Daniel Hakim

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

Austin D. Swafford, Kristen L. Beck, V. Salomaa, 2021, Genome research.

Scalable power analysis and effect size exploration of microbiome community differences with Evident

S. Peddada, D. McDonald, Y. Vázquez-Baeza, 2022, bioRxiv.

Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome

L. Metman, S. Mazmanian, A. Keshavarzian, 2022, bioRxiv.

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

Xiaoping Zhou, H. Weiner, A. Bar-Or, 2022, Cell.

BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations

James T. Morton, R. Knight, M. Estaki, 2023, bioRxiv.

Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References

Se Jin Song, Austin D. Swafford, Antonio Gonzalez, 2022, mSystems.

Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases

Y. Vázquez-Baeza, Lingjing Jiang, R. Knight, 2023, Genes.