Search Results - "Tamuri, Asif U"

A phylogenetic approach for weighting genetic sequences by De Maio, Nicola, Alekseyenko, Alexander V, Coleman-Smith, William J, Pardi, Fabio, Suchard, Marc A, Tamuri, Asif U, Truszkowski, Jakub, Goldman, Nick

“…Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the…”
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Health workforce needs in Malawi: analysis of the Thanzi La Onse integrated epidemiological model of care by She, Bingling, Mangal, Tara D, Prust, Margaret L, Heung, Stephanie, Chalkley, Martin, Colbourn, Tim, Collins, Joseph H, Graham, Matthew M, Jewell, Britta, Joshi, Purava, Li Lin, Ines, Mnjowe, Emmanuel, Mohan, Sakshi, Molaro, Margherita, Phillips, Andrew N, Revill, Paul, Smith, Robert Manning, Tamuri, Asif U, Twea, Pakwanja D, Manthalu, Gerald, Mfutso-Bengo, Joseph, Hallett, Timothy B

“…To make the best use of health resources, it is crucial to understand the healthcare needs of a population-including how needs will evolve and respond to…”
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chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians by Hendrix, Maurice, Clerx, Michael, Tamuri, Asif U, Keating, Sarah M, Johnstone, Ross H, Cooper, Jonathan, Mirams, Gary R

“…Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear…”
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Alignment Modulates Ancestral Sequence Reconstruction Accuracy by Vialle, Ricardo Assunção, Tamuri, Asif U, Goldman, Nick

“…Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying ancient proteins and comparing biochemical properties between…”
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A species-level timeline of mammal evolution integrating phylogenomic data by Álvarez-Carretero, Sandra, Tamuri, Asif U., Battini, Matteo, Nascimento, Fabrícia F., Carlisle, Emily, Asher, Robert J., Yang, Ziheng, Donoghue, Philip C. J., dos Reis, Mario

“…High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies 1 – 3 . However, state-of-the-art Bayesian methods for…”
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A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection by Tamuri, Asif U, dos Reis, Mario

“…Abstract We use first principles of population genetics to model the evolution of proteins under persistent positive selection (PPS). PPS may occur when…”
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Identifying changes in selective constraints: host shifts in influenza by Tamuri, Asif U, Dos Reis, Mario, Hay, Alan J, Goldstein, Richard A

“…The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through…”
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Genome sequencing of normal cells reveals developmental lineages and mutational processes by Behjati, Sam, Huch, Meritxell, van Boxtel, Ruben, Karthaus, Wouter, Wedge, David C., Tamuri, Asif U., Martincorena, Iñigo, Petljak, Mia, Alexandrov, Ludmil B., Gundem, Gunes, Tarpey, Patrick S., Roerink, Sophie, Blokker, Joyce, Maddison, Mark, Mudie, Laura, Robinson, Ben, Nik-Zainal, Serena, Campbell, Peter, Goldman, Nick, van de Wetering, Marc, Cuppen, Edwin, Clevers, Hans, Stratton, Michael R.

“…On the basis of whole-genome sequences of clonal lines derived from normal mouse tissues, variation in mutational patterns and load across different tissues…”
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Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models by Tamuri, Asif U, dos Reis, Mario, Goldstein, Richard A

“…Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods,…”
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Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination by Cudini, Juliana, Roy, Sunando, Houldcroft, Charlotte J., Bryant, Josephine M., Depledge, Daniel P., Tutill, Helena, Veys, Paul, Williams, Rachel, Worth, Austen J. J., Tamuri, Asif U., Goldstein, Richard A., Breuer, Judith

“…Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV) genome-wide intrahost diversity that rival those of persistent RNA viruses…”
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Rapid morphological evolution in placental mammals post-dates the origin of the crown group by Halliday, Thomas J D, Dos Reis, Mario, Tamuri, Asif U, Ferguson-Gow, Henry, Yang, Ziheng, Goswami, Anjali

“…Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the…”
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A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data by Tamuri, Asif U, Goldman, Nick, dos Reis, Mario

“…We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in…”
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A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi by Molaro, Margherita, Mohan, Sakshi, She, Bingling, Chalkley, Martin, Colbourn, Tim, Collins, Joseph H, Connolly, Emilia, Graham, Matthew M, Janoušková, Eva, Li Lin, Ines, Manthalu, Gerald, Mnjowe, Emmanuel, Nkhoma, Dominic, Twea, Pakwanja D, Phillips, Andrew N, Revill, Paul, Tamuri, Asif U, Mfutso-Bengo, Joseph, Mangal, Tara D, Hallett, Timothy B

“…An efficient allocation of limited resources in low-income settings offers the opportunity to improve population-health outcomes given the available health…”
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Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies by Venturini, Cristina, Pang, Juanita, Tamuri, Asif U, Roy, Sunando, Atkinson, Claire, Griffiths, Paul, Breuer, Judith, Goldstein, Richard A

“…Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and…”
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Factors associated with medical consumable availability in level 1 facilities in Malawi: a secondary analysis of a facility census by Mohan, Sakshi, Mangal, Tara D, Colbourn, Tim, Chalkley, Martin, Chimwaza, Chikhulupiliro, Collins, Joseph H, Graham, Matthew M, Janoušková, Eva, Jewell, Britta, Kadewere, Godfrey, Li Lin, Ines, Manthalu, Gerald, Mfutso-Bengo, Joseph, Mnjowe, Emmanuel, Molaro, Margherita, Nkhoma, Dominic, Revill, Paul, She, Bingling, Manning Smith, Robert, Tafesse, Wiktoria, Tamuri, Asif U, Twea, Pakwanja, Phillips, Andrew N, Hallett, Timothy B

“…Medical consumable stock-outs negatively affect health outcomes not only by impeding or delaying the effective delivery of services but also by discouraging…”
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ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments by Schwarz, Roland F, Tamuri, Asif U, Kultys, Marek, King, James, Godwin, James, Florescu, Ana M, Schultz, Jörg, Goldman, Nick

“…Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide…”
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ArchSchema: a tool for interactive graphing of related Pfam domain architectures by Tamuri, Asif U., Laskowski, Roman A.

“…ArchSchema is a Java Web Start application that generates a dynamic 2D network of related Pfam domain architectures. Each node corresponds to a different…”
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Charting the host adaptation of influenza viruses by dos Reis, Mario, Tamuri, Asif U, Hay, Alan J, Goldstein, Richard A

“…Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by…”
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cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians by Hendrix, Maurice, Clerx, Michael, Tamuri, Asif U, Keating, Sarah M, Johnstone, Ross H, Cooper, Jonathan, Mirams, Gary R

“…Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear…”
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SMIM1 underlies the Vel blood group and influences red blood cell traits by Cvejic, Ana, Haer-Wigman, Lonneke, Stephens, Jonathan C, Kostadima, Myrto, Smethurst, Peter A, Frontini, Mattia, van den Akker, Emile, Bertone, Paul, Bielczyk-Maczyńska, Ewa, Farrow, Samantha, Fehrmann, Rudolf S N, Gray, Alan, de Haas, Masja, Haver, Vincent G, Jordan, Gregory, Karjalainen, Juha, Kerstens, Hindrik H D, Kiddle, Graham, Lloyd-Jones, Heather, Needs, Malcolm, Poole, Joyce, Soussan, Aicha Ait, Rendon, Augusto, Rieneck, Klaus, Sambrook, Jennifer G, Schepers, Hein, Silljé, Herman H W, Sipos, Botond, Swinkels, Dorine, Tamuri, Asif U, Verweij, Niek, Watkins, Nicholas A, Westra, Harm-Jan, Stemple, Derek, Franke, Lude, Soranzo, Nicole, Stunnenberg, Hendrik G, Goldman, Nick, van der Harst, Pim, van der Schoot, C Ellen, Ouwehand, Willem H, Albers, Cornelis A

“…Ana Cvejic, Willem Ouwehand, Cornelis Albers and colleagues show that homozygosity for a null allele of SMIM1 is responsible for the Vel– blood group…”
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