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.


Department of Biology
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!


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


Department of Biology
371 Serra St.
Stanford University
Stanford, CA 94305-5020

Brief CV

I have been fortunate to receive support from: