bedford.io

bedford lab

The Bedford Lab at the Fred Hutch. Works at the interface of evolution, epidemiology and immunology. We apply computational and statistical methods to sequence data to understand viral dynamics, looking at the geographic circulation of viral strains and their evolution. We are interested in linking mutations in the virus to changes in acquired immunity in the human population, and then looking at how human immunity influences viral transmission patterns. Pathogen evolution, selection and immunity. Global...

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bedford lab | bedford.io Reviews

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The Bedford Lab at the Fred Hutch. Works at the interface of evolution, epidemiology and immunology. We apply computational and statistical methods to sequence data to understand viral dynamics, looking at the geographic circulation of viral strains and their evolution. We are interested in linking mutations in the virus to changes in acquired immunity in the human population, and then looking at how human immunity influences viral transmission patterns. Pathogen evolution, selection and immunity. Global...

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1 blog

2 papers

3 projects

4 team

5 bedford lab research

6 recent posts

7 new recruits

8 recent papers

9 active projects

10 by trvrb

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bedford lab | bedford.io Reviews

https://bedford.io

The Bedford Lab at the Fred Hutch. Works at the interface of evolution, epidemiology and immunology. We apply computational and statistical methods to sequence data to understand viral dynamics, looking at the geographic circulation of viral strains and their evolution. We are interested in linking mutations in the virus to changes in acquired immunity in the human population, and then looking at how human immunity influences viral transmission patterns. Pathogen evolution, selection and immunity. Global...

INTERNAL PAGES

bedford.io

1

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

http://www.bedford.io/papers/bedford-global-circulation

Global circulation patterns of seasonal influenza viruses vary with antigenic drift.

2

Trevor Bedford

http://www.bedford.io/team/trevor-bedford

Im an Assistant Member at the Fred Hutch. In the Vaccine and Infectious Disease Division. And the Computational Biology Program. Im also an Affiliate Assistant Professor in the Department of Epidemiology. At the University of Washington School of Public Health. I study the dynamics of virus populations. How do strains spread through the world? How do strains evolve in response to immune pressure? And ultimately, what makes a strain successful? And worked on viral phylogenetics with Andrew Rambaut. Geneti...

3

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.

4

bedford lab / team

http://www.bedford.io/team

Charles Y K Cheung.

5

bedford lab / blog

http://www.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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andersen-lab.com

Ebola paper in Cell | Andersen Lab

http://andersen-lab.com/new-ebola-paper-out-in-cell

Dudes & Dudettes. Dudes & Dudettes. Ebola paper out in Cell. June 18, 2015. In a large collaboration between the Viral Hemorrhagic Fever Consortium, Kenema Government Hospital, Harvard University, Broad Institute, Tulane University, Edinburgh University, the CDC, USAMRIID, and others we have just published a paper in. Detailing the epidemiology, transmission, and evolution of Ebola virus over seven months in Sierra Leone. The new study sequenced 232 new Ebola virus genomes, which were all released on NCBI.

cmb.washington.edu

Computational Molecular Biology program

http://cmb.washington.edu/faculty.htm

UW Computational Molecular Biology. Akeyj [ a t ] u.washington.edu. UW Biochemistry; Adjunct UW Genome Sciences, Bioengineering, Computer Science and Engineering, Chemical Engineering, and Physics. Dabaker [ a t ] u.washington.edu. UW Bioengineering; Adjunct UW Radiology. Jbb2 [ a t ] uw.edu. FHCRC; Affiliate UW Epidemiology. Trevor [ a t ] bedford.io. Cbergst [ a t ] uw.edu. FHCRC Basic Sciences; Affiliate UW Genome Sciences. Jbloom [ a t ] fhcrc.org. Hbolouri [ a t ] fhcrc.org. Rogerb [ a t ] uw.edu.

theshahlab.org

About

http://www.theshahlab.org/misc/about

Our new lab website has been directly inspired (in fact, borrowed) from Trevor Bedfords. Website. We have used Trevors GitHub code. With minimal modifications. We were also inspired by several stylistic aspects of Allan Drummonds. Detailed instructions on creating this website can be found here.

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).

theshahlab.org

Our new lab website

http://www.theshahlab.org/blog/new-website

Our new lab website. 18 Apr 2016 by Shah. We finally updated our website from the clunky iWeb based one. This was certainly a process. After several false starts and figuring out how html and css work, we made it. This was made possible almost entirely due to efforts of Trevor Bedford. And the detailed instructions. He provided. Our new lab website has been directly inspired (in fact, borrowed) from Trevors. Website. We have used Trevors GitHub code.

hi.nextflu.org

HI.nextflu / H3N2 / 6y

http://hi.nextflu.org/H3N2/6y

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...

hi.nextflu.org

HI.nextflu / H3N2 / 20y

http://hi.nextflu.org/H3N2/20y

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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bedford.io

bedford lab

The Bedford Lab at the Fred Hutch. Works at the interface of evolution, epidemiology and immunology. We apply computational and statistical methods to sequence data to understand viral dynamics, looking at the geographic circulation of viral strains and their evolution. We are interested in linking mutations in the virus to changes in acquired immunity in the human population, and then looking at how human immunity influences viral transmission patterns. Pathogen evolution, selection and immunity. Global...

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