[1] J. Chou, A. Gupta, S. Yaduvanshi, R. Davidson, M. Nute, S. Mirarab, and T. Warnow. (2015) “A comparative study of SVDquartets and other coalescent-based species tree estimation methods” RECOMB-Comparative Genomics and BMC Genomics. 2015.., 16 (Suppl 10): S2

[2] N. Nguyen, M. Nute, S. Mirarab, and T. Warnow. (2016) “HIPPI: Highly accurate protein family classification with ensembles of HMMs.” BMC Genomics 17 (Suppl 10):765, special issue for RECOMB-CG.

[3] M. Nute and T. Warnow. (2016) “Scaling statistical multiple sequence alignment to large datasets.” BMC Genomics 17(Suppl 10): 764, special issue for RECOMB-CG.

[4] M. Nute, E. Molloy, J. Chou, and T. Warnow. (2018) “The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data.”BMC Genomics, 19(Suppl 5):286, DOI: 10.1186/s12864-018-4619-8. Special issue for selected papers from RECOMB-CG, 2017

[5] S. Roch, M. Nute, T. Warnow. (2018) “Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods” arXiv preprint arXiv:1803.02800, In press, Systematic Biology

[6] K. Amato, J. Sanders, S. J. Song, M. Nute, J. Metcalf, L. Thompson, J. Morton, A. Amir, V. McKenzie, G. Humphrey, G. Gogul, J. Gaffney, A. Baden, G. Britton, F. Cuozzo, A. Di Fiore, N. Dominy, T. Goldberg, A. Gomez, M. Kowaleski, R. Lewis, A. Link, M. Sauther, S. Tecot, B. White, K. Nelson, R. Stumpf, R. Knight, and S. Leigh. (2018) “Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes” ISME J

[7] M. Nute, K. Yarlagadda and R. Stumpf. (2018) “A Picture Worth a Thousand Words: Visualizing Microbial Communities with Phylogenetic Histograms” (in preparation).

[8] M. Nute, E. Saleh, and T. Warnow. (2018) “Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets” Systematic Biology, syy068. (link)

[9] N. Shah, M. Nute, T. Warnow, and M. Pop. (2018) “Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.” Bioinformatics, byt833.