Publications

since 2010, for earlier publications see group member pages

preprints

2015

  1. nextflu: Real-time tracking of seasonal influenza virus evolution in humans. Richard A. Neher, Trevor Bedford. Bioinformatics, btv381
  2. 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

Popular press coverage (selection)

nextflu
Influenza prediction
HIV evolution