Search Results - "Blythe, Martin J"

Accelerated growth in the absence of DNA replication origins by Hawkins, Michelle, Malla, Sunir, Blythe, Martin J., Nieduszynski, Conrad A., Allers, Thorsten

“…When all origins of replication are deleted from the archaeon Haloferax volcanii , homologous recombination is used to initiate DNA replication and the growth…”
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Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing by Delmas, Stéphane, Pullan, Steven T, Gaddipati, Sanyasi, Kokolski, Matthew, Malla, Sunir, Blythe, Martin J, Ibbett, Roger, Campbell, Maria, Liddell, Susan, Aboobaker, Aziz, Tucker, Gregory A, Archer, David B

“…A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly…”
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The dynamics of genome replication using deep sequencing by Müller, Carolin A, Hawkins, Michelle, Retkute, Renata, Malla, Sunir, Wilson, Ray, Blythe, Martin J, Nakato, Ryuichiro, Komata, Makiko, Shirahige, Katsuhiko, de Moura, Alessandro P S, Nieduszynski, Conrad A

“…Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and…”
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Transient exposure to low levels of insecticide affects metabolic networks of honeybee larvae by Derecka, Kamila, Blythe, Martin J, Malla, Sunir, Genereux, Diane P, Guffanti, Alessandro, Pavan, Paolo, Moles, Anna, Snart, Charles, Ryder, Thomas, Ortori, Catharine A, Barrett, David A, Schuster, Eugene, Stöger, Reinhard

“…The survival of a species depends on its capacity to adjust to changing environmental conditions, and new stressors. Such new, anthropogenic stressors include…”
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Benchmarking B cell epitope prediction: Underperformance of existing methods by Blythe, Martin J., Flower, Darren R.

“…Sequence profiling is used routinely to predict the location of B‐cell epitopes. In the postgenomic era, the need for reliable epitope prediction is clear. We…”
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A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology by Blythe, Martin J, Kao, Damian, Malla, Sunir, Rowsell, Joanna, Wilson, Ray, Evans, Deborah, Jowett, Jamie, Hall, Amy, Lemay, Virginie, Lam, Sabrina, Aboobaker, A Aziz

“…The use of planarians as a model system is expanding and the mechanisms that control planarian regeneration are being elucidated. The planarian Schmidtea…”
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High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies by Blythe, Martin J, Malla, Sunir, Everall, Richard, Shih, Yu-huan, Lemay, Virginie, Moreton, Joanna, Wilson, Raymond, Aboobaker, A Aziz

“…Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms…”
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LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames by Blythe, Martin J., Kocer, Ayhan, Rubio-Roldan, Alejandro, Giles, Tom, Abakir, Abdulkadir, Ialy-Radio, Côme, Wheldon, Lee M., Bereshchenko, Oxana, Bruscoli, Stefano, Kondrashov, Alexander, Drevet, Joël R., Emes, Richard D., Johnson, Andrew D., McCarrey, John R., Gackowski, Daniel, Olinski, Ryszard, Cocquet, Julie, Garcia-Perez, Jose L., Ruzov, Alexey

“…Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs…”
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Metabolic activity in dormant conidia of Aspergillus niger and developmental changes during conidial outgrowth by Novodvorska, Michaela, Stratford, Malcolm, Blythe, Martin J., Wilson, Raymond, Beniston, Richard G., Archer, David B.

“…•Resting conidia are demonstrated to be metabolically active.•After triggering of conidial outgrowth fermentation occurs, followed by respiration.•Sorbic acid…”
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Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger by Ries, Laure, Pullan, Steven T, Delmas, Stéphane, Malla, Sunir, Blythe, Martin J, Archer, David B

“…A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce…”
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The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger by van Munster, Jolanda M., Daly, Paul, Delmas, Stéphane, Pullan, Steven T., Blythe, Martin J., Malla, Sunir, Kokolski, Matthew, Noltorp, Emelie C.M., Wennberg, Kristin, Fetherston, Richard, Beniston, Richard, Yu, Xiaolan, Dupree, Paul, Archer, David B.

“…•The transriptomic response of Aspergillus niger to wheat straw is sequential.•The early response consists of genes encoding hemicellulolytic enzymes.•The…”
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Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing by Novodvorska, Michaela, Hayer, Kimran, Pullan, Steven T, Wilson, Raymond, Blythe, Martin J, Stam, Hein, Stratford, Malcolm, Archer, David B

“…Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using both next generation RNA-sequencing and…”
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Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression by Daly, Paul, van Munster, Jolanda M., Kokolski, Matthew, Sang, Fei, Blythe, Martin J., Malla, Sunir, Velasco de Castro Oliveira, Juliana, Goldman, Gustavo H., Archer, David B.

“…[Display omitted] •First genome-wide transcriptional response in fungal mixed species straw cultures.•In mixed cultures, rRNA abundance was used to predict…”
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Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose by van Munster, Jolanda M, Daly, Paul, Blythe, Martin J, Ibbett, Roger, Kokolski, Matt, Gaddipati, Sanyasi, Lindquist, Erika, Singan, Vasanth R, Barry, Kerrie W, Lipzen, Anna, Ngan, Chew Yee, Petzold, Christopher J, Chan, Leanne Jade G, Arvas, Mikko, Raulo, Roxane, Pullan, Steven T, Delmas, Stéphane, Grigoriev, Igor V, Tucker, Gregory A, Simmons, Blake A, Archer, David B

“…Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic…”
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An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli by Nehring, Ralf B, Gu, Franklin, Lin, Hsin-Yu, Gibson, Janet L, Blythe, Martin J, Wilson, Ray, Bravo Núñez, María Angélica, Hastings, P J, Louis, Edward J, Frisch, Ryan L, Hu, James C, Rosenberg, Susan M

“…With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even…”
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JenPep: a database of quantitative functional peptide data for immunology by Blythe, Martin J., Doytchinova, Irini A., Flower, Darren R.

“…Motivation: The compilation of quantitative binding data underlies attempts to derive tools for the accurate prediction of epitopes in cellular immunology and…”
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Transcriptional landscape of Aspergillus nigerat breaking of conidial dormancy revealed by RNA-sequencing by Novodvorska, Michaela, Hayer, Kimran, Pullan, Steven T, Wilson, Raymond, Blythe, Martin J, Stam, Hein, Stratford, Malcolm, Archer, David B

“…Abstract Background Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using both next generation…”
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Additive Method for the Prediction of Protein−Peptide Binding Affinity. Application to the MHC Class I Molecule HLA-A0201 by Doytchinova, Irini A, Blythe, Martin J, Flower, Darren R

“…A method has been developed for prediction of binding affinities between proteins and peptides. We exemplify the method through its application to binding…”
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An analysis of the epitope knowledge related to Mycobacteria by Blythe, Martin J, Zhang, Qing, Vaughan, Kerrie, de Castro, Jr, Romulo, Salimi, Nima, Bui, Huynh-Hoa, Lewinsohn, David M, Ernst, Joel D, Peters, Bjoern, Sette, Alessandro

“…Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains a leading cause of infectious disease morbidity and mortality, and is responsible for…”
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Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments by Daly, Paul, van Munster, Jolanda M, Blythe, Martin J, Ibbett, Roger, Kokolski, Matt, Gaddipati, Sanyasi, Lindquist, Erika, Singan, Vasanth R, Barry, Kerrie W, Lipzen, Anna, Ngan, Chew Yee, Petzold, Christopher J, Chan, Leanne Jade G, Pullan, Steven T, Delmas, Stéphane, Waldron, Paul R, Grigoriev, Igor V, Tucker, Gregory A, Simmons, Blake A, Archer, David B

“…The capacity of fungi, such as to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks…”
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