The Experts below are selected from a list of 156423 Experts worldwide ranked by ideXlab platform
Ting Wang - One of the best experts on this subject based on the ideXlab platform.
-
Exploring the coronaVirus pandemic with the WashU Virus Genome Browser.
Nature Genetics, 2020Co-Authors: Jennifer Flynn, Deepak Purushotham, Mayank N. K. Choudhary, Xiaoyu Zhuo, Changxu Fan, Gavriel Matt, Ting WangAbstract:The WashU Virus Genome Browser is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral Genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.
-
Exploring the coronaVirus epidemic using the new WashU Virus Genome Browser
2020Co-Authors: Jennifer Flynn, Deepak Purushotham, Mayank N. K. Choudhary, Xiaoyu Zhuo, Changxu Fan, Gavriel Matt, Ting WangAbstract:Abstract Since its debut in mid-December, 2019, the novel coronaVirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the Virus have been sequenced and uploaded to NCBI’s GenBank [1], providing insight into the Virus’s evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing Virus genomic data. The browser is home to 16 complete 2019-nCoV Genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronaVirus (SARS-CoV), Middle East respiratory syndrome coronaVirus (MERS-CoV), and Ebola Virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU EpiGenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://Virusgateway.wustl.edu, and documentation is available at https://Virusgateway.readthedocs.io/.
Ashesh Nandy - One of the best experts on this subject based on the ideXlab platform.
-
Characterizing the Zika Virus Genome – A Bioinformatics Study
Current Computer - Aided Drug Design, 2016Co-Authors: Ashesh Nandy, Subhash C Basak, Sumanta Dey, Dorota Bielińska-wa̧ż, Piotr WazAbstract:Background: The recent epidemic of Zika Virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the Virus worldwide. The Zika Virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date. Objective: To carry out a bioinformatics study of the available Zika Virus genomic sequences to characterize the Virus. Method: 2D graphical representation method is used for visual rendering and compute sequence parameters and descriptors of the African and Asian-American groups of the Zika Viruses to characterize the sequences. We also used MEGA5.2 and other software to compute various biological properties of interest like phylogenetic relationships, transition-transversion ratios, amino acid usage, codon usage bias and hydropathy index of the Zika Genomes and virions. Results: The phylogenetic relationships show that the African and Asian-American Zika Virus Genomes are grouped in two clades. The 2D plots of typical Genomes of these types also show dramatic differences indicating that the gene sequences at the 5’-end coding regions for the structural proteins are rather strongly conserved. Among other characteristics, the transition/transversion ratio matrices for the sequences in each of the two clades show that analogous to the dengue Virus, the transition rates are about 10 to 15 times the transversion rates. Conclusion: These findings are important for computer-assisted approaches towards surveillance of emerging Zika Virus strains as well as in the design of drugs and vaccines to combat the growth and spread of the Zika Virus.
-
graphical representation and numerical characterization of h5n1 avian flu neuraminidase gene sequence
Journal of Chemical Information and Modeling, 2007Co-Authors: Ashesh Nandy, Subhash C Basak, Brian D GuteAbstract:The high degree of virulence and potential for development of a pandemic strain of the H5N1 avian flu has resulted in wide interest in characterization of the various genes of the H5N1 Virus Genome...
Dominique Rousset - One of the best experts on this subject based on the ideXlab platform.
-
zika Virus Genome from the americas
The Lancet, 2016Co-Authors: Antoine Enfissi, John Codrington, Jimmy Roosblad, Mirdad Kazanji, Dominique RoussetAbstract:www.thelancet.com Vol 387 January 16, 2016 227 3 Griffi ths CEM, Reich K, Lebwohl M, et al. Comparison of ixekizumab with etanercept or placebo in moderate-to-severe psoriasis (UNCOVER-2 and UNCOVER-3): results from two phase 3 randomised trials. Lancet 2015; 386: 541–51. 4 Beurel E, Harrington LE, Jope RS. Infl ammatory T helper 17 cells promote depression-like behavior in mice. Biol Psychiatry 2013; 73: 622–30. 5 Papp KA, Leonardi C, Menter A, et al. Brodalumab, an anti-interleukin-17-receptor antibody for psoriasis. N Engl J Med 2012; 366: 1181–89.
Chris Upton - One of the best experts on this subject based on the ideXlab platform.
-
african swine fever Virus replication and genomics
Virus Research, 2013Co-Authors: Linda K Dixon, David A G Chapman, Christopher L Netherton, Chris UptonAbstract:African swine fever Virus (ASFV) is a large icosahedral DNA Virus which replicates predominantly in the cytoplasm of infected cells. The ASFV double-stranded DNA Genome varies in length from about 170 to 193 kbp depending on the isolate and contains between 150 and 167 open reading frames. These are closely spaced and read from both DNA strands. The Virus Genome termini are covalently closed by imperfectly base-paired hairpin loops that are present in two forms that are complimentary and inverted with respect to each other. Adjacent to the termini are inverted arrays of different tandem repeats. Head to head concatemeric Genome replication intermediates have been described. A similar mechanism of replication to PoxViruses has been proposed for ASFV. Virus Genome transcription occurs independently of the host RNA polymerase II and Virus particles contain all of the enzymes and factors required for early gene transcription. DNA replication begins in perinuclear factory areas about 6h post-infection although an earlier stage of nuclear DNA synthesis has been reported. The Virus Genome encodes enzymes required for transcription and replication of the Virus Genome and virion structural proteins. Enzymes that are involved in a base excision repair pathway may be an adaptation to enable Virus replication in the oxidative environment of the macrophage cytoplasm. Other ASFV genes encode factors involved in evading host defence systems and modulating host cell function. Variation between the Genomes of different ASFV isolates is most commonly due to gain or loss of members of multigene families, MGFs 100, 110, 300, 360, 505/530 and family p22. These are located within the left terminal 40kbp and right terminal 20kbp. ASFV is the only member of the Asfarviridae, which is one of the families within the nucleocytoplasmic large DNA Virus superfamily.
Jennifer Flynn - One of the best experts on this subject based on the ideXlab platform.
-
Exploring the coronaVirus pandemic with the WashU Virus Genome Browser.
Nature Genetics, 2020Co-Authors: Jennifer Flynn, Deepak Purushotham, Mayank N. K. Choudhary, Xiaoyu Zhuo, Changxu Fan, Gavriel Matt, Ting WangAbstract:The WashU Virus Genome Browser is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral Genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.
-
Exploring the coronaVirus epidemic using the new WashU Virus Genome Browser
2020Co-Authors: Jennifer Flynn, Deepak Purushotham, Mayank N. K. Choudhary, Xiaoyu Zhuo, Changxu Fan, Gavriel Matt, Ting WangAbstract:Abstract Since its debut in mid-December, 2019, the novel coronaVirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the Virus have been sequenced and uploaded to NCBI’s GenBank [1], providing insight into the Virus’s evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing Virus genomic data. The browser is home to 16 complete 2019-nCoV Genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronaVirus (SARS-CoV), Middle East respiratory syndrome coronaVirus (MERS-CoV), and Ebola Virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU EpiGenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://Virusgateway.wustl.edu, and documentation is available at https://Virusgateway.readthedocs.io/.
