Publications

14. Garud NR, Messer P, Petrov D. “Detection of hard and soft sweeps from Drosophila melanogaster population genomic data.” BioRxiv (2020).

13. Harpak A, Garud NR, Rosenberg NA, Petrov DA, Combs M, Pennings PS, Munshi-South J. “Genetic adaptation in New York City rats.” BioRxiv (2020).

This perspective in Nature features our work.

12. Garud NR, Pollard KS. “Population Genetics in the Human Microbiome.” Trends in Genetics (2019) .

11. Garud NR*, Good BH*, Hallatschek O, and Pollard KS. “Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.” PLoS Biology (2019). *equal contributors.

This perspective by Isabel Gordo features our work.

10. Roodgar M*, Good BH*, Garud NR, Martis S, Avula S, Zhou W, Lancaster
S, Hayan Lee, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. “Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.” BioRxiv (2019).

9. Harris AM, Garud NR, and DeGiorgio M. “Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity.” Genetics (2018).

8. Battlay P., Leblanc P., Green L, Garud NR, Schmidt JM, Fournier-Level A, Robin A. “Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in the Drosophila Genetic Reference Panel.” G3 (2018)

7. Nayfach S, Rodriguez-Mueller B, Garud NR, and Pollard KS. “An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.” Genome Research (2016).

6. Garud NR and Petrov DA. “Elevated linkage disequilibrium and signatures of soft sweeps are common in Drosophila melanogaster.” Genetics (2016).

5. Wilson BA*, Garud NR*, Feder AF*, Assaf ZJ*, and Pennings PS. “The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.” Molecular Ecology (2015). *equal contributors

4. Garud NR and Rosenberg NA. “Enhancing the mathematical properties of haplotype homozygosity statistics for the detection of soft selective sweeps.” Theoretical Population Biology (2015).

3. Garud NR, Messer P, Buzbas E, and Petrov D. “Soft selective sweeps are the primary mode of adaptation in Drosophila.” PLoS Genetics 11: e1005004 (2015).

blog post featuring our paper is on Haldane’s Sieve. Also see my description of the project in this blog post and my GitHub repository of scripts for this project.

2. McCoy RC, Garud NR, Kelley JL, Boggs CL, and Petrov DA. “Genomic inference accuratelypredicts the timing and severity of a recent bottleneck in a non‐model insect population.” Molecular Ecology (2013).

1. Molina J, Sikora M, Garud NR, Flowers J, Rubinstein S, Reynolds A, Huang P et al. “Molecular evidence for a single evolutionary origin of domesticated rice.” Proceedings of the National Academy of Sciences 108, no. 20 (2011): 8351-8356.

Articles about this work in the press: BBC NewsAsia Times OnlineAnthropoligist in the attic blog post, and Discover Magazine blog