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
 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.
 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.
 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
 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
 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
 M. Nute, K. Yarlagadda and R. Stumpf. (2018) “A Picture Worth a Thousand Words: Visualizing Microbial Communities with Phylogenetic Histograms” (in preparation).
 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)
 N. Shah, M. Nute, T. Warnow, and M. Pop. (2018) “Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.” Bioinformatics, byt833.