Publications

Bold = Garud lab members


24. Chen D.W. and Garud N.R. “Rapid evolution and strain turnover in the infant gut microbiome.” Genome Research2022.


23. Briscoe L, Balliu B, Sankararaman S, Halperin E, Garud NR. “Evaluating supervised and unsupervised background noise correction in human gut microbiome data.” PLoS Comp. Bio (2022).


22. Harris M. and Garud N.R.“Enrichment of hard sweeps on the X chromosome of Drosophila melanogaster.” bioRxiv (2022).


21. Briscoe L., Halperin E., and Garud N.R.“Microbiome source tracking using single nucleotide variants.”bioRxiv (2022).


20. Madi N, Chen D, Wolff R, Shapiro BJ, Garud NR. Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. BioRxiv (2022).


19. Garud NR. “Microbial Evolution: An overlooked biomarker of host diet.” Cell Host and Microbe (2022).


18. Wolff, R., Shoemaker W.R., and Garud N.R. “Ecological stability emerges at the level of strains in the human gut microbiome.” BioRxiv [Preprint]. September 30, 2021. Available from https://doi.org/10.1101/2021.09.30.462616.


17. Singh G., Haileselassie Y., Briscoe L., Bai L, Patel A, Sanjines E, Hendler S, Singh P, Garud NR, Limketkai BN, Habtezion A. “The effect of gastric acid suppression on probiotic colonization in a double blinded randomized clinical trial.” Clinical Nutrition ESPEN (2021). 


16. Garud NR. “The Tempo and Mode of Adaptation in a Complex Natural Population: the Microbiome.” mSystems(2021).


15. Shoemaker W, Chen D, Garud NR. “Comparative population genetics in the human gut microbiome.” GBE (2021).


14. Garud NR, Messer P, Petrov D. “Detection of hard and soft sweeps from Drosophila melanogaster population genomic data.” PLoS Genetics (2021).


13. Roodgar M*, Good BH*, Garud NR, Martis S, Avula S, Zhou W, Lancaster S, Lee H, 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.” Genome Research (2021).


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

This perspective in Nature features our work.


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


10. 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.


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 our blog post and the associated GitHub repository 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