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, to appear. Special issue for selected papers from RECOMB-CG, 2017
 M. Nute, K. Yarlagadda and R. Stumpf. (2018) “A Picture Worth a Thousand Words: Visualizing Microbial Communities with Phylogenetic Histograms” Submitted to mSystems.
 M. Nute, E. Saleh, and T. Warnow. (2018) “Benchmarking statistical multiple sequence alignment” Submitted to PLoS ONE.