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Quality control of next-generation sequencing data without a reference.

Frontiers in genetics

Trivedi UH, Cézard T, Bridgett S, Montazam A, Nichols J, Blaxter M, Gharbi K.
PMID: 24834071
Front Genet. 2014 May 06;5:111. doi: 10.3389/fgene.2014.00111. eCollection 2014.

Next-generation sequencing (NGS) technologies have dramatically expanded the breadth of genomics. Genome-scale data, once restricted to a small number of biomedical model organisms, can now be generated for virtually any species at remarkable speed and low cost. Yet non-model...

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Trivedi UH, Cézard T, Bridgett S, et al. Quality control of next-generation sequencing data without a reference. Front Genet. 2014;5:111doi: 10.3389/fgene.2014.00111.
Trivedi, U. H., Cézard, T., Bridgett, S., Montazam, A., Nichols, J., Blaxter, M., & Gharbi, K. (2014). Quality control of next-generation sequencing data without a reference. Frontiers in genetics, 5111. https://doi.org/10.3389/fgene.2014.00111
Trivedi, Urmi H, et al. "Quality control of next-generation sequencing data without a reference." Frontiers in genetics vol. 5 (2014): 111. doi: https://doi.org/10.3389/fgene.2014.00111
Trivedi UH, Cézard T, Bridgett S, Montazam A, Nichols J, Blaxter M, Gharbi K. Quality control of next-generation sequencing data without a reference. Front Genet. 2014 May 06;5:111. doi: 10.3389/fgene.2014.00111. eCollection 2014. PMID: 24834071; PMCID: PMC4018527.
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Of monkeys and men: immunomic profiling of sera from humans and non-human primates resistant to schistosomiasis reveals novel potential vaccine candidates.

Frontiers in immunology

Pearson MS, Becker L, Driguez P, Young ND, Gaze S, Mendes T, Li XH, Doolan DL, Midzi N, Mduluza T, McManus DP, Wilson RA, Bethony JM, Nausch N, Mutapi F, Felgner PL, Loukas A.
PMID: 25999951
Front Immunol. 2015 May 05;6:213. doi: 10.3389/fimmu.2015.00213. eCollection 2015.

Schistosoma haematobium affects more than 100 million people throughout Africa and is the causative agent of urogenital schistosomiasis. The parasite is strongly associated with urothelial cancer in infected individuals and as such is designated a group I carcinogen by...

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Pearson MS, Becker L, Driguez P, et al. Of monkeys and men: immunomic profiling of sera from humans and non-human primates resistant to schistosomiasis reveals novel potential vaccine candidates. Front Immunol. 2015;6:213doi: 10.3389/fimmu.2015.00213.
Pearson, M. S., Becker, L., Driguez, P., Young, N. D., Gaze, S., Mendes, T., Li, X. H., Doolan, D. L., Midzi, N., Mduluza, T., McManus, D. P., Wilson, R. A., Bethony, J. M., Nausch, N., Mutapi, F., Felgner, P. L., & Loukas, A. (2015). Of monkeys and men: immunomic profiling of sera from humans and non-human primates resistant to schistosomiasis reveals novel potential vaccine candidates. Frontiers in immunology, 6213. https://doi.org/10.3389/fimmu.2015.00213
Pearson, Mark S, et al. "Of monkeys and men: immunomic profiling of sera from humans and non-human primates resistant to schistosomiasis reveals novel potential vaccine candidates." Frontiers in immunology vol. 6 (2015): 213. doi: https://doi.org/10.3389/fimmu.2015.00213
Pearson MS, Becker L, Driguez P, Young ND, Gaze S, Mendes T, Li XH, Doolan DL, Midzi N, Mduluza T, McManus DP, Wilson RA, Bethony JM, Nausch N, Mutapi F, Felgner PL, Loukas A. Of monkeys and men: immunomic profiling of sera from humans and non-human primates resistant to schistosomiasis reveals novel potential vaccine candidates. Front Immunol. 2015 May 05;6:213. doi: 10.3389/fimmu.2015.00213. eCollection 2015. PMID: 25999951; PMCID: PMC4419842.
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Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni.

Journal of extracellular vesicles

Nowacki FC, Swain MT, Klychnikov OI, Niazi U, Ivens A, Quintana JF, Hensbergen PJ, Hokke CH, Buck AH, Hoffmann KF.
PMID: 26443722
J Extracell Vesicles. 2015 Oct 05;4:28665. doi: 10.3402/jev.v4.28665. eCollection 2015.

BACKGROUND: Penetration of skin, migration through tissues and establishment of long-lived intravascular partners require Schistosoma parasites to successfully manipulate definitive host defences. While previous studies of larval schistosomula have postulated a function for excreted/secreted (E/S) products in initiating these...

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Nowacki FC, Swain MT, Klychnikov OI, et al. Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. J Extracell Vesicles. 2015;4:28665doi: 10.3402/jev.v4.28665.
Nowacki, F. C., Swain, M. T., Klychnikov, O. I., Niazi, U., Ivens, A., Quintana, J. F., Hensbergen, P. J., Hokke, C. H., Buck, A. H., & Hoffmann, K. F. (2015). Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. Journal of extracellular vesicles, 428665. https://doi.org/10.3402/jev.v4.28665
Nowacki, Fanny C, et al. "Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni." Journal of extracellular vesicles vol. 4 (2015): 28665. doi: https://doi.org/10.3402/jev.v4.28665
Nowacki FC, Swain MT, Klychnikov OI, Niazi U, Ivens A, Quintana JF, Hensbergen PJ, Hokke CH, Buck AH, Hoffmann KF. Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. J Extracell Vesicles. 2015 Oct 05;4:28665. doi: 10.3402/jev.v4.28665. eCollection 2015. PMID: 26443722; PMCID: PMC4595467.
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T-bet Expression by Foxp3(+) T Regulatory Cells is Not Essential for Their Suppressive Function in CNS Autoimmune Disease or Colitis.

Frontiers in immunology

McPherson RC, Turner DG, Mair I, O'Connor RA, Anderton SM.
PMID: 25741342
Front Immunol. 2015 Feb 18;6:69. doi: 10.3389/fimmu.2015.00069. eCollection 2015.

Accumulation of T regulatory (Treg) cells within the central nervous system (CNS) during experimental autoimmune encephalomyelitis (EAE) is essential for the resolution of disease. CNS Treg cells have been shown to uniformly express the Th1-associated molecules, T-bet and CXCR3....

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McPherson RC, Turner DG, Mair I, et al. T-bet Expression by Foxp3(+) T Regulatory Cells is Not Essential for Their Suppressive Function in CNS Autoimmune Disease or Colitis. Front Immunol. 2015;6:69doi: 10.3389/fimmu.2015.00069.
McPherson, R. C., Turner, D. G., Mair, I., O'Connor, R. A., & Anderton, S. M. (2015). T-bet Expression by Foxp3(+) T Regulatory Cells is Not Essential for Their Suppressive Function in CNS Autoimmune Disease or Colitis. Frontiers in immunology, 669. https://doi.org/10.3389/fimmu.2015.00069
McPherson, Rhoanne C, et al. "T-bet Expression by Foxp3(+) T Regulatory Cells is Not Essential for Their Suppressive Function in CNS Autoimmune Disease or Colitis." Frontiers in immunology vol. 6 (2015): 69. doi: https://doi.org/10.3389/fimmu.2015.00069
McPherson RC, Turner DG, Mair I, O'Connor RA, Anderton SM. T-bet Expression by Foxp3(+) T Regulatory Cells is Not Essential for Their Suppressive Function in CNS Autoimmune Disease or Colitis. Front Immunol. 2015 Feb 18;6:69. doi: 10.3389/fimmu.2015.00069. eCollection 2015. PMID: 25741342; PMCID: PMC4332357.
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Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities.

PLoS computational biology

Estrela S, Brown SP.
PMID: 24385891
PLoS Comput Biol. 2013;9(12):e1003398. doi: 10.1371/journal.pcbi.1003398. Epub 2013 Dec 26.

Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships),...

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Estrela S, Brown SP. Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities. PLoS Comput Biol. 2013;9(12):e1003398doi: 10.1371/journal.pcbi.1003398.
Estrela, S., & Brown, S. P. (2013). Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities. PLoS computational biology, 9(12), e1003398. https://doi.org/10.1371/journal.pcbi.1003398
Estrela, Sylvie, and Brown, Sam P. "Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities." PLoS computational biology vol. 9,12 (2013): e1003398. doi: https://doi.org/10.1371/journal.pcbi.1003398
Estrela S, Brown SP. Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities. PLoS Comput Biol. 2013;9(12):e1003398. doi: 10.1371/journal.pcbi.1003398. Epub 2013 Dec 26. PMID: 24385891; PMCID: PMC3873226.
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Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects.

Evolutionary applications

Cameron A, Reece SE, Drew DR, Haydon DT, Yates AJ.
PMID: 23467678
Evol Appl. 2013 Feb;6(2):365-76. doi: 10.1111/eva.12005. Epub 2012 Oct 10.

Parasites may alter their behaviour to cope with changes in the within-host environment. In particular, investment in transmission may alter in response to the availability of parasite resources or host immune responses. However, experimental and theoretical studies have drawn...

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Cameron A, Reece SE, Drew DR, et al. Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects. Evol Appl. 2012;6(2):365-76doi: 10.1111/eva.12005.
Cameron, A., Reece, S. E., Drew, D. R., Haydon, D. T., & Yates, A. J. (2013). Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects. Evolutionary applications, 6(2), 365-76. https://doi.org/10.1111/eva.12005
Cameron, Angus, et al. "Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects." Evolutionary applications vol. 6,2 (2013): 365-76. doi: https://doi.org/10.1111/eva.12005
Cameron A, Reece SE, Drew DR, Haydon DT, Yates AJ. Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects. Evol Appl. 2013 Feb;6(2):365-76. doi: 10.1111/eva.12005. Epub 2012 Oct 10. PMID: 23467678; PMCID: PMC3586624.
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SSE: a nucleotide and amino acid sequence analysis platform.

BMC research notes

Simmonds P.
PMID: 22264264
BMC Res Notes. 2012 Jan 20;5:50. doi: 10.1186/1756-0500-5-50.

BACKGROUND: There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes.FINDING: A simple sequence editor (SSE) was developed...

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Simmonds P. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes. 2012;5:50doi: 10.1186/1756-0500-5-50.
Simmonds, P. (2012). SSE: a nucleotide and amino acid sequence analysis platform. BMC research notes, 550. https://doi.org/10.1186/1756-0500-5-50
Simmonds, Peter. "SSE: a nucleotide and amino acid sequence analysis platform." BMC research notes vol. 5 (2012): 50. doi: https://doi.org/10.1186/1756-0500-5-50
Simmonds P. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes. 2012 Jan 20;5:50. doi: 10.1186/1756-0500-5-50. PMID: 22264264; PMCID: PMC3292810.
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Plasma markers of oxidative stress are uncorrelated in a wild mammal.

Ecology and evolution

Christensen LL, Selman C, Blount JD, Pilkington JG, Watt KA, Pemberton JM, Reid JM, Nussey DH.
PMID: 26640685
Ecol Evol. 2015 Oct 19;5(21):5096-108. doi: 10.1002/ece3.1771. eCollection 2015 Nov.

Oxidative stress, which results from an imbalance between the production of potentially damaging reactive oxygen species versus antioxidant defenses and repair mechanisms, has been proposed as an important mediator of life-history trade-offs. A plethora of biomarkers associated with oxidative...

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Christensen LL, Selman C, Blount JD, et al. Plasma markers of oxidative stress are uncorrelated in a wild mammal. Ecol Evol. 2015;5(21):5096-108doi: 10.1002/ece3.1771.
Christensen, L. L., Selman, C., Blount, J. D., Pilkington, J. G., Watt, K. A., Pemberton, J. M., Reid, J. M., & Nussey, D. H. (2015). Plasma markers of oxidative stress are uncorrelated in a wild mammal. Ecology and evolution, 5(21), 5096-108. https://doi.org/10.1002/ece3.1771
Christensen, Louise L, et al. "Plasma markers of oxidative stress are uncorrelated in a wild mammal." Ecology and evolution vol. 5,21 (2015): 5096-108. doi: https://doi.org/10.1002/ece3.1771
Christensen LL, Selman C, Blount JD, Pilkington JG, Watt KA, Pemberton JM, Reid JM, Nussey DH. Plasma markers of oxidative stress are uncorrelated in a wild mammal. Ecol Evol. 2015 Oct 19;5(21):5096-108. doi: 10.1002/ece3.1771. eCollection 2015 Nov. PMID: 26640685; PMCID: PMC4662306.
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Anthelmintic resistance in equine nematodes.

International journal for parasitology. Drugs and drug resistance

Matthews JB.
PMID: 25516842
Int J Parasitol Drugs Drug Resist. 2014 Oct 25;4(3):310-5. doi: 10.1016/j.ijpddr.2014.10.003. eCollection 2014 Dec.

Anthelmintics have been applied indiscriminately to control horse nematodes for over 40 years. Three broad-spectrum anthelmintic classes are currently registered for nematode control in horses: benzimidazoles (fenbendazole, oxibendazole), tetrahydropyrimidines (pyrantel) and macrocyclic lactones (ivermectin, moxidectin). Generally, control strategies have...

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Matthews JB. Anthelmintic resistance in equine nematodes. Int J Parasitol Drugs Drug Resist. 2014;4(3):310-5doi: 10.1016/j.ijpddr.2014.10.003.
Matthews, J. B. (2014). Anthelmintic resistance in equine nematodes. International journal for parasitology. Drugs and drug resistance, 4(3), 310-5. https://doi.org/10.1016/j.ijpddr.2014.10.003
Matthews, Jacqueline B. "Anthelmintic resistance in equine nematodes." International journal for parasitology. Drugs and drug resistance vol. 4,3 (2014): 310-5. doi: https://doi.org/10.1016/j.ijpddr.2014.10.003
Matthews JB. Anthelmintic resistance in equine nematodes. Int J Parasitol Drugs Drug Resist. 2014 Oct 25;4(3):310-5. doi: 10.1016/j.ijpddr.2014.10.003. eCollection 2014 Dec. PMID: 25516842; PMCID: PMC4266799.
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Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.

PLoS currents

Dudas G, Rambaut A.
PMID: 24860690
PLoS Curr. 2014 May 02;6. doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d.

Members of the genus Ebolavirus have caused outbreaks of haemorrhagic fever in humans in Africa. The most recent outbreak in Guinea, which began in February of 2014, is still ongoing. Recently published analyses of sequences from this outbreak suggest...

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Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLoS Curr. 2014;6doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d.
Dudas, G., & Rambaut, A. (2014). Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLoS currents, 6. https://doi.org/10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d
Dudas, Gytis, and Rambaut, Andrew. "Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak." PLoS currents vol. 6 (2014). doi: https://doi.org/10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d
Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLoS Curr. 2014 May 02;6. doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d. PMID: 24860690; PMCID: PMC4024086.
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Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring.

Evolutionary applications

Pollitt LC, Sim D, Salathé R, Read AF.
PMID: 25861387
Evol Appl. 2015 Mar;8(3):296-304. doi: 10.1111/eva.12194. Epub 2014 Aug 11.

Artemisinin-based drugs are the front-line weapon in the treatment of human malaria cases, but there is concern that recent reports of slow clearing infections may signal developing resistance to treatment. In the absence of molecular markers for resistance, current...

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Pollitt LC, Sim D, Salathé R, et al. Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring. Evol Appl. 2014;8(3):296-304doi: 10.1111/eva.12194.
Pollitt, L. C., Sim, D., Salathé, R., & Read, A. F. (2015). Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring. Evolutionary applications, 8(3), 296-304. https://doi.org/10.1111/eva.12194
Pollitt, Laura C, et al. "Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring." Evolutionary applications vol. 8,3 (2015): 296-304. doi: https://doi.org/10.1111/eva.12194
Pollitt LC, Sim D, Salathé R, Read AF. Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring. Evol Appl. 2015 Mar;8(3):296-304. doi: 10.1111/eva.12194. Epub 2014 Aug 11. PMID: 25861387; PMCID: PMC4380923.
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Parasitism in early life: environmental conditions shape within-brood variation in responses to infection.

Ecology and evolution

Granroth-Wilding HM, Burthe SJ, Lewis S, Reed TE, Herborn KA, Newell MA, Takahashi EA, Daunt F, Cunningham EJ.
PMID: 25535557
Ecol Evol. 2014 Sep;4(17):3408-19. doi: 10.1002/ece3.1192. Epub 2014 Aug 18.

Parasites play key ecological and evolutionary roles through the costs they impose on their host. In wild populations, the effect of parasitism is likely to vary considerably with environmental conditions, which may affect the availability of resources to hosts...

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Granroth-Wilding HM, Burthe SJ, Lewis S, et al. Parasitism in early life: environmental conditions shape within-brood variation in responses to infection. Ecol Evol. 2014;4(17):3408-19doi: 10.1002/ece3.1192.
Granroth-Wilding, H. M., Burthe, S. J., Lewis, S., Reed, T. E., Herborn, K. A., Newell, M. A., Takahashi, E. A., Daunt, F., & Cunningham, E. J. (2014). Parasitism in early life: environmental conditions shape within-brood variation in responses to infection. Ecology and evolution, 4(17), 3408-19. https://doi.org/10.1002/ece3.1192
Granroth-Wilding, Hanna M V, et al. "Parasitism in early life: environmental conditions shape within-brood variation in responses to infection." Ecology and evolution vol. 4,17 (2014): 3408-19. doi: https://doi.org/10.1002/ece3.1192
Granroth-Wilding HM, Burthe SJ, Lewis S, Reed TE, Herborn KA, Newell MA, Takahashi EA, Daunt F, Cunningham EJ. Parasitism in early life: environmental conditions shape within-brood variation in responses to infection. Ecol Evol. 2014 Sep;4(17):3408-19. doi: 10.1002/ece3.1192. Epub 2014 Aug 18. PMID: 25535557; PMCID: PMC4228615.
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Showing 1 to 12 of 27 entries