nextflu.org

nextflu / H3N2 / 3y

Real-time tracking of seasonal influenza virus evolution in humans. Input mutations as position amino acid, i.e. 159Y. Clades as clade name, i.e. 3c2.a. And add locations as /AS. By default, positions are interpreted as residues in HA1. You can specify the subunit as HA2:18V. Alternatively, simply click on variable positions in the graph below. Use the date slider. Use the drop down menu. To color viruses by number of epitope mutations. Or receptor binding mutations. Use the input box. The default is HA1.

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nextflu / H3N2 / 3y | nextflu.org Reviews

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Real-time tracking of seasonal influenza virus evolution in humans. Input mutations as position amino acid, i.e. 159Y. Clades as clade name, i.e. 3c2.a. And add locations as /AS. By default, positions are interpreted as residues in HA1. You can specify the subunit as HA2:18V. Alternatively, simply click on variable positions in the graph below. Use the date slider. Use the drop down menu. To color viruses by number of epitope mutations. Or receptor binding mutations. Use the input box. The default is HA1.

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1 virus

2 b/vic

3 b/yam

4 time

5 ha phylogeny

6 legend

7 color by

8 epitope mutations

9 non epitope mutations

10 receptor binding mutations

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virus,b/vic,b/yam,time,ha phylogeny,legend,color by,epitope mutations,non epitope mutations,receptor binding mutations,local branching index,geographic region,sampling date,frequency change,region,africa,china,europe,japan / korea,north america,oceania

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nextflu / H3N2 / 3y | nextflu.org Reviews

https://nextflu.org

Real-time tracking of seasonal influenza virus evolution in humans. Input mutations as position amino acid, i.e. 159Y. Clades as clade name, i.e. 3c2.a. And add locations as /AS. By default, positions are interpreted as residues in HA1. You can specify the subunit as HA2:18V. Alternatively, simply click on variable positions in the graph below. Use the date slider. Use the drop down menu. To color viruses by number of epitope mutations. Or receptor binding mutations. Use the input box. The default is HA1.

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hi.nextflu.org

HI.nextflu / H3N2 / 3y

Real-time tracking of seasonal influenza. Virus evolution in humans. HI distance from focus. Click (repeatedly) on a branch to zoom. Input mutations as position amino acid, i.e. 159Y. Clades as clade name, i.e. 3c2.a. And add locations as /AS. By default, positions are interpreted as residues in HA1. You can specify the subunit as HA2:18V. Alternatively, simply click on variable positions in the graph below. For help with the nextflu interface or watch the tutorial video below. In the color by. To select...

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nextflu.org

1

nextflu / help

http://www.nextflu.org/help

Real-time tracking of influenza virus evolution. The date slider allows exploration of viruses isolations through time. Color tree by epitope evolution. Are based on HA structure and exposed residues. Multiple recent mutations at epitope sites have been suggested. To be predictive for strains dominating future seasons. Color tree by evolution outside epitopes. Mutations outside of the epitopes (see above) - termed non-epitope sites. Color tree by evolution at the receptor binding site. Use the input box.

2

nextflu / methods

http://www.nextflu.org/methods

Real-time tracking of influenza virus evolution. All source code is publicly available. And the exact steps of the nextflu algorithms are detailed in the processing pipeline files: H3N2 process.py. And Yam process.py. Here we give an overview of these methods. Broadly, nextflu. Contains two separate functions, the augur. Pipeline that processes FASTA sequence data and compiles JSON files, and auspice. Visualization package that displays these results in the browser. Sun et al, 2013.

3

nextflu / acknowledgements

http://www.nextflu.org/acknowledgements

Real-time tracking of influenza virus evolution. We acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu Database. On which this research is based. The list is detailed below.

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bedford.io

nextflu: real-time tracking of seasonal influenza virus evolution in humans

http://www.bedford.io/papers/neher-nextflu

Nextflu: real-time tracking of seasonal influenza virus evolution in humans. Neher RA, Bedford T. 2015. Bioinformatics 31: 3546-3548. Python and Javascript source code is freely available from github.com/blab/nextflu. While the web-application is live at nextflu.org.

pandemiedegrippe.com

Uncategorized Archives - Pandemiedegrippe.com

http://www.pandemiedegrippe.com/category/uncategorized

Archives de catégorie : Uncategorized. Vaccin contre la grippe. La grippe a causé un nombre record de décès au Québec pendant l’hiver 2014-2015. Décembre 9, 2015. La grippe a causé plus de décès en janvier 2015 que lors de la pandémie de H1N1. Mauvaise conjoncture des planètes pour la saison grippale 2014-2015. Vaccin contre la grippe. Vaccin contre la grippe. Votre enfant a la grippe: ne l’envoyez pas à l’hôpital avec un sirop contre la toux. Octobre 25, 2015. Causés par la grippe. En 2009, Santé Canada...

neherlab.wordpress.com

join us – neherlab

https://neherlab.wordpress.com/friends

Evolution, population genetics, and infectious diseases. All positions are currently filled. For informal inquiries contact Richard Neher at:. Firstname.lastname at tuebingen.mpg.de. For informal inquiries, contact me via email. If you feel the need to encrypt your correspondence, here is my public key. BEGIN PGP PUBLIC KEY BLOCK- - - Version: GnuPG v1 mQENBFH3z7ABCAC2UGGsP46o1 oS1esHr30ZwXRtJN4Pv8Liok9voVP7RtFqmHxf 3TdS1EN86Z0oFaD70kw eZPr8TUA4B/Dj23b7980sbS3 wXv226angk tk4kj/n3 3CCfx66cZcXdcgYN2gfuzVlv...

bedford.io

nextflu/

http://www.bedford.io/projects/nextflu

Real-time tracking of influenza evolution. 18 Oct 2016 - Update H3N2 outliers. 14 Oct 2016 - Merge pull request #139 from blab/checkDirectoriesAdd function to check for and create output directories. 12 Oct 2016 - Add function to check for and create output directories.Called in process.py process init. 01 Oct 2016 - Include Michigan/2015 as H1 vaccine strain. 25 Sep 2016 - Update outlier lists. Nextflu is live at nextflu.org. File of flu sequences and builds an annotated phylogeny, and auspice. AGPL) ne...

neherlab.wordpress.com

nextflu.org – neherlab

https://neherlab.wordpress.com/2015/02/23/nextflu-org

Evolution, population genetics, and infectious diseases. Together with Trevor Bedford. I have been working on a new version of the interactive tool to explore influenza evolution. It is now up and running at http:/ nextflu.org. In addition to a tree of the most recent influenza strains, we now also include frequencies of mutations, more complex genotypes, and clades of the tree. February 23, 2015. February 23, 2015. Leave a Reply Cancel reply. Enter your comment here. Address never made public).

neherlab.wordpress.com

Which flu strain will dominate 2015/2016? – neherlab

https://neherlab.wordpress.com/2015/01/09/which-flu-strain-will-dominate-20152016

Evolution, population genetics, and infectious diseases. Which flu strain will dominate 2015/2016? In November, Boris Shraiman. And myself published a paper on predicting evolution. Building on two projects by Trevor Bedford. To automatically construct influenza trees ( augur. And visualize them using javascript ( augur. I developed a tool for interactive exploration of seasonal influenza evolution and prediction. The dynamics of A/H3N2 viruses over the last 3 years are illustrated in the above figure&#4...

neherlab.wordpress.com

Is evolution predictable? – neherlab

https://neherlab.wordpress.com/2014/06/05/is-evolution-predictable

Evolution, population genetics, and infectious diseases. 8212; a collaboration with Colin Russell. How does it work? Individuals adapt to a changing environment by accumulating beneficial mutations, while avoiding deleterious mutations. We model this process assuming that there are many such mutations which change fitness in small increments. Using this model, we calculate the probability that an individual that lived in the past at time. And with an individual B that lived at a later time. The joint pro...

pandemiedegrippe.com

Grippe Archives - Pandemiedegrippe.com

http://www.pandemiedegrippe.com/category/grippe

Archives de catégorie : Grippe. Vaccin contre la grippe. Vaccin contre la grippe en spray nasal chez les enfants: quoi choisir? Août 17, 2016. Flumist et Fluenz sont des vaccin contre la grippe en spray nasal. Vaccin contre la grippe en spray nasal ou en injection: lequel est meilleur chez les enfants. Il y a quelque mois les experts des CDC recommandaient que le vaccin contre la grippe en spray nasal. Ne soit plus utilisé aux États-Unis. La controverse continue…. Vaccin contre la grippe. Juillet 17, 2016.

bedford.io

bedford lab / blog

http://bedford.io/blog

Zika sequencing in Brazil (or Trevor does fieldwork). 10 Jun 2016 by trvrb. I'm at the Rio airport now, heading home after 9 days in Brazil as part of the ground team of the ZiBRA project. As part of the team, I traveled from Natal to Recife along the northeastern coast collecting clinical samples for mobile Zika genome sequencing and analysis. This has been an illuminating experience and I'm grateful to Nick. And the rest of the team. For inviting me to be part of this. The RT diagnostic is particularly...

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nextflu.org

nextflu / H3N2 / 3y

Real-time tracking of seasonal influenza virus evolution in humans. Input mutations as position amino acid, i.e. 159Y. Clades as clade name, i.e. 3c2.a. And add locations as /AS. By default, positions are interpreted as residues in HA1. You can specify the subunit as HA2:18V. Alternatively, simply click on variable positions in the graph below. Use the date slider. Use the drop down menu. To color viruses by number of epitope mutations. Or receptor binding mutations. Use the input box. The default is HA1.

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