Works matching DE "VIRAL population genetics"

Results: 57

IVA: accurate de novo assembly of RNA virus genomes.

Published in:

Bioinformatics, 2015, v. 31, n. 14, p. 2374, doi. 10.1093/bioinformatics/btv120

By:

Hunt, Martin;
Gall, Astrid;
Swee Hoe Ong;
Brener, Jacqui;
Ferns, Bridget;
Goulder, Philip;
Nastouli, Eleni;
Keane, Jacqueline A.;
Kellam, Paul;
Otto, Thomas D.

Publication type:

Article

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 682, doi. 10.1093/bioinformatics/btu726

By:

Skums, Pavel;
Artyomenko, Alexander;
Glebova, Olga;
Ramachandran, Sumathi;
Mandoiu, Ion;
Campo, David S.;
Dimitrova, Zoya;
Zelikovsky, Alex;
Khudyakov, Yury

Publication type:

Article

Accurate viral population assembly from ultra-deep sequencing data.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. i329, doi. 10.1093/bioinformatics/btu295

By:

Mangul, Serghei;
Wu, Nicholas C.;
Mancuso, Nicholas;
Zelikovsky, Alex;
Sun, Ren;
Eskin, Eleazar

Publication type:

Article

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Published in:

Scientific Reports, 2013, p. 1, doi. 10.1038/srep02837

By:

Prosperi, Mattia C. F.;
Li Yin;
Nolan, David J.;
Lowe, Amanda D.;
Goodenow, Maureen M.;
Salemi, Marco

Publication type:

Article

Natural scrub typhus antibody suppresses HIV CXCR4(X4) viruses.

Published in:

Infectious Disease Reports, 2013, v. 5, n. 1, p. 27, doi. 10.4081/idr.2013.e8

By:

Watt, George;
Pacharee Kantipong;
Burnouf, Thierry;
Shikuma, Cecilia;
Philpott, Sean

Publication type:

Article

Nearly full-length genome sequence of a novel astrovirus isolated from chickens with 'white chicks' condition.

Published in:

2016

By:

Sajewicz-Krukowska, Joanna;
Domanska-Blicharz, Katarzyna

Publication type:

Report

Genomoviridae: a new family of widespread single-stranded DNA viruses.

Published in:

Archives of Virology, 2016, v. 161, n. 9, p. 2633, doi. 10.1007/s00705-016-2943-3

By:

Krupovic, Mart;
Ghabrial, Said;
Jiang, Daohong;
Varsani, Arvind

Publication type:

Article

A phylogeographical study of the cauliflower mosaic virus population in mid-Eurasia Iran using complete genome analysis.

Published in:

Archives of Virology, 2014, v. 159, n. 6, p. 1329, doi. 10.1007/s00705-013-1910-5

By:

Farzadfar, Shirin;
Pourrahim, Reza;
Ebrahimi, Hassan

Publication type:

Article

The population genetics of maize dwarf mosaic virus in Spain.

Published in:

2012

By:

Achon, M.;
Larrañaga, A.;
Alonso-Dueñas, N.

Publication type:

Report

On the classification and evolution of endogenous retrovirus: human endogenous retroviruses may not be 'human' after all.

Published in:

APMIS, 2016, v. 124, n. 1/2, p. 44, doi. 10.1111/apm.12489

By:

Escalera‐Zamudio, Marina;
Greenwood, Alex D.

Publication type:

Article

Previously unknown and highly divergent ssDNA viruses populate the oceans.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 11, p. 2169, doi. 10.1038/ismej.2013.110

By:

Labonté, Jessica M;
Suttle, Curtis A

Publication type:

Article

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.

Published in:

Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0064-x

By:

Zukurov, Jean P.;
do Nascimento-Brito, Sieberth;
Volpini, Angela C.;
Oliveira, Guilherme C.;
Janini, Luiz Mario R.;
Antoneli, Fernando

Publication type:

Article

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy.

Published in:

Retrovirology, 2015, v. 12, p. 1, doi. 10.1186/s12977-015-0212-2

By:

Kearney, Mary F.;
Anderson, Elizabeth M.;
Coomer, Charles;
Smith, Luke;
Wei Shao;
Johnson, Nicholas;
Kline, Christopher;
Spindler, Jonathan;
Mellors, John W.;
Coffin, John M.;
Ambrose, Zandrea

Publication type:

Article

High-throughput profiling of point mutations across the HIV-1 genome.

Published in:

Retrovirology, 2014, v. 11, n. 1, p. 1, doi. 10.1186/s12977-014-0124-6

By:

Al-Mawsawi, Laith Q.;
Wu, Nicholas C.;
Anders Olson, C.;
Cai Shi, Vivian;
Hangfei Qi;
Xiaojuan Zheng;
Ting-Ting Wu;
Ren Sun

Publication type:

Article

Denoising PCR-amplified metagenome data.

Published in:

BMC Bioinformatics, 2012, v. 13, n. 1, p. 1, doi. 10.1186/1471-2105-13-283

By:

Rosen, Michael J.;
Callahan, Benjamin J.;
Fisher, Daniel S.;
Holmes, Susan P.

Publication type:

Article

Human Papillomavirus in Thai Women and Men with Anogenital Warts.

Published in:

Intervirology, 2018, v. 61, n. 5, p. 223, doi. 10.1159/000497351

By:

Nilyanimit, Pornjarim;
Chansaenroj, Jira;
Srisomboon, Jatupol;
Rodrangnok, Wanida;
Rajakom, Ngamta;
Daengsaard, Ekkachai;
Sookrak, Nutthavit;
Poovorawan, Yong

Publication type:

Article

Survival of Viruses in Water.

Published in:

Intervirology, 2018, v. 61, n. 5, p. 214, doi. 10.1159/000484899

By:

Pinon, Anthony;
Vialette, Michèle

Publication type:

Article

Genotype-to-Protein Map and Collective Adaptation in a Viral Population.

Published in:

Biophysica, 2022, v. 2, n. 4, p. 381, doi. 10.3390/biophysica2040034

By:

Villanueva, Ariadna;
Secaira-Morocho, Henry;
Seoane, Luis F.;
Lázaro, Ester;
Manrubia, Susanna

Publication type:

Article

Increasing the Clinical Potential and Applications of Anti-HIV Antibodies.

Published in:

Frontiers in Immunology, 2017, p. 1, doi. 10.3389/fimmu.2017.01655

By:

Hua, Casey K.;
Ackerman, Margaret E.

Publication type:

Article

Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations.

Published in:

Viruses (1999-4915), 2015, v. 7, n. 7, p. 3625, doi. 10.3390/v7072788

By:

Barbe, Valérie;
Chateigner, Aurélien;
Bézier, Annie;
Herniou, Elisabeth A.;
Labrousse, Carole;
Jiolle, Davy

Publication type:

Article

Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing.

Published in:

Viruses (1999-4915), 2014, v. 6, n. 3, p. 1049, doi. 10.3390/v6031049

By:

Sijmons, Steven`;
Van Ranst, Marc;
Maes, Piet

Publication type:

Article

Erratum to: Genetic structure and diversity of the Banana bunchy top virus population on Sumatra Island, Indonesia.

Published in:

2015

By:

Chiaki, Yuya;
Nasir, Nasril;
Herwina, Henny;
Jumjunidang;
Sonoda, Ayaka;
Fukumoto, Tomohiro;
Nakamura, Masayuki;
Iwai, Hisashi

Publication type:

Erratum

Inferring population genetics parameters of evolving viruses using time-series data.

Published in:

Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vez011

By:

Zinger, Tal;
Gelbart, Maoz;
Miller, Danielle;
Pennings, Pleuni S;
Stern, Adi

Publication type:

Article

Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.

Published in:

Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vey043

By:

Scotch, Matthew;
Tahsin, Tasnia;
Weissenbacher, Davy;
O'Connor, Karen;
Magge, Arjun;
Vaiente, Matteo;
Suchard, Marc A;
Gonzalez-Hernandez, Graciela

Publication type:

Article

Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection.

Published in:

Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vez008

By:

Zhao, Lei;
Abbasi, Ali B;
Illingworth, Christopher J R

Publication type:

Article

Measurements of intrahost viral diversity require an unbiased diversity metric.

Published in:

Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vey041

By:

Zhao, Lei;
Illingworth, Christopher J R

Publication type:

Article

Genetic shift of env V3 loop viral sequences in patients with HIV-associated neurocognitive disorder during antiretroviral therapy.

Published in:

Journal of NeuroVirology, 2013, v. 19, n. 6, p. 523, doi. 10.1007/s13365-013-0207-5

By:

Eggers, Christian;
Müller, Oliver;
Thordsen, Ingo;
Schreiber, Michael;
Methner, Axel

Publication type:

Article

A decade of viral mutations and associated drug resistance in a population of HIV-1<sup>+</sup> Puerto Ricans: 2002–2011.

Published in:

PLoS ONE, 2017, v. 12, n. 5, p. 1, doi. 10.1371/journal.pone.0177452

By:

Sepúlveda-Torres, Lycely del C.;
Rishishwar, Lavanya;
Rogers, Maria Luisa;
Ríos-Olivares, Eddy;
Boukli, Nawal;
Jordan, I. King;
Cubano, Luis A.

Publication type:

Article

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00822

By:

Laffy, Patrick W.;
Wood-Charlson, Elisha M.;
Turaev, Dmitrij;
Weynberg, Karen D.;
Botté, Emmanuelle S.;
van Oppen, Madeleine J. H.;
Webster, Nicole S.;
Rattei, Thomas;
Delmont, Tom O.;
Jeffries, Thomas C.

Publication type:

Article

Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses.

Published in:

Virology Journal, 2015, v. 12, n. 1, p. 1, doi. 10.1186/s12985-015-0305-5

By:

Conceição-Neto, Nádia;
Zeller, Mark;
Heylen, Elisabeth;
Lefrère, Hanne;
Mesquita, João Rodrigo;
Matthijnssens, Jelle

Publication type:

Article

Genotypic but not phenotypic historical contingency revealed by viral experimental evolution.

Published in:

BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-46

By:

Bedhomme, Stéphanie;
Lafforgue, Guillaume;
Elena, Santiago F.

Publication type:

Article

Emergence of novel domains in proteins.

Published in:

BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-47

By:

Toll-Riera, Macarena;
Albà, M. Mar

Publication type:

Article

INFLUENCE OF VIRAL REPLICATION MECHANISMS ON WITHIN-HOST EVOLUTIONARY DYNAMICS.

Published in:

Evolution, 2012, v. 66, n. 11, p. 3462, doi. 10.1111/j.1558-5646.2012.01687.x

By:

Loverdo, Claude;
Park, Miran;
Schreiber, Sebastian J.;
Lloyd-Smith, James O.

Publication type:

Article

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.

Published in:

Nature, 2014, v. 513, n. 7517, p. 242, doi. 10.1038/nature13459

By:

Deng, Li;
Ignacio-Espinoza, J. Cesar;
Gregory, Ann C.;
Poulos, Bonnie T.;
Weitz, Joshua S.;
Hugenholtz, Philip;
Sullivan, Matthew B.

Publication type:

Article

Genomic diversity contributes to the neuroinvasiveness of the Yellow fever French neurotropic vaccine.

Published in:

NPJ Vaccines, 2021, v. 6, n. 1, p. 1, doi. 10.1038/s41541-021-00318-3

By:

Bakoa, Florian;
Préhaud, Christophe;
Beauclair, Guillaume;
Chazal, Maxime;
Mantel, Nathalie;
Lafon, Monique;
Jouvenet, Nolwenn

Publication type:

Article

Phylogeographic distribution of very virulent infectious bursal disease virus isolates in the Iberian Peninsula.

Published in:

Avian Pathology, 2012, v. 41, n. 3, p. 277, doi. 10.1080/03079457.2012.682562

By:

Cortey, Martí;
Bertran, Kateri;
Toskano, Jennifer;
Majó, Natàlia;
Dolz, Roser

Publication type:

Article

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-96

By:

Chen-Harris, Haiyin;
Borucki, Monica K.;
Torres, Clinton;
Slezak, Tom R.;
Allen, Jonathan E.

Publication type:

Article

De novo assembly of highly diverse viral populations.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 475, doi. 10.1186/1471-2164-13-475

By:

Xiao Yang;
Charlebois, Patrick;
Gnerre, Sante;
Coole, Matthew G.;
Lennon, Niall J.;
Levin, Joshua Z.;
Qu, James;
Ryan, Elizabeth M.;
Zody, Michael C.;
Henn, Matthew R.

Publication type:

Article

Circulating Virus Load Determines the Size of Bottlenecks in Viral Populations Progressing within a Host.

Published in:

PLoS Pathogens, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.ppat.1003009

By:

Gutiérrez, Serafín;
Yvon, Michel;
Pirolles, Elodie;
Garzo, Eliza;
Fereres, Alberto;
Michalakis, Yannis;
Blanc, Stéphane

Publication type:

Article

Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing.

Published in:

BMC Infectious Diseases, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2334-13-52

By:

Bansode, Vijay;
McCormack, Grace P.;
Crampin, Amelia C.;
Ngwira, Bagrey;
Shrestha, Ram K.;
French, Neil;
Glynn, Judith R.;
Travers, Simon A.

Publication type:

Article

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV.

Published in:

PLoS Genetics, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pgen.1004000

By:

Pennings, Pleuni S.;
Kryazhimskiy, Sergey;
Wakeley, John

Publication type:

Article

Diversity of the major capsid genes ( g23) of T4-like bacteriophages in the eutrophic Lake Kotokel in East Siberia, Russia.

Published in:

Archives of Microbiology, 2013, v. 195, n. 7, p. 513, doi. 10.1007/s00203-013-0884-8

By:

Butina, Tatyana;
Belykh, Olga;
Potapov, Sergey;
Sorokovikova, Ekaterina

Publication type:

Article

Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses – Target Selection and Optimized Screening.

Published in:

PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150110

By:

Stern, Daniel;
Pauly, Diana;
Zydek, Martin;
Miller, Lilija;
Piesker, Janett;
Laue, Michael;
Lisdat, Fred;
Dorner, Martin B.;
Dorner, Brigitte G.;
Nitsche, Andreas

Publication type:

Article

Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review.

Published in:

PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0147021

By:

Kim, Kiyeon;
Omori, Ryosuke;
Ueno, Keisuke;
Iida, Sayaka;
Ito, Kimihito

Publication type:

Article

Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing.

Published in:

PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0142473

By:

Choudhury, Md Abu;
Lott, William B;
Banu, Shahera;
Cheng, Anthony Youzhi;
Teo, Yik-Ying;
Ong, Rick Twee-Hee;
Aaskov, John

Publication type:

Article

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.

Published in:

PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0135903

By:

Iyer, Shyamala;
Casey, Eleanor;
Bouzek, Heather;
Kim, Moon;
Deng, Wenjie;
Larsen, Brendan B.;
Zhao, Hong;
Bumgarner, Roger E.;
Rolland, Morgane;
Mullins, James I.

Publication type:

Article

A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province.

Published in:

PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0129845

By:

Shi, Chenyan;
Liu, Yi;
Hu, Xiaomin;
Xiong, Jinfeng;
Zhang, Bo;
Yuan, Zhiming

Publication type:

Article

Superinfection between Influenza and RSV Alternating Patterns in San Luis Potosí State, México.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0115674

By:

Velasco-Hernández, Jorge Xicoténcatl;
Núñez-López, Mayra;
Comas-García, Andreu;
Cherpitel, Daniel Ernesto Noyola;
Ocampo, Marcos Capistrán

Publication type:

Article

Quantification and Localization of Watermelon Chlorotic Stunt Virus and Tomato Yellow Leaf Curl Virus (Geminiviridae) in Populations of Bemisia tabaci (Hemiptera, Aleyrodidae) with Differential Virus Transmission Characteristics.

Published in:

PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0111968

By:

Kollenberg, Mario;
Winter, Stephan;
Götz, Monika

Publication type:

Article

A Very Low Geno2pheno False Positive Rate Is Associated with Poor Viro-Immunological Response in Drug-Naïve Patients Starting a First-Line HAART.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0105853

By:

Armenia, Daniele;
Soulie, Cathia;
Di Carlo, Domenico;
Fabeni, Lavinia;
Gori, Caterina;
Forbici, Federica;
Svicher, Valentina;
Bertoli, Ada;
Sarmati, Loredana;
Giuliani, Massimo;
Latini, Alessandra;
Boumis, Evangelo;
Zaccarelli, Mauro;
Bellagamba, Rita;
Andreoni, Massimo;
Marcelin, Anne-Geneviève;
Calvez, Vincent;
Antinori, Andrea;
Ceccherini-Silberstein, Francesca;
Perno, Carlo-Federico

Publication type:

Article