Publications

The easiest way to find all our publications is google scholar. Most of our publications are also on arxiv. Code associated with the manuscripts can be found on github. Some of our work has been covered by the popular press.

preprints

2016

  1. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.
    Richard A. Neher, Trevor Bedford, Rodney S. Daniels, Colin A. Russell, Boris I. Shraiman. PNAS, vol. 113, E1701-E1709. doi:10.1073/pnas.1525578113
  2. Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus. Hassouna et al, Molecular Psychiatry
  3. Establishment and stability of the latent HIV-1 DNA reservoir.
    Johanna Brodin, Fabio Zanini, Lina Thebo, Christa Lanz, Göran Bratt, Richard Neher, Jan Albert
    eLife, in press, doi:10.1101/053983
  4. HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell
    Mikael Boulle, et al. …., Alex Sigal
    PLoS Pathogens, 12(11): e1005964. 10.1371/journal.ppat.1005964

2015

  1. Population genomics of intrapatient HIV-1 evolution.
    Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A. Neher. eLIFE, 11282
  2. nextflu: Real-time tracking of seasonal influenza virus evolution in humans.
    Richard A. Neher, Trevor Bedford. Bioinformatics, btv381
  3. Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing.
    J Brodin, C Hedskog, A Heddini, E Benard, RA Neher, M Mild, J Albert. PloS one 10 (3)

2014

  1. Predicting evolution from the shape of genealogical trees.
    Richard A Neher, Colin A Russel, Boris I Shraiman. eLIFE, 03568
  2. Characterization of Genetic Diversity in the Nematode Pristionchus Pacificus from Population-Scale Resequencing Data.
    C Rödelsperger, RA. Neher, Andreas M. Weller, G Eberhardt, H Witte, WE Mayer, Dieterich, and RJ Sommer. Genetics. doi:10.1534/genetics.113.159855
  3. Interference limits resolution of selection pressures from linked neutral diversity.
    Benjamin H. Good, Aleksandra M. Walczak, Richard A. Neher, Michael M. Desai. PLoS Genetics, 10(3): e1004222.

2013

  1. Quantifying the range of a lipid phosphate signal in vivo.
    Amrita Mukherjee, Richard A. Neher, Andrew D. Renault. J. Cell Science, epub
  2. Quantifying selection against synonymous mutations in HIV-1 env evolution.
    Fabio Zanini, Richard A. Neher. Journal of Virology, doi:10.1128/JVI.01529-13
  3. Coalescence and genetic diversity in sexual populations under selection
    Richard A. Neher, Taylor A. Kessinger, Boris I. Shraiman. PNAS 110 (39) 15836-15841
  4. Inferring HIV escape rates from multi-locus genotype data
    Taylor A. Kessinger, Alan S. Perelson and Richard A. Neher. Front. Immunol. 4:252. doi: 10.3389/fimmu.2013.00252
  5. Genetic draft, selective interference, and population genetics of rapid adaptation
    Richard A. Neher, Annual Reviews of Ecology, Evolution, and Systematics, vol 44.
  6. Genealogies of rapidly adapting populations
    Richard Neher, Oskar Hallatschek. PNAS 110 (2), 437-442
  7. Emergence of clones in sexual populations
    Richard Neher, Marjia Vucelja, Marc Mezard, Boris Shraiman. JSTAT 2013 (01), P01008
  8. Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses
    Vitaly Ganusov, Richard Neher, Alan Perelson. JSTAT 2013 (01), P01010

2012

  1. FFPopSim: an efficient forward simulation package for the evolution of large populations
    Fabio Zanini, Richard Neher. Bioinformatics 28 (24), 3332-3333
  2. Dynamic Mutation–Selection Balance as an Evolutionary Attractor
    Sid Goyal, Dan Balick, Elisabeth Jerison, Richard Neher, Boris Shraiman, Michael Desai. Genetics 191 (4), 1309-1319
  3. Estimating the Strength of Selective Sweeps from Deep Population Diversity Data
    Philipp Messer, Richard Neher. Genetics 191 (2), 593-605
  4. Fluctuations of Fitness Distributions and the Rate of Muller’s Ratchet
    Richard Neher, Boris Shraiman. Genetics. 191 (4), 1283-1293

2011

  1. Correlated evolution of nearby residues in Drosophilid proteins
    Benjamin Callahan, Richard Neher, Doris Bachtrog, Peter Andolfatto, Boris Shraiman. PLoS Genetics 7 (2), e1001315
  2. Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations
    Richard Neher, Boris Shraiman. Genetics 188 (4), 975-996
  3. Statistical Genetics and Evolution of Quantitative Traits
    Richard Neher, Boris Shraiman. Rev. Mod. Phys. 83, 1283–1300 (2011)Target search on a dynamic DNA molecule
  4. Target search on a dynamic DNA molecule
    Thomas Schötz, Richard Neher, and Ulrich Gerland. Phys. Rev. E 84, 051911

2010

  1. Rate of adaptation in large sexual populations
    Richard Neher, Boris Shraiman, Daniel Fisher. Genetics 184 (2), 467
  2. Recombination rate and selection strength in HIV intra-patient evolution
    RA Neher, T Leitner. PLoS computational biology 6 (1), e1000660

Miscellaneous

Popular press coverage (selection)

nextflu

Influenza prediction

HIV evolution