Search Results - "Jeffares, Daniel C."

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast by Jeffares, Daniel C., Jolly, Clemency, Hoti, Mimoza, Speed, Doug, Shaw, Liam, Rallis, Charalampos, Balloux, Francois, Dessimoz, Christophe, Bähler, Jürg, Sedlazeck, Fritz J.

“…Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic…”
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A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome by Jeffares, Daniel C, Tomiczek, Bartłomiej, Sojo, Victor, dos Reis, Mario

“…The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding…”
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Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast by Tusso, Sergio, Nieuwenhuis, Bart P S, Sedlazeck, Fritz J, Davey, John W, Jeffares, Daniel C, Wolf, Jochen B W

“…Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that…”
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Identification of individual root-knot nematodes using low coverage long-read sequencing by Sellers, Graham S, Jeffares, Daniel C, Lawson, Bex, Prior, Tom, Lunt, David H

“…Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are…”
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R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements by Ellis, David A, Reyes-Martín, Félix, Rodríguez-López, María, Cotobal, Cristina, Sun, Xi-Ming, Saintain, Quentin, Jeffares, Daniel C, Marguerat, Samuel, Tallada, Víctor A, Bähler, Jürg

“…Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a…”
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Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites by Dirkx, Laura, Van Acker, Sara I, Nicolaes, Yasmine, Cunha, João Luís Reis, Ahmad, Rokaya, Hendrickx, Rik, Caljon, Ben, Imamura, Hideo, Ebo, Didier G, Jeffares, Daniel C, Sterckx, Yann G-J, Maes, Louis, Hendrickx, Sarah, Caljon, Guy

“…Addressing the challenges of quiescence and post-treatment relapse is of utmost importance in the microbiology field. This study shows that Leishmania infantum…”
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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 by Rogerio, Luana Aparecida, Takahashi, Talita Yuri, Cardoso, Luria, Takamiya, Nayore Tamie, de Melo, Enaldo Vieira, de Jesus, Amelia Ribeiro, de Oliveira, Fabricia Alvisi, Forrester, Sarah, Jeffares, Daniel C., da Silva, João Santana, Ribeiro, José Marcos, Almeida, Roque Pacheco, Maruyama, Sandra Regina

“…•Severe visceral leishmaniasis with non-ulcerated cutaneous leishmaniasis.•A Crithidia-related parasite was isolated from bone marrow aspirate and…”
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LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq by Bitton, Danny A, Rallis, Charalampos, Jeffares, Daniel C, Smith, Graeme C, Chen, Yuan Y C, Codlin, Sandra, Marguerat, Samuel, Bähler, Jürg

“…Both canonical and alternative splicing of RNAs are governed by intronic sequence elements and produce transient lariat structures fastened by branch points…”
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Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells by Ellis, David A, Mustonen, Ville, Rodríguez-López, María, Rallis, Charalampos, Malecki, Michał, Jeffares, Daniel C, Bähler, Jürg

“…Quantitative traits often show large variation caused by multiple genetic factors . One such trait is the chronological lifespan of non-dividing yeast cells,…”
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Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies by Pilling, Olivia A, Reis-Cunha, João L, Grace, Cooper A, Berry, Alexander S F, Mitchell, Matthew W, Yu, Jane A, Malekshahi, Clara R, Krespan, Elise, Go, Christina K, Lombana, Cláudia, Song, Yun S, Amorim, Camila F, Lago, Alexsandro S, Carvalho, Lucas P, Carvalho, Edgar M, Brisson, Dustin, Scott, Phillip, Jeffares, Daniel C, Beiting, Daniel P

“…In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of…”
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Parasite Genotype Is a Major Predictor of Mortality from Visceral Leishmaniasis by Grace, Cooper Alastair, Sousa Carvalho, Kátia Silene, Sousa Lima, Mayara Ingrid, Costa Silva, Vladimir, Reis-Cunha, João Luís, Brune, Matthew J, Forrester, Sarah, Pedrozo E Silva de Azevedo, Conceição de Maria, Costa, Dorcas Lamounier, Speed, Doug, Mottram, Jeremy C, Jeffares, Daniel C, Costa, Carlos H N

“…Visceral leishmaniasis (VL) is a potentially fatal disease caused mainly by Leishmania infantum in South America and Leishmania donovani in Asia and Africa…”
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Spotsizer: High-throughput quantitative analysis of microbial growth by Bischof, Leanne, Převorovský, Martin, Rallis, Charalampos, Jeffares, Daniel C, Arzhaeva, Yulia, Bähler, Jürg

“…Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although…”
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Genome variation and evolution of the malaria parasite Plasmodium falciparum by Dermitzakis, Emmanouil T, Berriman, Matthew, Jeffares, Daniel C, Pain, Arnab, Berry, Andrew, Cox, Anthony V, Stalker, James, Ingle, Catherine E, Thomas, Alan, Quail, Michael A, Siebenthall, Kyle, Uhlemann, Anne-Catrin, Kyes, Sue, Krishna, Sanjeev, Newbold, Chris

“…Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and…”
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Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms by Hendrickx, Sarah, Reis-Cunha, João Luís, Forrester, Sarah, Jeffares, Daniel C, Caljon, Guy

“…The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug…”
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PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing by Long, Quan, Jeffares, Daniel C, Zhang, Qingrun, Ye, Kai, Nizhynska, Viktoria, Ning, Zemin, Tyler-Smith, Chris, Nordborg, Magnus

“…With the advance of next-generation sequencing (NGS) technologies, increasingly ambitious applications are becoming feasible. A particularly powerful one is…”
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The natural diversity and ecology of fission yeast by Jeffares, Daniel C.

“…While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I…”
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Long- and short-term selective forces on malaria parasite genomes by Nygaard, Sanne, Braunstein, Alexander, Malsen, Gareth, Van Dongen, Stijn, Gardner, Paul P, Krogh, Anders, Otto, Thomas D, Pain, Arnab, Berriman, Matthew, McAuliffe, Jon, Dermitzakis, Emmanouil T, Jeffares, Daniel C

“…Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ∼23 Mb…”
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Rapidly regulated genes are intron poor by Jeffares, Daniel C, Penkett, Christopher J, Bähler, Jürg

“…We show that genes with rapidly changing expression levels in response to stress contain significantly lower intron densities in yeasts, thale cress and mice…”
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Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13 by Coppée, Romain, Jeffares, Daniel C., Miteva, Maria A., Sabbagh, Audrey, Clain, Jérôme

“…Numerous mutations in the Plasmodium falciparum Kelch13 (K13) protein confer resistance to artemisinin derivatives, the current front-line antimalarial drugs…”
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Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites by Reis-Cunha, João L, Pimenta-Carvalho, Samuel A, Almeida, Laila V, Coqueiro-Dos-Santos, Anderson, Marques, Catarina A, Black, Jennifer A, Damasceno, Jeziel, McCulloch, Richard, Bartholomeu, Daniella C, Jeffares, Daniel C

“…Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal…”
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