Alison F. Feder
I am an evolutionary biologist studying intra-patient pathogen
evolution to understand how adaptation proceeds
in space and time. I've just finished up my PhD in the
biology
department at Stanford University advised by Dmitri Petrov.As of August 1, 2018, I am a Miller fellow at Berkeley. My new (although nearly identical) website can be found here.
Contact
- e-mail: afeder@stanford.edu
371 Serra St.
Stanford University
Stanford, CA 94305-5020
You can also find me on Twitter.
I'm planning to attend several conferences this summer (2018). Let me know if you want to meet up at the IDM symposium, HIV Dynamics & Evolution, PEQG, or SMBE!
Research
I'm generally interested in evolution, and how we can use mathematics and computation to better understand evolutionary processes. I am particularly interested in how these processes play out in pathogen populations rapidly evolving within their hosts.
Here are some of the projects I've worked on over the past several years, and you can find a current list of publications on Google scholar.
Rapid adaptation reveals structure in populations that are
effectively panmictic under neutrality.This is ongoing work with Pleuni Pennings, Dmitri Petrov and Joachim Hermisson
Within-patient HIV mutation frequencies reveal fitness costs of CpG
dinucleotides, drastic amino acid changes and G->A mutations
(2018) [paper]
with K. Theys, Maoz Gelbart, Marion Hartl, Adi Stern, Pleuni Pennings
High resolution spatio-temporal assessment of SHIV evolution reveals a highly dynamic
process within the host (2017) [paper,video
abstract]
with Dmitri Petrov, Pleuni Pennings, Zandrea Ambrose
More effective drugs lead to harder selective sweeps in the evolution
of drug
resistance in
HIV-1 (2016)[paper, video abstract]
with Soo-Yon Rhee, Susan Holmes, Bob Shafer, Dmitri Petrov and Pleuni Pennings
The population genetics of drug resistance evolution in natural
populations of viral, bacterial and eukaryotic pathogens. (2016) [paper]
with Ben Wilson, Nandita Garud, Zoe Assaf, and Pleuni Pennings
Comparative analysis of derived mutations across human
populations (2013)
[MSc
thesis]
with Gil McVean
Identifying Signatures of Selection in Genetic Time Series (2014) [paper]
with Sergey Kryazhimskiy and Joshua Plotkin
Estimating linkage disequilibrium from pooled paired end NGS reads using an approximate maximum likelihood approach. [paper, download LDx]
with Dmitri Petrov and Alan Bergland - Summer 2011
Investigating the correlation between recombination rate and mean allelic frequency in the context of different regimes of natural selection. [paper]
with Kirk Lohmueller and Rasmus Nielsen - Summer 2010
Estimating the bias incurred when estimating phylogenetic timescales with incorrect nucleotide substitution models
with Warren Ewens - Spring 2009
Other media
- Here's a seminar I gave at the Center for the Inference and
Dynamics of Infectious Disease (CIDID) at the Fred Hutch in September,
2017: [Flyer,
Video]
- Video abstract for 'A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host':
- A Muller diagram I drew was featured
as part of the cover of Molecular Ecology's special issue on 'Detecting Selection in Natural Populations.'
- Video abstract for 'More efficient drugs lead to harder sweeps in the evolution of drug resistance in HIV-1':
Contact
- e-mail: afeder@stanford.edu
371 Serra St.
Stanford University
Stanford, CA 94305-5020
Brief CV
- PhD Biology
Stanford University, 2018
- MSc (Res) Statistics
University of Oxford, 2013
- BA Mathematics
University of Pennsylvania, 2012
I have been fortunate to receive support from:
