10.1038/ncomms14061.

8.

Spotsizer: High-throughput quantitative analysis of microbial growth.

Bischof L, Převorovský M, Rallis C, Jeffares DC, Arzhaeva Y, Bähler J.

Biotechniques. 2016 Oct 1;61(4):191-201. doi: 10.2144/000114459.

9.

Does the Ribosome Challenge our Understanding of the RNA World?

Poole AM, Jeffares DC, Hoeppner MP, Penny D.

J Mol Evol. 2016 Jan;82(1):1-4. No abstract available.

PMID:
27148607
10.

Selected Schizosaccharomyces pombe Strains Have Characteristics That Are Beneficial for Winemaking.

Benito Á, Jeffares D, Palomero F, Calderón F, Bai FY, Bähler J, Benito S.

PLoS One. 2016 Mar 23;11(3):e0151102. doi: 10.1371/journal.pone.0151102. eCollection 2016.

11.

Does the Ribosome Challenge our Understanding of the RNA World?

Poole AM, Jeffares DC, Hoeppner MP, Penny D.

J Mol Evol. 2016 Jan;82(1):1-4. doi: 10.1007/s00239-015-9720-x. Epub 2015 Nov 18.

PMID:
26582049
12.

The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J.

Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215. Epub 2015 Feb 9.

13.

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

Jeffares DC, Tomiczek B, Sojo V, dos Reis M.

Methods Mol Biol. 2015;1201:65-90. doi: 10.1007/978-1-4939-1438-8_4.

PMID:
25388108
14.

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

Bitton DA, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat S, Bähler J.

Genome Res. 2014 Jul;24(7):1169-79. doi: 10.1101/gr.166819.113. Epub 2014 Apr 7.

15.

PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.

Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C, Nordborg M.

PLoS One. 2011 Jan 5;6(1):e15292. doi: 10.1371/journal.pone.0015292.

16.

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

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.

PLoS Genet. 2010 Sep 9;6(9):e1001099. doi: 10.1371/journal.pgen.1001099.

17.

An overview of the introns-first theory.

Penny D, Hoeppner MP, Poole AM, Jeffares DC.

J Mol Evol. 2009 Nov;69(5):527-40. doi: 10.1007/s00239-009-9279-5. Epub 2009 Sep 24.

PMID:
19777149
18.

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

Hoeppner MP, White S, Jeffares DC, Poole AM.

Genome Biol Evol. 2009 Nov 5;1:420-8. doi: 10.1093/gbe/evp045.

19.

Rapidly regulated genes are intron poor.

Jeffares DC, Penkett CJ, Bähler J.

Trends Genet. 2008 Aug;24(8):375-8. doi: 10.1016/j.tig.2008.05.006. Epub 2008 Jun 27. Erratum in: Trends Genet. 2008 Oct;24(10):488.

PMID:
18586348
20.

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

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 Res. 2008 Feb;18(2):281-92. Epub 2007 Dec 20.

21.

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

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 MA, 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 LR, Barrell B, Cruz AK, Mottram JC, Smith DF, Berriman M.

Nat Genet. 2007 Jul;39(7):839-47. Epub 2007 Jun 17.

22.

Genome variation and evolution of the malaria parasite Plasmodium falciparum.

Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann AC, Kyes S, Krishna S, Newbold C, Dermitzakis ET, Berriman M.

Nat Genet. 2007 Jan;39(1):120-5. Epub 2006 Dec 10. Erratum in: Nat Genet. 2007 Apr;39(4):567. Nat Genet. 2007 Mar;39(3):422.

23.

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

Neumann N, Jeffares DC, Poole AM.

Evol Bioinform Online. 2007 Feb 27;2:23-34.

24.

The biology of intron gain and loss.

Jeffares DC, Mourier T, Penny D.

Trends Genet. 2006 Jan;22(1):16-22. Epub 2005 Nov 14.

PMID:
16290250
25.

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

Anderson GH, Alvarez ND, Gilman C, Jeffares DC, Trainor VC, Hanson MR, Veit B.

Plant Mol Biol. 2004 Mar;54(5):653-70.

PMID:
15356386
26.

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

Jacobsen N, Nielsen PS, Jeffares DC, Eriksen J, Ohlsson H, Arctander P, Kauppinen S.

Nucleic Acids Res. 2004 Apr 19;32(7):e64.

27.

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

Zagrobelny M, Jeffares DC, Arctander P.

Gene. 2004 Apr 14;330:61-6.

PMID:
15087124
28.

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

Jeffares DC, Phillips MJ, Moore S, Veit B.

Dev Genes Evol. 2004 Mar;214(3):149-58. Epub 2004 Feb 17.

PMID:
14986133
29.

Eukaryotic intron loss.

Mourier T, Jeffares DC.

Science. 2003 May 30;300(5624):1393. No abstract available.

30.

Early evolution: prokaryotes, the new kids on the block.

Poole A, Jeffares D, Penny D.

Bioessays. 1999 Oct;21(10):880-9. Review.

PMID:
10497339
31.

Relics from the RNA world.

Jeffares DC, Poole AM, Penny D.

J Mol Evol. 1998 Jan;46(1):18-36. Review.

PMID:
9419222
32.

The path from the RNA world.

Poole AM, Jeffares DC, Penny D.

J Mol Evol. 1998 Jan;46(1):1-17. Review.

PMID:
9419221
33.

Pre-rRNA processing and the path from the RNA world.

Jeffares DC, Poole AM, Penny D.

Trends Biochem Sci. 1995 Aug;20(8):298-9. No abstract available.

PMID:
7545338

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