Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Deliverables

Other (12)

GUI Epidemiological analysis tools for pilot study

Epidemiological tracing tool

GUI entire platform for pilot study

GUI entire platform for pilot study

Virome comparison tool

Report on use of HPM for NGS data analysis

Pan-viral typing tool

NGS assembly tool

Classification tool

Phylogenetic analysis method for reticulation

GUI NGS assembly tool for pilot study

GUI Virome comparison tools for pilot study

GUI Pan-viral typing tool for pilot study

Documents, reports (4)

Colloquium

Plan for the dissemination and exploitation of results

Report pilot studies

Training module NGS data analysis

Publications

Peer reviewed articles (7)

Phylogenetic analysis as a forensic tool in HIV transmission investigations

Author(s): Ana B. Abecasis, Marta Pingarilho, Anne-Mieke Vandamme
Published in: AIDS, 2018, Page(s) 1, ISSN 0269-9370
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/QAD.0000000000001728

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Author(s): Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Published in: Molecular Biology and Evolution, 33/8, 2016, Page(s) 2167-2169, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw082

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author(s): Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D’Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adri
Published in: Nature, 544/7650, 2017, Page(s) 309-315, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22040

The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data

Author(s): B. Vrancken, D. Adachi, M. Benedet, A. Singh, R. Read, S. Shafran, G.D. Taylor, K. Simmonds, C. Sikora, P. Lemey, C.L. Charlton, J.W. Tang
Published in: Infection, Genetics and Evolution, 52, 2017, Page(s) 100-105, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2017.04.005

Challenges in the analysis of viral metagenomes

Author(s): Rebecca Rose, Bede Constantinides, Avraam Tapinos, David L Robertson, Mattia Prosperi
Published in: Virus Evolution, 2/2, 2016, Page(s) vew022, ISSN 2057-1577
Publisher: Oxford Journals
DOI: 10.1093/ve/vew022

Visual programming for next-generation sequencing data analytics

Author(s): Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Published in: BioData Mining, 9/1, 2016, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-016-0095-3

Genome Sequences of a Novel Vietnamese Bat Bunyavirus

Author(s): Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten
Published in: Genome Announcements, 4/6, 2016, Page(s) e01366-16, ISSN 2169-8287
Publisher: Genome Announcements
DOI: 10.1128/genomeA.01366-16